From 5b755c2f34dfc07dbc2eea53efad7936fc879a0f Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 12:05:01 +0100 Subject: [PATCH 1/7] update schema, bump version --- CMakeLists.txt | 2 +- .../schema/ZEN/flatten/ImageMetadata.xsd | 20694 ++++++++-------- documentation/version-history.md | 1 + 3 files changed, 10922 insertions(+), 9775 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 2a411d7..2ce6b28 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.15) project(CZICheck - VERSION 0.6.0 + VERSION 0.6.1 HOMEPAGE_URL "https://github.com/ZEISS/czicheck" DESCRIPTION "CZICheck is a validator for CZI-documents") diff --git a/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd b/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd index 2bb2634..074c0fd 100644 --- a/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd +++ b/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd @@ -1,10055 +1,11201 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Use this element as the root element for stand-alone image metadata XML file. - - - - - - - - - - - - Contains information about "topography data items", which can be thought of - as a group of channels, where each channel (within this group) can be - attributed as "heightmap" or "texture". - NOTES: - (1) The Id of the Appliances node specifying a "topography data item" must be "Topography:1". - Everything else will not be recognized as specifying a "topography data item". - (2) It is _not_ recommended to rely on Metadata.Information.Document.SubType in order - to detect the presence of "topography data items" in a document. Instead, it is - recommended to actively discover whether this information is present (and if - the document is usable for the respective application). - - - - - - - - - - - - - - - This node exists for legacy reasons - its content is not used. - - - - - - - - - - - - - - An identifier to uniquely identify this Topography data. - - - - - - - - - - The ShuttleAndFindData contains the calibration of the marker points for Shuttle and Find. - This data is added to metadata via the Appliances node (path: Appliances/Appliance/Data/ShuttleAndFindData). - NOTE: Ensure that the Id of the respective Appliance node obeys the following naming guideline: - Id="ShuttleAndFind:*". - ('*' generally is an integer but might be anything.) - Hence, algorithms can search for Ids which start with "ShuttleAndFind:". - - - - - - - - - - An identifier to uniquely identify this ShuttleAndFind data. - - - - - - - - - The SEMData appliances hold the SEM parameters. - - - - - - - - - - An identifier to uniquely identify this SEM data. - - - - - - - - - This data contains the initial parameter values for SIM Plugin viewers, as defined by the user for the SIM experiment. - - - - - - - - - - An identifier to uniquely identify this SIM data. - - - - - - - - A simple type that restricts the value to a float between 0 and 1 (inclusive). - - - - - - - - - - - - The distance value in meters. - - - - - - - If the format parameter is not specified in a UnitItem method that expects a format value, - then this DefaultUnitFormat is used. - Note that this is "just a hint" which unit of measurement should be used to present - the distance value to the user, it does not change the unit of the Value-field (which is - always meters, irrespective of the content of this element). - - - - - - - - - - - - - - - The date time value in ticks. - - - - - - - If the format parameter is not specified in a UnitItem method that expects a format value, - then this DefaultUnitFormat is used. - Note that this is "just a hint" which unit of measurement should be used to present - the date-time value to the user, it does not change the unit of the Value-field (which is - always 'ticks', irrespective of the content of this element). - - - - - - - - - - - - - - - The time value in seconds. - - - - - - - If the format parameter is not specified in a UnitItem method that expects a format value, - then this DefaultUnitFormat is used. - Note that this is "just a hint" which unit of measurement should be used to present - the time value to the user, it does not change the unit of the Value-field (which is - always 'ticks', irrespective of the content of this element). - - - - - - - - - - - - + + + + - - The number of pixels (no unit). - + A simple type that restricts the value to a float between 0 and 1 + (inclusive). - - + + + + + + + + + + + The distance value in meters. + + + + + + If the format parameter is not specified in a + UnitItem method that expects a format value, then this + DefaultUnitFormat is used. Note that this is "just a hint" which + unit of measurement should be used to present the distance value + to the user, it does not change the unit of the Value-field (which is + always meters, irrespective of the content of this element). + + + + + + + + + + + + + + + The date time value in ticks. + + + + + + + If the format parameter is not specified in a + UnitItem method that expects a format value, then this + DefaultUnitFormat is used. Note that this is "just a hint" which + unit of measurement should be used to present the date-time + value to the user, it does not change the unit of the Value-field (which is + always 'ticks', irrespective of the content of this element). + + + + + + + + + + + + + + + The time value in seconds. + + + + + + If the format parameter is not specified in a + UnitItem method that expects a format value, then this + DefaultUnitFormat is used. Note that this is "just a hint" which + unit of measurement should be used to present the time value to + the user, it does not change the unit of the Value-field (which is + always 'ticks', irrespective of the content of this element). + + + + + + + + + + + + + + + The number of pixels (no unit). + + + + + + If the format parameter is not specified in a + UnitItem method that expects a format value, then this + DefaultUnitFormat is used. Note that this is "just a hint" which + unit of measurement should be used to present the value 'number + of pixels' to the user, it does not change the unit of the Value-field + (which is always 'number of pixels', irrespective of the content + of this element). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - If the format parameter is not specified in a UnitItem method that expects a format value, - then this DefaultUnitFormat is used. - Note that this is "just a hint" which unit of measurement should be used to present - the value 'number of pixels' to the user, it does not change the unit of the Value-field (which is - always 'number of pixels', irrespective of the content of this element). - + Application Tags - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Application Tags - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Characteristics - - - - - - - - - - - - - - - - - - - - - - - - Angles for the image or scene composite image (index 0) and for individual scenes - (starting from index 1 for the first scene). - - - - - - - - - - - True if channel-merge display is enabled. - - - - - - The bit range for the histogram display. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + + + + + + - - - - - - Defines the display setting for a single channel. - - - - - The normalized low (=black) value of the mapping range. - - - - - The normalized high (=white) value of the mapping range. - - - - - The gamma value to be applied to the mapping range. - - - - - - Indicates whether the command specified in AutoApplyMode is applied each time a new image - subset is selected (e.g. when the player is running). - - - - - - - A value indicating whether this instance uses color NaN mode. - This option affects only float images, which contain NaN values. - - - - - - The color for display of NaN values in float images. - - - - - - If "true" a fix histogramm range is used for float images otherwise minimum and maximum - values are determined from image data. - Range is determined by FixFloatImageMinValue and FixFloatImageMaxValue. - - - - - - - The minimum value of fixed histogramm range for float images. - - - - - - - The maximum value of fixed histogramm range for float images. - - - - - - - - - - - - - - - The lower threshold for the BestFit operation. - The value is useful e.g. to skip large nearly black areas with some noise. - - - - - - - The upper threshold for the BestFit operation. - The value is useful e.g. to skip large white or nearly white areas. - - - - - - - The bit range. (Default: 8) - BitCountRange and Pixeltype are only persisted as indication for the 'optimal' range for the histogram. - Necessary for import of display setting for acquisition channels and for adjusting Low and High values if the bit range - of the imported display setting does not match the bit depth of the camera (setting) of the acquisition channel. - Note: - To persist the histogram range selected by the user, use the element HistogramRange of DisplaySetting. - - - - - - - The pixel type. (Default: Gray8) - BitCountRange and Pixeltype are only persisted as indication for the 'optimal' range for the histogram. - Necessary for import of display setting for acquisition channels and for adjusting Low and High values if the bit range - of the imported display setting does not match the bit depth of the camera (setting) of the acquisition channel. - - - - - - The mode: can be Spline, Ramp or None. Default is None. - - - - - - - - - - - - - If mode is Spline, these are the Spline Points. - If mode is Ramp, these are the Points for the Ramp mode. - If mode is None, there is supposed to be no Points node, i.e. Points are ignored. - - - - - - User-defined description of the channel. - - - - - - - - - - - - The color in which to display the channel if ColorMode=Color. - - - - - The color mode in which to display the channel. - - - - - - - - - - - - - - - The original color of the channel, i.e. the color the channel had on the most recent save event. - - - - - - If the DisplaySetting is in MergeChannels mode, - the channel is only displayed if IsSelected is true. - - - - - - - If ColorMode=Palette, the channel is displayed with the lookup-table (LUT) - defined by the PaletteName. - - - - - - - This optional element allows to embed a custom palette in a Channel. - It is used only when the ColorMode is Palette. - - You must also ensure that the PaletteName of the Channel is not one of the built-in palette names, - otherwise the custom palette will be ignored. It is recommended to use a - URN as the PaletteName of custom palettes. - - - - - - - - The Blue components of the palette RGB triples in their natural order encoded as a Base64 string. - For each palette entry there is one byte. - Blue, Green, and Red must have the same length, usually 256 bytes. - - - - - - - The Green components of the palette RGB triples in their natural order encoded as a Base64 string. - For each palette entry there is one byte. - Blue, Green, and Red must have the same length, usually 256 bytes. - - - - - - - The Green components of the palette RGB triples in their natural order encoded as a Base64 string. - For each palette entry there is one byte. - Blue, Green, and Red must have the same length, usually 256 bytes. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - The channel weight (ratio among all selected channels). - - - - - - The ChannelUnit contains scaling factor, offset and unit for each image - channel. The data are currently used by images with ion concentration - data. The display value is calculated by - - DisplayValue = Factor * PixelIntensity / MaxPixelIntensity + Offset. - - where "MaxPixelIntensity" is the maximum possible pixel intensity for the - data type (4095 or 255). - - - - - - - A new factor value for the channel. - - - - - A new offset value for the channel. - - - - - The Unit identifier. - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Characteristics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Angles for the image or scene composite image + (index 0) and for individual scenes (starting from index 1 for + the first scene). + + + + - - - The channel type identifier. - - + + + + + True if channel-merge display is enabled. + + + + + + The bit range for the histogram display. + + - - - - - - - - - - - + + + + + + - - - - - - - - - - An identifier to uniquely identify this channel. - Use this Id to refer to the respective Channel node within Dimensions/Channels/Channel. - - - - - - - The (user-defined) channel name. - - - - - - - The index of the channel. - In general, the channel elements in the channels collection are indexed by 0, 1, 2, etc. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - abstract - - Manufacturer info to be added to various microscope components. E.g Objective, Filter etc. - Provides attributes for recording common properties of these components such as Manufacturer name, Model etc, - all of which are optional. - - - - - - The manufacturer of the component. [plain text string] - - - - - The Model of the component. [plain text string] - - - - - The serial number of the component. [plain text string] - - - - - The lot number of the component. [plain text string] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The Tube Lenses collection holds all the tube lenses that are available from within the - microscope's tube lens revolver, optovar revolver or reflector changer. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A list of components where each part is divided by a colon. The purpose is to name the whole system. - For a confocal system the schema is "[LsmName][, RtScannerName][, CameraName][, StandName]". - - - - - - - - - - - - - - - - - - - An optional name, set by the user to identify different microscopes of the same stand type. - - - - - - - An identifier to uniquely identify this Microscope (unique among all microscope in this document). - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - The lightsource for the instrument. An instrument may have several light sources. - The type of lightsource is specified by one of the child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'. - Each of the light source types has its own Type attribute to further differentiate the light source - (eg, Nd-YAG for Laser or Hg for Arc). - - - - - - The light-source power. Units milliwatts[mW] - - - - - - - - - - A LightSource ID must be specified for each light source, and the individual - light sources can be referred to by their LightSource IDs (eg from Channel). - - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - - - - - - - - - - The LightEmittingDiode element is used to describe - various kinds of LED lamps. The content model is yet unspecific. - - - - - - - - - - - The type of filament. - - - - - - - - - - - - - - - - The type of Arc lamp. - - - - - - - - - - - - - - - Laser types are specified using two elements - the Type and the LaserMedium. - - - - - - The Laser element may contain a Pump sub-element which refers to - a LightSource used as a laser pump. - - - - + + + + + - Type is the general category of laser. + Defines the display setting for a single channel. - - - - - - - - - - - - - - - - - The Medium attribute specifies the actual laser medium - for a given laser type. - - Possible media for type MetalVapor: - Cu, Ag - - Possible media for type Excimer: - ArFl, ArCl, KrFl, KrCl, XeFl, XeCl, XeBr - - Possible media for type Gas: - N, Ar, Kr, Xe, HeNe, HeCd, CO, CO2, H2O, HFl - - Possible media for type SolidState: - NdGlass, NdYAG, ErGlass, ErYAG, HoYLF, HoYAG, Ruby, TiSapphire, Alexandrite - - Possible media for type Dye: - Rhodamine6G, CoumarinC30 - - Possible media for type Semiconductor: - GaAs, GaAlAs - - Possible media for type FreeElectron: - EMinus - - Possible media for type Other: - Other - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The Wavelength of the laser in nanometres[nm] - - - - - FrequencyMultiplication that may be specified. [units:none] - - - - - Whether or not the laser is tuneable [flag] - - - - - The Pulse mode of the laser. - - - - - - - - - - - - - - - If true the laser has a PockelCell to rotate the polarization of the beam. [flag] - - - - - - The rate in Hz at which the laser pulses if the Pulse type is 'Repetitive'. hertz[Hz] - - - - - - - - - - This describes a TIRF light-source. - - - - - - - - - - - The detector used to capture the image. - The Detector ID can be used as a reference within the Channel element in the Image element. - - - - - - - The Detector Gain for this detector, as a float. [units:none] - - - - - The Voltage of the detector (e.g. PMT voltage) as a float. volts[V] - - - - - The Detector Offset. [units:none] - - - - - The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] - - - - - - Gain applied to the detector signal. - This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] - - - - - - - Offset applied to the detector signal. [units:none] - - - - - - - The Type of detector. - E.g. - CCD - Charge-Coupled Device - PMT - Photomultiplier tube - EMCCD - Electron Multiplying Charge Coupled Device - FTIR - Fourier transform infrared spectroscopy - APD - Avalanche Photodiode - CMOS - complementary metal oxide semiconducto - EBCCD - electron-bombarded charge-coupled device - etc. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If the detector type is supposed to have an adapter, this is the respective adapter data. - E.g. a CCD can have a camera adapter with a magnification; a PMT or a Photodiode doesn't - have an adapter. - - - - - - - The default gamma value. [units:none] - The Reset function of the DisplaySetting will reset the gamma to this value. - The default is 1.0. - - - - - - - - An identifier to uniquely identify this Detector (unique among all detectors in this document). - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - The type of detector adapter used to capture the image. - - - - - - - The magnification of the detector adapter [units:none]. - - - - - - - - - A description of the microscope's objective lens. - Required elements include the lens numerical aperture, - and the magnification, both of which are floating - point (real) numbers. - The values are those that are fixed for a particular - objective: either because it has been manufactured to - this specification or the value has been measured on - this particular objective. - - - - - - - This is the type of correction coating applied to this lens. - - - - - - - - - - - - - - - - - - - - - - - - - This is the type of immersion medium the lens is designed to work with. - It is not the same as 'Medium' in Information/Image/ObjectiveSettings - (a single type) as here Immersion can have compound values like 'Multi'. - - - - - - - - - - - - - - - - - - The refractive index of the immersion. [units:none] - If this field is empty, the refractive index is assumed to be the default refractive index of the specified immersion. - - - - - - - The numerical aperture of the lens expressed as a floating point (real) number. - Expected range 0.02 - 1.5 [units:none] - The depth of focus can be retrieved via the formula: depthOfField = 2 * n * w / (lensNA)^2. - where: n = ImmersionRefractiveIndex, w = emission wavelength. - - - - - - The magnification of the lens as specified by the manufacturer - i.e. '40' is a 40x lens. [units:none] - - - - - The magnification of the lens as measured by a calibration process - i.e. '39.987' for a 40x lens. [units:none] - - - - - The working distance of the lens expressed as a floating point (real) number. Units are microns[um]. - - - - - Records whether or not the objective was fitted with an Iris. [flag] - - - - - - Records what type of phase-rings ("Phasenringe") the objective has. - Possible values: - Circular - Circular geometry - Annular - Annular geometry - PhaseRing0 - Phase ring 0 geometry - PhaseRing1 - Phase ring 1 geometry - PhaseRing2 - Phase ring 2 geometry - PhaseRing3 - Phase ring 3 geometry - Other - a phase ring is present, but its geometry is neither of the above ones. - - The rules are: - - If it is known for sure that the objective has no phase-rings, set the value "Circular" here. - - If one has no idea whether there is a phase-ring (and what type) or not, do not set this field at all. - - "Other" means: there is a phase-ring present, it is not of the type "Annular", "PhaseRing1", "PhaseRing2", - "PhaseRing3". In a future version it will be possible to parametrize the phasering in this case. - - "Annular" phase-ring currently is not supported by ZEN (however, it is a valid entry). - - - - - - - - - - - - - - - - - - Focal length [unit:micrometers] - - - - - - - Slit Aperture [unit.none] - - - - - - - - The refractive index of the cover glass this objective was designed for. [units:none] - - - - - - - The thickness of the cover glass this objective was designed for. [units:µm] - - - - - - - - An identifier to uniquely identify this Objective. - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - A description of the tube lens. - Required elements include the magnification. - A tube lens might be a tube lens, an optovar lens or a Bertrand lens. - - - - - - - The magnification of the lens as specified by the manufacturer [units:none] - - - - - - The type of the lens in the revolver element (might be a tube lens (aka "Optovar-lens") or a Bertrand lens or "other"). - - - - - - - - - - - - - - - An identifier to uniquely identify this TubeLens. - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - Filter set manufacturer specification. - Reflector information can be stored in a filter set: - - Excitation Wavelength: - lower wavelength -> ExcitationFilter.TransmittanceRange.CutIn, - upper wavelength -> ExcitationFilter.TransmittanceRange.CutOut, - - Emission Wavelength: - lower wavelength -> EmissionFilter.TransmittanceRange.CutIn, - upper wavelength -> EmissionFilter.TransmittanceRange.CutOut, - - BeamSplitter: store within Dichroic element. - - - - - - - The Filters placed in the Excitation light path. - - - - - - - - - - - The Filters placed in the Emission light path. - - - - - - - - - - - - An identifier to uniquely identify this FilterSet (unique among all filter-sets in this document). - - - - - - The name can be used to store the reflector name. - However, the canonical place for a human-readable name is Manufacturer.Model. - - - - - - - - A filter is either an excitation or emission filter. - It can be associated with an optional FilterWheel - Note: this is not the same as a FilterSet. - - - - - - - - - - - - - - - - - - - - - A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string] - - - - - - - An identifier to uniquely identify this Filter (unique among all filters in this document). - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - This records the range of wavelengths that are transmitted by the filter. It also records the maximum amount of light transmitted. - - - - - CutIn is the wavelength below which there is less than 50% transmittance for a filter. Units: nanometres[nm]. - - - - - CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units: nanometres[nm]. - - - - - CutInTolerance. Units: nanometres[nm]. - - - - - CutOutTolerance. Units: nanometres[nm]. - - - - - - The amount of light the filter transmits at a maximum [units:none]. - A fraction, as a value from 0.0 to 1.0. - - - - - - - An identifier to uniquely identify this TransmittanceRange (unique among all transmittance ranges in this document). - - - - - - The dichromatic beamsplitter or dichroic mirror used for this filter combination. - - - - - - - The beamsplitter for a filter combination may consist of more than one components, - e.g. if the respective filter set has three emission and three excitation wavelength ranges, - the beam splitter is supposed to consist of 3 splitter components. - Each is described by a wavelength. - - - - - - - - Wavelength in nm. - Light with a wavelength lower than this specified wavelength is reflected whereas light - with a larger wavelength is transmitted. Yet, this does not mean "perfectly reflected" or "perfectly - transmitted", it only gives an appropriate description of the beamsplitter. - - - - - - - - - - - An identifier to uniquely identify this Dichroic (unique among all dichroics in this document). - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - Description of a cylindrical lens (used for SPIM). - - - - - - - The focal length of the cylindrical lens. If this parameter is not given (or if it is NaN) - this means that no cylinder lens is present. The special value "0" means: a cylinder lens - is present, but its focal length is unknown. - [units: millimeter] - - - - - - - - An identifier to uniquely identify this CylindricalLens (unique among all cylindrical lenses in this document). - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - Description of a device with which a SIM (= Structured Illumination Microscopy) acquisition is performed - (e.g. ApoTome, Elyra HR-SIM). - - - - - - - The hardware version used for the acquisition. - - - - - - - - - - - - - - - - - An identifier to uniquely identify this SIMDevice (unique among all SIM-devices in this document). - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - - The optical transfer function. FilterSetRef refers to the set of - filters used in computing the OTF. - This element must contain a BinData element containing the - Base64-encoded OTF. These work the same way as they do for the - Data element within Image. - - - - - - - - - The variable type used to specify the size of pixel the OTF is designed for. - - - - - - The OpticalAxisAveraged is a boolean specifying whether or not - optical axis averaging was done. [flag] - - - - - - The width of the OTF. [units:none] - - - - - The height of the OTF. [units:none] - - - - - - - - - - This holds the setting applied to an objective as well as a - reference to the objective. - The ID is the objective used in this case. - - - - - - This ID refers to an instance of InstrumentObjective in Information/Instrument/Objectives. - - - - - - - A description of a Medium used for the lens. - The Medium is the actual immersion medium used in this case. - - - - - - - - - - - - - - - The position of the (first) correction collar (= correction ring) of an objective. - The CorrectionCollar is an adjustable ring on the objective. - If the parameter is not available, double.NaN is returned. - Each correction collar has an arbitrary scale on it. So, use percentage as unit. [units:percentage]. - - - - - - - The position of the second correction collar (= correction ring) of an objective. - The CorrectionCollar is an adjustable ring on the objective. - If the parameter is not available, double.NaN is returned. - Each correction collar has an arbitrary scale on it. So, use percentage as unit. [units:percentage]. - - - - - - - A description of a correction controller operating mode used for the lens. - Depending on the mode, either values of CorrectionCollar and CorrectionCollar2, - or values of CorrectionControllerBottomThickness and CorrectionControllerImagingDepth are available. - - - - - - - The parameter cover bottom thickness of the correction controller [unit: microns]. - - - - - - - The parameter imaging depth of the correction controller [unit: microns]. - - - - - - - The RefractiveIndex is that of the immersion medium. This is - a ratio so it is also unit-less. [units:none] - - - - - - - - - - By the Id value, a microscope contained in the Instrument list can be referenced. Ensure - there exists a microscope with the referenced Id. - - - - - - - - By the Id value, a LightSource contained in the Instrument list can be referenced. Ensure - there exists a LightSource with the referenced Id. - - - - - - - - By the Id value, a Detector contained in the Instrument list can be referenced. Ensure - there exists a Detector with the referenced Id. - - - - - - - - By the Id value, an Objective contained in the Instrument list can be referenced. Ensure - there exists an Objective with the referenced Id. - - - - - - - - By the Id value, a cylindrical lens contained in the Instrument list can be referenced. Ensure - there exists a CylindricalLens with the referenced Id. - - - - - - - - By the Id value, a Tube Lens contained in the Instrument list can be referenced. Ensure - there exists a Tube Lens with the referenced Id. - - - - - - - - By the Id value, a FilterSet contained in the Instrument list can be referenced. Ensure - there exists a FilterSet with the referenced Id. - - - - - - - - By the Id value, a Filter contained in the Instrument list can be referenced. Ensure - there exists a Filter with the referenced Id. - - - - - - - - By the Id value, a Dichroic contained in the Instrument list can be referenced. Ensure - there exists a Dichroic with the referenced Id. - - - - - - - - By the Id value, a SIMDevice contained in the Instrument list can be referenced. Ensure - there exists a SIMDevice with the referenced Id. - - - - - - - - By the Id value, an OTF contained in the Instrument list can be referenced. Ensure - there exists an OTF with the referenced Id. - - - - - - - - The EM detector used to capture the image using an electron microscope. - The Detector ID can be used as a reference within the Channel element in the Image element. - - - - - - - - An identifier to uniquely identify this EM Detector. - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - The Type of detector. - E.g. - EBSD - Other - etc. - - - - - - - - - - - - The Brightness for this detector, as a double in percent on range [0..100]. - - - - - The Contrast for this detector, as a double in percent on range [0..100]. - - - - - - The Detector Technology of this detector. - E.g. - PhotomultiplierTube - A PMT based detector characterized by 'fast' response and non-linear response to contrast control, such as SE2. - Diode - A diode-based detector characterized by 'slower' response and a more linear response to contrast control, such as BSD4. - Other - Any other detector technology. - - - - - - - - - - - - - - - The Electron Sensitivity of this detector: which kind of electrons can be detected? - E.g. - Unknown - Unknown, should not occur in a well configured system. - PrimaryElectrons - Sensitive to primary electrons, like STEM. - SecondaryElectrons - Sensitive to secondary electrons, like SE2. - BackScatteredElectrons - sensitive to back scattered electrons, like BSD4. - Cathodoluminescence - Sensitive to cathodoluminescence, like CL. - Mixed - The detector has no clear main sensitivity. - Other - Other kinds of sensitivity. - - - - - - - - - - - - - - - - - - The Ion Sensitivity for this detector. - E.g. - Unknown - Unknown, should not occur in a well configured system. - IonInsensitive - The detector is not sensitive to secondary ions, as in most non-SESI other detectors. - IonSensitive - The detector is or can be configured to be sensitive to secondary ions, like SESI. - - - - - - - - - - - - - - - - The column used to acquire the image using an electron microscope. - - - - - - - - An identifier to uniquely identify this Column. - - - - - - Use of this field is depreciated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - The beam current. - Unit: "A" - - - - - - - The estimated electron dose. - Unit: "e/nm²" - - - - - - - electrical high tension (accelerating voltage) in effect. - When the column is off, the value can be set but has no effect. When the column is turned on, - it will go to the LSV. Setting the value when the column is on will change the EHT immediately. - This should report as continuously variable but not all values will be achievable so writers - should expect differences between CurrentValue and LastSetValue. - Unit: "V" - - - - - - - The distance from the lower lens to the expected tightest convergence point of the beam. - Unit: "m" - - - - - - - The stigmation value in the (scan rotation zero) column X direction. Should be unitless on range [-1..1]. - - - - - - - The stigmation value in the (scan rotation zero) column Y direction. Should be on unitless range [-1..1]. - - - - - - - The full swing deflection of a scan perpendicular to the optical axis. This is not necessarily the image width or height. - If the scanner is using the full range in X, it would be the image width, but this is not known to the column. - A value of 300um means the beam is deflected +/-150um from the optical axis by a full range scan in the X or Y direction. - Settings on other interfaces (tilt correction) may cause the deflection amplitude in Y to be less than in X. - Unit: "m" - - - - - - - The shift FROM the center of the optical axis TO the center of the image in the (scan rotated) IMAGE X axis direction. - Note: this definition means that if a feature in the center of the image does not shift as scan rotation is varied, - then the beam shift values reported will change as the scan is rotated (as in SmartSEM Jan 2019). - Unit: "m" - - - - - - - The shift FROM the center of the optical axis TO the center of the image in the (scan rotated) IMAGE Y axis direction. - Note: this definition means that if a feature in the center of the image does not shift as scan rotation is varied, - then the beam shift values reported will change as the scan is rotated (as in SmartSEM Jan 2019). - Unit: "m" - - - - - - - The angle FROM the microscope reference +X axis direction TO the image +X axis direction around the microscope - reference +Z axis by the right-hand rule. When scan rotation is changed, the feature in the center of the image - should rotate but not translate, even if beam shift is set (as in SmartSEM Jan 2019). - - A positive rotation causes the image of the surface of a perpendicular sample to rotate clockwise, meaning that - the features in the image are moving counterclockwise. - Unit: "Degree" - - - - - - - Is the beam currently blanked?. May be disabled based on column state. - - - - - - - The liner voltage (for FESem). - Unit: "V" - - - - - - - The condenser lens voltage (for FIB). - Unit: "V" - - - - - - - The objective lens voltage (for FIB). - Unit: "V" - - - - - - - - The stage used to acquire the image using an electron microscope. - - - - - - - - An identifier to uniquely identify this Stage. - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - The stage type, such as eucentric or cartesian. - Values: - UnknownStage - The stage type is unknown. This should not occur in a well configured system. - CartesianStage - The stage is a cartesian stage with Z, X, Y, T, R stacking order. - EucentricStage - The stage is an eucentric stage with Z, T, X, Y, M, R stacking order. - - - - - - - - - - - - - - The position of the stage in the microscope reference X direction. The positive direction is oriented EAST. - The values will be calibrated to be correct in scale, and the zero position will place the center of the - dovetail mount under the optical axis. - Unit: "m" - - - - - - - The position of the sample stage in the microscope reference Y direction when the tilt is zero. - In a Eucentric Type stage, the Y axis direction is rotated around the X axis by the tilt value. - The positive direction is oriented NORTH at a tilt of zero. The values will be calibrated to be - correct in scale, and the zero position will place the center of the dovetail mount under the optical - axis at a tilt of zero. - Unit: "m" - - - - - - - The position of the sample stage in the microscope reference Z direction. The positive direction is oriented UP. - The values will be calibrated to be correct in scale, and the zero position will be the DOWN limit of travel. - Unit: "m" - - - - - - - The rotation of the sample stage around the microscope reference Z direction when the tilt is zero. - The rotation axis is tilted around the X axis by the tilt value. The positive direction is determined by - the right-hand rule and the stage positive Z direction. The stage value reported must follow this convention. - The value will be calibrated to be correct in scale, and the zero position will be calibrated to be the position - that places the dovetail in the upright orientation (backstop to the left, threads for the transfer rod on the right) - in a scan rotation zero image. - Unit: "Degree" - - - - - - - The rotation of the sample stage around the stage X axis. The positive direction is determined by the right-hand - rule and the stage positive X direction. The stage value reported must follow this convention. The values will be - calibrated to be correct in scale, and the zero position will place the dovetail surface perpendicular to the - microscope Z reference direction. - Unit: "Degree" - - - - - - - The position of the sample stage in the microscope reference Z direction. In Eucentric Type stages, the M axis - is rotated around the positive X axis by the tilt value. The positive direction is oriented UP. The values will - be calibrated to be correct in scale, and the zero position will be the DOWN limit of travel. - - In relation to Z and M, two calibration values are required.The first is the distance from the tilt axis to the - lens when Z is at the lowest travel. This is similar to the current lens to flat value. The second is the distance - from the dovetail flat to the tilt axis when M is at the lowest travel. With these two calibrations, it should be - possible to place a sample at tilt eucentric and at a specific working distance if the dovetail flat to sample - surface measurement is known. - Unit: "m" - - - - - - - The information whether tilt correction is on. - - - - - - - The stage tilt correction angle. - Unit: "Degree" - - - - - - - - The particle beam scan generator used to acquire the image using an electron microscope. - - - - - - - - An identifier to uniquely identify this Scan component. - - - - - - Use of this field is deprecated. The canonical place for a human-readable - name is Manufacturer.Model. - - - - - - - The scan type. - Values: - Raster - Serpentine - DoubleSerpentine - BidirectionalLineMill - UnidirectionalLineMill - UnidirectionalLineScan - Other - - - - - - - - - - - - - - - - - - The dwell time that will be used for the image acquisition. The clock interval can be reflected in the datapoint SmallestIncrement - value. Scan speed-based systems should take the last set value, configure to the closest scan speed in log(time) space and reflect - the dwell time of the selected scan speed in the current value. Be sure to check the SmallestIncrement for dwell time. - It is not continuously variable. - Unit: "s" - - - - - - - The number of times to scan a line at the selected dwell time before the scan progresses to the next line in the frame. - LineAverages = 1 means a line will be scanned once. - LineAverages = 2 means a line will be scanned twice. - LineAverages = 0 is invalid. - - - - - - - An acquisition is made of a number of frames, were only every Nth line in each frame is scanned, where N is the Interlacing. - With Interlacing = 1, it is a conventional scan. - With Interlacing = 2, the acquisition is scanned in 2 frames. - In the first frame, the 1st, 3rd, 5th… lines are scanned. - In the second frame, the 2nd, 4th, 6th… lines are scanned. - With Interlacing = 3, in the first frame, the 1st, 4th, 7th… lines are scanned. - . - The pixel data in the MMF should update with the partial scan data as the scan progresses. - - - - - - - An acquisition is made of a number of full frames, and the resulting image is the average of all the frames. - In live acquisition the provided pixel data is a rolling average and is updated on a line/block basis as the acquisition progresses. - FrameAverages = 1 means the frame is scanned once. - FrameAverages = 2 means the frame is scanned twice. - FrameAverages = 0 is invalid. - . - In a single acquisition, the pixel data is provided on a line/block basis as the acquisition progresses. - I.e., the user sees a live image that is continuously updating will the acquisition is progressing. - - - - - - - - - - - - - - - - - - - - Specifies at which event a track switch has been performed. Possible values are: - Line - after each scan line - Frame - after each frame - FrameFast - after each frame without movement of slow hardware and - ZStack - after each z stack. - The value is the same for all tracks in a recording. - - - - - - - - - - + + + + The normalized low (=black) value of the mapping + range. + - - - - The switch order of the tracks. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This associates a timestamp to each t-coordinate. The data must not be confused - with the "acquisition time" of a camera frame. It has just the meaning of "some - representative and informative" timestamp which is associated with each t-coordinate. - For a simple timelapse document this might be the real acquisition time, but for a - tiled image there is no simple "acquisition time for an x-y-plane". In addition, we make - no promises if this corresponds to the "real acquisition time" or the interval which - was specified when setting up the experiment (=theoretical interval vs real interval). - - The basic idea is: we have one absolute point in time (given by the StartTime field) which - acts as a reference point in time. Then we give the relative time to this reference for t=0, - t=1 and so on. Note that specifying the reference point is optional - if it is not given - then we just have time offsets for each t-coordinate. - - Remarks: - - Specifying just the StartTime but not the TimeStamps is quite pointless, although it - is not forbidden. - - If there are less offsets given than there are t-coordinates in the documents it means - "no timestamp available" for the surplus t-coordinates. - - If there are more offsets given, they are simply ignored. [Unit: Seconds] - - Time Stamps: - For each index in a time series acquisition, a time stamp can be stored in a list. - I.e. the number of time stamps equals Information/Image/SizeT. - (Time stamps must not be mixed up with the subblock/slice-specific acquisition time! - E.g. in case of an image with SizeT = 10 and SizeZ = 20, there are 10 time stamps, - but 200 different acquisition time items.) - - In most LSM cases, there will be a large number of time stamps and then the time stamps will be - stored in an attachment. - Yet, for a small number of time stamps, they can be stored within this xml data. - - - - - - - - Reference point in time (optional), as round trip format string. - - + + + The normalized high (=white) value of the mapping + range. + - - - - Definition of the offsets for each T Index. This may be given as - start+offset or as an explicit list [unit:s]. - - + + + The gamma value to be applied to the mapping + range. + - - - - - - - This associates a spatial point for each Z Index. The data must not be confused - with the "focus position" of a camera frame. It has just the meaning of "some - representative and informative" position which is associated with each z-index. - The offsets may be positive or negative. They could also be not monotone - although - this would be an unusual experiment. - The position of Z=0 is StartZPosition + Start (in case of ZInterval) or Start + ZOffsetList[0]. - This approach avoids ambiguities when StartZPosition is not given. [unit:micrometers] - - - - - - - - The shear definition of the z-axis with respect to x-y. - - - - - - - - No shear present, the z-axis is strictly orthogonal to x-y planes - (e.g. µSPIM fully de-skewed or standard z-stack). - - - - - - - The image data in z-direction is sheared and rotated about the x axis by 60 degrees (e.g. µSPIM raw data). - - - - - - - The image data in z-direction is pixel interpolated x-shear corrected and rotated about the x axis by 60 degrees (e.g. de-sheared µSPIM raw data). - - - - - - - The image data in z-direction is integer x-shear corrected by the bounds and rotated about the x axis by 60 degrees (e.g. roughly de-sheared µSPIM raw data). - - - - - - - - - - Specifies the chirality of the coordinate system defined by - - X axis in a subblock, from left to right - - Y axis in a subblock, from top to bottom (-> origin in the top-left corner) - - Z axis given by Z-index - - This chirality is used when arranging the z-slices spatially according to their Z-index. - It is recommended to ensure that the chirality (and the order of the z-slices) is unchanged - when arranging the z-slices according to their associated distances (as given by ../Dimensions/Z/Positions). - - - - - - - - The coordinate-system is orientated left-handed. - - - - - - - The coordinate-system is orientated right-handed. - - - - - - - The orientation of the coordinate-system is undefined or not known. - This is the default to be assumed if this field is not present. - - - - - + + + Indicates whether the command specified in + AutoApplyMode is applied each time a new image subset is + selected (e.g. when the player is running). + - - - - THIS IS AN EXPERIMENTAL DEFINITION! - - We define the z-axis to be collinear with the optical axis. On this axis the z-coordinates - of the focal plane are measured, and their distances are found in the Z-labels - (defined under ../Dimensions/Z/Positions) and the FocusPosition-field found in subblock-metadata. - The direction of the axis may either be “from specimen to objective” or “from objective to specimen”. - In this coordinate system the specimen is at a fixed position. Note that the origin of the coordinate - system is _not_ defined here. - Possible values are: FromSpecimenToObjective, FromObjectiveToSpecimen and undefined. - Undefined is the default (and to be assumed if this element is not present). - - Note that the coordinate system defined here is different to the one defined with "XYZHandedness". - - - - - - - - The z-axis is pointing from specimen to objective. - - - - - - - The z-axis is pointing from objective to specimen. - - - - - - - The direction of the z-axis is undefined/not known. - This is the default to be assumed if this field is not present. - - - - - - - - - - Description of mode of operation of the Z-Drive. "Continuous" means that - the z-drive did not stop while acquiring the image. "Step" means that the - Z-drive did not move during the acquisition of the image. - Used for SPIM. - - - - - - - - + + + A value indicating whether this instance uses + color NaN mode. This option affects only float images, which + contain NaN values. + - - - - In Continuous-mode, this specifies the speed of the z-drive. - Used for SPIM. [unit:µm/s]. - - + + + The color for display of NaN values in float + images. + - - - - Reference position [unit=µm]. - - + + + If "true" a fix histogramm range is used for + float images otherwise minimum and maximum values are determined + from image data. Range is determined by FixFloatImageMinValue + and FixFloatImageMaxValue. + - - - - Definition of the offsets for each Z index. This may be given as - start+offset or as an explicit list [unit=µm]. - - + + + The minimum value of fixed histogramm range for + float images. + - - - - - - - - This associates a rotation angle to each R index. [unit: degrees] - - - - - - - - Reference position [unit=degrees]. - - + + + The maximum value of fixed histogramm range for + float images. + - - - - Definition of the angles (for each R index). - - + + + + + + + - - - - - - - - This associates a phase to each H index. [unit: none] - Used in SIM acquisitions where the data is recorded from various illumination grating phase shifts. - - If a channel in this document is marked as an Airy-scan image (by Channel/ChannelType), then - the H-dimension has a different meaning - then the H-dimension is used to label the images - from the different fibers of an Airy-scan-detector-array. - - - - - - - - Reference position [unit=µm]. - - + + + The lower threshold for the BestFit operation. + The value is useful e.g. to skip large nearly black areas with some noise. + + - - - - Definition of the phase offsets for each H index. - This may be given as an explicit list or as start+offset [unit=none]. - - + + + The upper threshold for the BestFit operation. + The value is useful e.g. to skip large white or nearly white areas. + + - - - - - - - - This associates an illumination direction to each I index. Values: e.g. from left=0, from right=1. - [unit: none] - - - - - - - - Reference position [unit=µm]. - - + + + The bit range. (Default: 8) + BitCountRange and Pixeltype are only persisted as indication for the + 'optimal' range for the histogram. Necessary for import of + display setting for acquisition channels and for adjusting Low and High + values if the bit range of the imported display setting does + not match the bit depth of the camera (setting) of the acquisition channel. + Note: To persist the histogram range selected by the user, use + the element HistogramRange of DisplaySetting. + - - - - Definition of the illumination values for each I index. [unit: none] - - + + + The pixel type. (Default: Gray8) + BitCountRange and Pixeltype are only persisted as indication for the + 'optimal' range for the histogram. Necessary for import of + display setting for acquisition channels and for adjusting Low and High + values if the bit range of the imported display setting does + not match the bit depth of the camera (setting) of the acquisition channel. + + - - - - - - - - This associates a rotation angle to each V index. This dimension is used - with SPIM-acquisitions, where it denotes the rotation of the - specimen [unit: degrees] - - - - - - - - Directional vector specifying the axis of rotation. We have three numbers - which give the components in (physical) x-, y- and z-direction (in a left-handed - coordinate-system). - The scaling used for the numbers is arbitrary (since only the direction is what matters), - however the scaling must be the same for x-y- and z-direction. - A rotation around the y-axis corresponds to "0 1 0", rotation - around the x-axis corresponds to "1 0 0". - For the time being, only these two values are expected. - If this parameter is not given, we default to "rotation around y-axis ("0 1 0"). - - - - - - - - - - + + + The mode: can be Spline, Ramp or None. Default is + None. + + + + + + + + - - - - Tentative definition: Position of the "center of the image" in stage coordinates, - given as three doubles for the X-,Y- and Z-position. [unit:µm] - - - - - - - - - - + + + If mode is Spline, these are the Spline Points. + If mode is Ramp, these are the Points for the Ramp mode. If mode + is None, there is supposed to be no Points node, i.e. Points are ignored. + + - - - - Reference position [unit=degrees]. - - + + + User-defined description of the channel. + - - - - Definition of the angles (for each V-index). - - + + + + + + + + + + The color in which to display the channel if + ColorMode=Color. + - - - - - - - - Regions from Tiles Acquisition. - - - - - - - - - - + + + The color mode in which to display the + channel. + + + + + + + + + + + - - - - - - - - Mosaic Tiles. - - - - - - - - Reference position for X dimension [unit=µm]. - - + + + The original color of the channel, i.e. the color the channel + had on the most recent save event. + - - - - Reference position for Y dimension [unit=µm]. - - + + + If the DisplaySetting is in MergeChannels mode, + the channel is only displayed if IsSelected is true. + + - - - - Tile offset in X [unit: micrometers] - - + + + If ColorMode=Palette, the channel is displayed + with the lookup-table (LUT) defined by the PaletteName. + + - - - - Tile offset in Y [unit: micrometers] - - + + + This optional element allows to embed a custom + palette in a Channel. It is used only when the ColorMode is + Palette. You must also ensure that the PaletteName of the + Channel is not one of the built-in palette names, otherwise the + custom palette will be ignored. It is recommended to use a URN + as the PaletteName of custom palettes. + + + + + + The Blue components of the + palette RGB triples in their natural order encoded as a Base64 + string. For each palette entry there is one + byte. Blue, Green, and Red must have the same + length, usually 256 bytes. + + + + + The Green components of the + palette RGB triples in their natural order encoded as a Base64 + string. For each palette entry there is one + byte. Blue, Green, and Red must have the same + length, usually 256 bytes. + + + + + The Green components of the + palette RGB triples in their natural order encoded as a Base64 + string. For each palette entry there is one + byte. Blue, Green, and Red must have the same + length, usually 256 bytes. + + + + - - - - - - - - This element contains information about the "X-dimension". - - - - - - - - The stage orientation for the axis. Possible values: 1, -1. Undefined: 0 or all other values. - - + + + The channel weight (ratio among all selected + channels). + - - - - - - - This element contains information about the "Y-dimension". - - - - - - - - The stage orientation for the axis. Possible values: 1, -1. Undefined: 0 or all other values. - - + + + The ChannelUnit contains scaling factor, offset + and unit for each image channel. The data are currently used by + images with ion concentration data. The display value is + calculated by DisplayValue = Factor * PixelIntensity / + MaxPixelIntensity + Offset. where "MaxPixelIntensity" is the + maximum possible pixel intensity for the data type (4095 or + 255). + + + + + + A new factor value for the + channel. + + + + + A new offset value for the + channel. + + + + + The Unit identifier. + + + + + + + + + + + + + + + The channel type identifier. + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - Information about pyramid for this scene. - - - - - - - The unique identifier of the corresponding region (tile region or single tile region). - - - - - - - An optional hint string to be specified with the scene. - - - - - - - - - - - - - - - - The array name if the scene was acquired from a single position which is part of an array. - - - - - - - The category which is optionally specified for the scene/region. - - - - - - - The contour center position (X and Y) of the scene/region in absolute stage coordinates (µm). This specifies the center position of the bounding box. - Note the string representation of the center position: value for X and Y are separated by comma, e.g. "-8000.2,6000.5". - - - - - - - The contour size of the scene/region in absolute stage coordinates (µm). This specifies the bounding box size of the contour which was defined to setup the region. - It makes only sense for extended regions, e.g. tile regions with more than one tile. - - - - - - - - - - - - - - - - Shape definition from which this scene/region is part of. This is relevant if the region - was setup from an underlying sample carrier, e.g. a multiwell. - - - - - - - - - - - - - - - - - - If the region is rectangular, this is the column number of tiles in the region. - This parameter only makes sense if the tiling is like a checkerboard. - - - - - - - If the region is rectangular, this is the row number of tiles in the region. - This parameter only makes sense if the tiling is like a checkerboard. - - - - - - - The "Positions" define a list of all stage positions for acquired tiles. - This list might not be complete. For example, if the number of positions is too large, - it might only contain the first acquired position. - - - - - - - - - - - - - The zero based scene index which corresponds to the StartS immage coordinate. - - - - - - - - - - - - Specifies whether the pyramid is complete. It it is marked as sane, then we assume - that the whole scene is covered by the pyramid _and_ that all pyramid-layers are present - and have the correct content. - If this element is not present, we assume that the pyramid is broken (and it might not be leveraged - in some cases). - - - - - - - The number of pyramid layers. Counting starts with the layer above the original resolution layer. - - - - - - - A boolean describing whether the tiles provide a minimal coverage. - - - - - - - The factor by which consecutive pyramid layers have been shrunken. - - - - - - - Specifies the method that was used for minifying the pyramid tiles. - - - - - - - - - - - - - - - - - - - - - - - - - Format: "X1,Y1 X2,Y2 .. Xn,Yn" - - - - - - - - - The X, Y and Z attributes are the real hardware device positions (stage and focus). [unit: micrometers] - - - - - - - - - The TheM attribute defines the corresponding M index for this position. - It is numbered from 0 and corresponds to the StartM-index of the subblocks of this image document. - NOTE: - If there is a TheM defined, the stage position refers to the center of the tile with index=TheM. - If there is no TheM defined, then the stage position refers to the center of the complete scene. - - - - - - - - There must be at least one element per channel in the Image, even for a single-plane image. - Information about how each channel was acquired is stored here. - - - - - - - - - AiryScan Draft - - This field (in a sense) has the highest precedence when determining/assigning - the microscopy method how a channel was acquired. Usually, the AcquisitionMode-field - is used to give an indication which microscopy method was used. But if this field - "ChannelType" is present, it has higher precedence - i. e. it should be checked first. - - - - - - - - This channel represents a heightmap. Note that additional restrictions apply when declaring a channel as heightmap. - Some of the restrictions are: a corresponding "TopographyDataItem"-structure has to be present, the channel must - be of pixel-type Gray32Float. - For details see DS_TopoImageExtensions.docx. - - - - - - - - - - - AiryScan Draft - - This channel contains a processed (combined) super-resolution from an Airy-scan-acquisition in draft quality - - for preview purposes. - TODO: - Do we find this one for all Airy-Scan-types or only for Super-Resolution? - - Do we need to distinguish between super-resolution and virtual pinhole and multibeam? - - - - - - AiryScan Draft - - This channel contains the images of all sensors in the Airy-Scan-sensor- - array. The scan is intended to give a higher-resolution image. - This also implies that an H-dimension is present in this document, and - that (in this document) the H-dimension is used to label the images - captured from the different sensors in the Airy-Scan-sensor-array. - Note that this value is used for all types of Airy-Scan (currently, this is - Super-Resolution, Virtual-Pinhole and Multibeam). - Note: this value "AiryScanRawSr" is deprecated, use "AiryScanRaw" instead. - - - - - - AiryScan Draft - - This channel contains the images of all sensors in the Airy-Scan-sensor- - array. The scan is intended to give a higher-resolution image. - This also implies that an H-dimension is present in this document, and - that (in this document) the H-dimension is used to label the images - captured from the different sensors in the Airy-Scan-sensor-array. - Note that this value is used for all types of Airy-Scan (currently, this is - Super-Resolution, Virtual-Pinhole and Multibeam). - Note: this value is synonymous to "AiryScanRawSr", this one is the recommended one. - - - - - - AiryScan Draft - - This channel contains the (processed) super-resolution image (typically processed - from a raw image of ChannelType=AiryScanRaw, all the different H-dimension - images have been condensed into a resolution-enhanced image). - - - - - - AiryScan Draft - - This channel contains the (processed) "virtual pinhole" image (typically processed - from a raw image of ChannelType=AiryScanRaw, all the different H-dimension - images have been condensed into a "virtual-pinhole" image). - TODO - find better wording... - - - - - - AiryScan Draft - - This channel contains the (processed) "multi-beam" image (typically processed - from a raw image of ChannelType=AiryScanRaw, all the different H-dimension - images have been condensed into a "multi-beam" image). - TODO - find better wording... + + + + An identifier to uniquely identify this channel. + Use this Id to refer to the respective Channel node within + Dimensions/Channels/Channel. + + + + + The (user-defined) channel name. - - - - - AiryScan Draft - - This channel contains the Sheppard-sum created from 4 fiber-rings. - TODO: add explanation... + + + + + The index of the channel. In general, the + channel elements in the channels collection are indexed by 0, 1, 2, etc. - - - - - - This channel contains the result of an online unmixing acquisition with a laser-scanning microscope. (i.e. Online-Fingerprinting) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + abstract + Manufacturer info to be added to various microscope + components. E.g Objective, Filter etc. Provides attributes for recording + common properties of these components such as Manufacturer name, Model etc, + all of which are optional. + + + + + The manufacturer of the component. [plain text + string] + + + + + The Model of the component. [plain text + string] + + + + + The serial number of the component. [plain text + string] + + + + + The lot number of the component. [plain text + string] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The Tube Lenses collection holds all the tube + lenses that are available from within the microscope's tube lens + revolver, optovar revolver or reflector changer. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A list of components where each part is divided + by a colon. The purpose is to name the whole system. For a + confocal system the schema is "[LsmName][, RtScannerName][, CameraName][, + StandName]". + + + + + + + + + + + + + + + + + An optional name, set by the user to identify + different microscopes of the same stand type. + + + + + + An identifier to uniquely identify this Microscope (unique among + all microscope in this document). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. - - - - - - - - - - - - - This channel may contain NaN values - used to determine if IP functions can work with this type of images. - - - - - - - - AcquisitionMode describes the type of microscopy performed for each channel. - Possible modes: - WideField - LaserScanningConfocalMicroscopy - CLSM or LSCM - SpinningDiskConfocal - SlitScanConfocal - StructuredIllumination - SingleMoleculeImaging - TotalInternalReflection - FluorescenceLifetime - SpectralImaging - FluorescenceCorrelationSpectroscopy - NearFieldScanningOpticalMicroscopy - NSOM - SecondHarmonicGenerationImaging - Second harmonic imaging microscopy (SHIM) - PALM - photo-activated localization microscopy, photo-activation localization microscopy - STORM - stochastic optical reconstruction microscopy - STED - stimulated emission depletion - TIRF - total internal reflection fluorescence (TIRFM) - FSM - Fluorescence speckle microscopy - LCM - Laser capture microdissection - SPIM - Selective Plane Illumination - SEM - Scanning Electron Microscopy - FIB - Focus Ion Beam - FIB-SEM - Focus Ion Beam - Scanning Electron Microscopy - AngularIllumination - Angular illumination, uses bright field illumination via LED Matrix - LatticeLightsheet - Lattice lightsheet - StructuredIlluminationSr - Structured Illumination with super resolution (Elyra, Lattice SIM) - LightField - Light field microscope (LFM) based on micro lens array - Other - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The method of illumination used to capture the channel. - Possible values: - Transmitted - Epifluorescence - Oblique - NonLinear - Other - "Epifluorescence" in this context just describes the fact that the objective is used to bring - the fluorescence inducing light ("the illumination") to the specimen (in contrast to transmitted illumination e.g.). - This does not neccessarily require that we do a fluorescence acquisition. - - - - - - - - - - - - - - - - ContrastMethod describes the technique used to achieve contrast for each channel. - Possible values: - Brightfield - Phase - DIC - Differential Interference Contrast - HoffmanModulation - Hoffman Modulation Contrast (HMC) - ObliqueIllumination - PolarizedLight - Polarization Microscopy - Darkfield - Fluorescence - MultiPhotonFluorescence - multi-photon excitation was employed - TIE - Transport Of Intensity Equation - Other - - - - - - - - - - - - - - - - - - - - - - Illumination Wavelength as either a single Peak or a list of Ranges. - This characterizes the light used for illuminating the specimen. - More specific, it is about the light that actually hits the specimen, not the light as it leaves the light source. - - - - - - - Detection Wavelength as either a single Peak or a list of Ranges. - This characterizes the part of the spectrum for which the detector used for this channel is actually sensitive for. - It gives in any case the "net result" - it does not matter what technique is used to limit the detection range. - - - - - - - Wavelength of excitation for this channel in nanometers. - This characterizes the fluorochrome - the fluorochrome one was interested in this channel. - It has just an informative meaning - it is not meant to characterize the fluorochrome in depth, - that is what the DyeId is meant for. [units:nanometers]. - - - - - - - Wavelength of emission for this particular channel, in nanometres[nm]. - This information refers to the fluorochrome. - - - - - - - Gives the "effective numerical aperture" of the optical imaging used for acquiring this channel. The "effective NA" may include other circumstances - than merely the NA of the objective lens, so the two are not necessarily interchangeable. - - - - - - The dye id which is unique within the original dye database. - - - - - The id (Guid) of the original database this dye is taken from. - - - - - - The optional PinholeSize element allows specifying adjustable pinhole diameters for confocal microscopes. - The Pinhole is track specific. I.e. channels of the same track need to have the same value here. - [units:micrometers]. - - - - - - - The size of the pinhole in units of the airy disc. Since this value cannot (easily) - be derived from the above PinholeSize (in micrometers), the rule is that we store this - value separately. - [units:none]. - - - - - - The geometry of the pinhole, either circular or rectangular. + + + + + + + The lightsource for the instrument. An instrument may have + several light sources. The type of lightsource is specified by one of the + child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'. + Each of the light source types has its own Type attribute to further differentiate + the light source (eg, Nd-YAG for Laser or Hg for Arc). + - - - - - - - - - + + + + The light-source power. Units + milliwatts[mW] + + + + + + + + + A LightSource ID must be specified for each light + source, and the individual light sources can be referred to by their + LightSource IDs (eg from Channel). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + + + + + + + + + - - The Fluor element is used for fluorescence images. - This is the name of the fluorophor used to produce this channel [plain text string]. - This element is just for informative purposes. The fluorochrome is far better identified by the - DyeId. However - if you do not have a DyeId at hand, you may use this field in order to give at least - an informative string. - + The LightEmittingDiode element is used to describe + various kinds of LED lamps. The content model is yet unspecific. + - - + + + + + + + + + + The type of filament. + + + + + + + + + + + + + + + + + The type of Arc lamp. + + + + + + + + + + + + + + + + + Laser types are specified using two elements - the Type and the + LaserMedium. + + + + + The Laser element may contain a Pump sub-element + which refers to a LightSource used as a laser pump. + + + + + + Type is the general category of laser. + + + + + + + + + + + + + + + + + The Medium attribute specifies the actual laser + medium for a given laser type. Possible media for + type MetalVapor: Cu, Ag Possible media for type + Excimer: ArFl, ArCl, KrFl, KrCl, XeFl, XeCl, XeBr + Possible media for type Gas: N, Ar, Kr, Xe, HeNe, HeCd, CO, CO2, + H2O, HFl Possible media for type SolidState: + NdGlass, NdYAG, ErGlass, ErYAG, HoYLF, HoYAG, Ruby, TiSapphire, Alexandrite + Possible media for type Dye: Rhodamine6G, CoumarinC30 + Possible media for type Semiconductor: GaAs, GaAlAs + Possible media for type FreeElectron: EMinus + Possible media for type Other: Other + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The Wavelength of the laser in + nanometres[nm] + + + + + FrequencyMultiplication that may be specified. + [units:none] + + + + + Whether or not the laser is tuneable [flag] + + + + + The Pulse mode of the laser. + + + + + + + + + + + + + + + If true the laser has a PockelCell to rotate the polarization + of the beam. [flag] + + + + + The rate in Hz at which the laser pulses if the + Pulse type is 'Repetitive'. hertz[Hz] + + + + + + + + - - The NDfilter element is used to specify the combined effect of any neutral density filters used. - [units:optical density expressed as a PercentFraction] - + This describes a TIRF light-source. + - - + + + + + + + + + + - - The PockelCellSetting used for this channel. - This is the amount the polarization of the beam is rotated by. [units:none] - + The detector used to capture the image. The Detector + ID can be used as a reference within the Channel element in the Image element. + - - + + + + + The Detector Gain for this detector, as a float. + [units:none] + + + + + The Voltage of the detector (e.g. PMT voltage) as a float. + volts[V] + + + + + The Detector Offset. [units:none] + + + + + The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. + [units:none] + + + + + Gain applied to the detector signal. + This is the electronic gain (as apposed to the inherent gain) that is set + for the detector. [units:none] + + + + + Offset applied to the detector signal. + [units:none] + + + + + The Type of detector. E.g. + CCD - Charge-Coupled Device PMT - Photomultiplier tube + EMCCD - Electron Multiplying Charge Coupled Device FTIR - + Fourier transform infrared spectroscopy APD - Avalanche + Photodiode CMOS - complementary metal oxide semiconducto + EBCCD - electron-bombarded charge-coupled device etc. + + + + + + + + + + + + + + + + + + + + + + + + + + + + If the detector type is supposed to have an + adapter, this is the respective adapter data. E.g. a CCD can + have a camera adapter with a magnification; a PMT or a Photodiode doesn't + have an adapter. + + + + + The default gamma value. [units:none] + The Reset function of the DisplaySetting will reset the gamma to this value. + The default is 1.0. + + + + + + + + An identifier to uniquely identify this Detector (unique among all + detectors in this document). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + - - The original color of the channel (the color that was defined by the dye or the user before the acquisition). - + The type of detector adapter used to capture the image. + - - - - - Exposure time used to acquire this channel for informative purposes. - The value may be given as a single number or a range. - Examples: "4000" "89944" "887-1100" "100-1000" - This element gives just an informative value for the exposure time used to acquire this channel. - It must not be understood to have the meaning of "exposure time is constant for all pictures in this channel". - If the exposure time is not constant, then a range may be given here. - If it does not apply at all (e. g. because no CCD-camera or similar was used as detector), leave it out. [units:nanoseconds]. - - - - - - - - - + + + + + The magnification of the detector adapter + [units:none]. + + + + + + + + + A description of the microscope's objective lens. + Required elements include the lens numerical aperture, and the + magnification, both of which are floating point (real) numbers. The + values are those that are fixed for a particular objective: either because + it has been manufactured to this specification or the value has been + measured on this particular objective. + + + + + + This is the type of correction coating applied to this + lens. + + + + + + + + + + + + + + + + + + + + + + + + This is the type of immersion medium the lens is + designed to work with. It is not the same as 'Medium' in + Information/Image/ObjectiveSettings (a single type) as here + Immersion can have compound values like 'Multi'. + + + + + + + + + + + + + + + + + The refractive index of the immersion. + [units:none] If this field is empty, the refractive index is + assumed to be the default refractive index of the specified immersion. + + + + + + The numerical aperture of the lens expressed as a + floating point (real) number. Expected range 0.02 - 1.5 + [units:none] The depth of focus can be retrieved via the + formula: depthOfField = 2 * n * w / (lensNA)^2. where: n = + ImmersionRefractiveIndex, w = emission wavelength. + + + + + + The magnification of the lens as specified by the manufacturer + - i.e. '40' is a 40x lens. [units:none] + + + + + The magnification of the lens as measured by a calibration + process - i.e. '39.987' for a 40x lens. [units:none] + + + + + The working distance of the lens expressed as a floating point + (real) number. Units are microns[um]. + + + + + Records whether or not the objective was fitted with an Iris. + [flag] + + + + + + Records what type of phase-rings ("Phasenringe") + the objective has. Possible values: Circular - + Circular geometry Annular - Annular geometry + PhaseRing0 - Phase ring 0 geometry PhaseRing1 - Phase ring 1 + geometry PhaseRing2 - Phase ring 2 geometry + PhaseRing3 - Phase ring 3 geometry Other - a phase ring is + present, but its geometry is neither of the above ones. + The rules are: - If it is known for sure that the objective has + no phase-rings, set the value "Circular" here. - If one has no + idea whether there is a phase-ring (and what type) or not, do not set this + field at all. - "Other" means: there is a phase-ring present, it + is not of the type "Annular", "PhaseRing1", "PhaseRing2", + "PhaseRing3". In a future version it will be possible to parametrize the + phasering in this case. - "Annular" phase-ring currently is not + supported by ZEN (however, it is a valid entry). + + + + + + + + + + + + + + + + + + + + + + + Focal length [unit:micrometers] + + + + + + Slit Aperture [unit.none] + + + + + + + + + The refractive index of the cover glass this + objective was designed for. [units:none] + + + + + The thickness of the cover glass this objective + was designed for. [units:µm] + + + + + + + An identifier to uniquely identify this + Objective. + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + A description of the tube lens. Required elements + include the magnification. A tube lens might be a tube lens, an optovar lens + or a Bertrand lens. + + + + + + The magnification of the lens as specified by the manufacturer + [units:none] + + + + + + The type of the lens in the revolver element + (might be a tube lens (aka "Optovar-lens") or a Bertrand lens or "other"). + + + + + + + + + + + + + + + An identifier to uniquely identify this + TubeLens. + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + Filter set manufacturer specification. Reflector + information can be stored in a filter set: - Excitation Wavelength: + lower wavelength -> ExcitationFilter.TransmittanceRange.CutIn, upper + wavelength -> ExcitationFilter.TransmittanceRange.CutOut, - Emission + Wavelength: lower wavelength -> EmissionFilter.TransmittanceRange.CutIn, + upper wavelength -> EmissionFilter.TransmittanceRange.CutOut, - BeamSplitter: + store within Dichroic element. + + + + + + The Filters placed in the Excitation light + path. + + + + + + + + + + + The Filters placed in the Emission light + path. + + + + + + + + + + + + An identifier to uniquely identify this FilterSet (unique among + all filter-sets in this document). + + + + + The name can be used to store the reflector name. However, + the canonical place for a human-readable name is + Manufacturer.Model. + + + + + + + A filter is either an excitation or emission filter. + It can be associated with an optional FilterWheel - Note: this is not the same as a + FilterSet. + + + + + + + + + + + + + + + + + + + + A filter 'wheel' in OME can refer to any arrangement of + filters in a filter holder of any shape. It could, for example, be a filter + slider. [plain text string] + + + + + + + An identifier to uniquely identify this Filter (unique among all + filters in this document). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + This records the range of wavelengths that are transmitted by the + filter. It also records the maximum amount of light transmitted. + + + + + CutIn is the wavelength below which there is less than 50% + transmittance for a filter. Units: nanometres[nm]. + + + + + CutOut is the wavelength above which there is less than 50% + transmittance for a filter. Units: nanometres[nm]. + + + + + CutInTolerance. Units: nanometres[nm]. + + + + + CutOutTolerance. Units: nanometres[nm]. + + + + + The amount of light the filter transmits at a + maximum [units:none]. A fraction, as a value from 0.0 to 1.0. + + + + + + + An identifier to uniquely identify this TransmittanceRange (unique + among all transmittance ranges in this document). + + + + + + + The dichromatic beamsplitter or dichroic mirror used for this filter + combination. + + + + + + The beamsplitter for a filter combination may + consist of more than one components, e.g. if the respective + filter set has three emission and three excitation wavelength ranges, + the beam splitter is supposed to consist of 3 splitter components. + Each is described by a wavelength. + + + + + + Wavelength in nm. + Light with a wavelength lower than this specified wavelength is + reflected whereas light with a larger + wavelength is transmitted. Yet, this does not mean "perfectly + reflected" or "perfectly transmitted", it only + gives an appropriate description of the beamsplitter. + + + + + + + + + + + An identifier to uniquely identify this Dichroic (unique among all + dichroics in this document). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + + + + Description of a cylindrical lens (used for SPIM). + + + + + + The focal length of the cylindrical lens. If this + parameter is not given (or if it is NaN) this means that no + cylinder lens is present. The special value "0" means: a cylinder lens + is present, but its focal length is unknown. [units: millimeter] + + + + + + + + An identifier to uniquely identify this CylindricalLens (unique + among all cylindrical lenses in this document). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + Description of a device with which a SIM (= Structured + Illumination Microscopy) acquisition is performed (e.g. ApoTome, Elyra + HR-SIM). + + + + + + + + The hardware version used for the + acquisition. + + + + + + + + + + + + + + + + + + + + + An identifier to uniquely identify this SIMDevice (unique among + all SIM-devices in this document). + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + + + The optical transfer function. FilterSetRef refers to the set + of filters used in computing the OTF. This element must contain a + BinData element containing the Base64-encoded OTF. These work the same way + as they do for the Data element within Image. + + + + + + + + The variable type used to specify the size of pixel the OTF is + designed for. + + + + + The OpticalAxisAveraged is a boolean specifying + whether or not optical axis averaging was done. [flag] + + + + + + The width of the OTF. [units:none] + + + + + The height of the OTF. [units:none] + + + + + + + + - - The depth of focus [unit: micrometers]. - There are several formulas how to evaluate the depth of focus. - The following one is used for images acquired on ZENblue: - depth of focus = 2 * n * w / (objectiveNA)^2. - where: n = ImmersionRefractiveIndex, w = emission wavelength, objectiveNA = numerical aperture of objective lens. - + This holds the setting applied to an objective as well as a + reference to the objective. The ID is the objective used in this case. + - - + + + + This ID refers to an instance of InstrumentObjective in + Information/Instrument/Objectives. + + + + + + A description of a Medium used for the + lens. The Medium is the actual immersion medium used in + this case. + + + + + + + + + + + + + The position of the (first) correction collar (= + correction ring) of an objective. The CorrectionCollar is an + adjustable ring on the objective. If the parameter is not + available, double.NaN is returned. Each correction collar has an + arbitrary scale on it. So, use percentage as unit. [units:percentage]. + + + + + + The position of the second correction collar (= + correction ring) of an objective. The CorrectionCollar is an + adjustable ring on the objective. If the parameter is not + available, double.NaN is returned. Each correction collar has an + arbitrary scale on it. So, use percentage as unit. [units:percentage]. + + + + + + A description of a correction controller + operating mode used for the lens. Depending on the mode, either + values of CorrectionCollar and CorrectionCollar2, or values of + CorrectionControllerBottomThickness and CorrectionControllerImagingDepth are + available. + + + + + The parameter cover bottom thickness of the + correction controller [unit: microns]. + + + + + The parameter imaging depth of the correction + controller [unit: microns]. + + + + + The RefractiveIndex is that of the immersion + medium. This is a ratio so it is also unit-less. [units:none] + + + + + + + + - - The thickness of the section (e.g. for SIM acquisition). [unit: micrometers]. - + By the Id value, a microscope contained in the Instrument + list can be referenced. Ensure there exists a microscope with the referenced + Id. - - - - - + + + + - Refers to an instance of InstrumentFilterSet in Information/Instrument/FilterSets. + By the Id value, a LightSource contained in the Instrument + list can be referenced. Ensure there exists a LightSource with the + referenced Id. - - + + + + - - Same as element 'FilterSetRef', this is the legacy-element-name (and here for backwards-compatibility reasons). This element - should not be written. If both elements are present, then 'FilterSetRef' takes precedence. - + By the Id value, a Detector contained in the Instrument list + can be referenced. Ensure there exists a Detector with the referenced Id. + - - + + + + - Here we find information how the laser operated when scanning the field. + By the Id value, an Objective contained in the Instrument + list can be referenced. Ensure there exists an Objective with the referenced + Id. - - + + + + - - Here we find information about the details of the illumination for a SPIM-acquisition. - This element is only expected to be present if AcquisitionMode=SPIM. - + By the Id value, a cylindrical lens contained in the + Instrument list can be referenced. Ensure there exists a CylindricalLens + with the referenced Id. - - + + + + - - Here we find information about the details of the detection lightpath for a SPIM-acquisition. - This element is only expected to be present if AcquisitionMode=SPIM. - + By the Id value, a Tube Lens contained in the Instrument list + can be referenced. Ensure there exists a Tube Lens with the referenced Id. + - - + + + + - - Information about the details of a SIM acquisition. - This element is only expected to be present if AcquisitionMode=StructuredIllumination. - + By the Id value, a FilterSet contained in the Instrument list + can be referenced. Ensure there exists a FilterSet with the referenced Id. + - - + + + + - - Information about the details of a lattice SIM acquisition. - This element is only expected to be present if AcquisitionMode=StructuredIllumination and the device is a - lattice device. - + By the Id value, a Filter contained in the Instrument list + can be referenced. Ensure there exists a Filter with the referenced Id. + - - + + + + - - Information about the details of a polarizing. - This element is only expected to be present if polarizing filter was used. - + By the Id value, a Dichroic contained in the Instrument list + can be referenced. Ensure there exists a Dichroic with the referenced Id. + - - + + + + - - Information about the details of the Transport Of Intensity Equation. - This element is only expected to be present if TIE was used. - + By the Id value, a SIMDevice contained in the Instrument list + can be referenced. Ensure there exists a SIMDevice with the referenced Id. + - - + + + + - - Information about the details of a Airyscan acquisition. - + By the Id value, an OTF contained in the Instrument list can + be referenced. Ensure there exists an OTF with the referenced Id. + - - + + + + - The name of the reflector which was used for this channel. + The EM detector used to capture the image using an electron + microscope. The Detector ID can be used as a reference within the Channel + element in the Image element. - - + + + + + + An identifier to uniquely identify this EM + Detector. + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + The Type of detector. E.g. EBSD + Other etc. + + + + + + + + + + + The Brightness for this detector, as a double in percent on range + [0..100]. + + + + + The Contrast for this detector, as a double in percent on range + [0..100]. + + + + + The Detector Technology of this detector. + E.g. PhotomultiplierTube - A PMT based detector characterized by + 'fast' response and non-linear response to contrast control, such as SE2. + Diode - A diode-based detector characterized by 'slower' + response and a more linear response to contrast control, such as BSD4. + Other - Any other detector technology. + + + + + + + + + + + + + + The Electron Sensitivity of this detector: which kind + of electrons can be detected? E.g. Unknown + - Unknown, should not occur in a well configured system. + PrimaryElectrons - Sensitive to primary electrons, like STEM. + SecondaryElectrons - Sensitive to secondary electrons, like SE2. + BackScatteredElectrons - sensitive to back scattered electrons, like BSD4. + Cathodoluminescence - Sensitive to cathodoluminescence, like CL. + Mixed - The detector has no clear main sensitivity. + Other - Other kinds of sensitivity. + + + + + + + + + + + + + + + + + The Ion Sensitivity for this detector. E.g. + Unknown - Unknown, should not occur in a well configured system. + IonInsensitive - The detector is not sensitive to secondary ions, as in + most non-SESI other detectors. IonSensitive - The detector is + or can be configured to be sensitive to secondary ions, like SESI. + + + + + + + + + + + + + + - The condenser contrast that was used for this channel. + The column used to acquire the image using an electron + microscope. - - + + + + + + An identifier to uniquely identify this Column. + + + + + Use of this field is depreciated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + The beam current. Unit: "A" + + + + + + The estimated electron dose. Unit: "e/nm²" + + + + + + electrical high tension (accelerating voltage) in + effect. When the column is off, the value can be set but has no + effect. When the column is turned on, it will go to the LSV. Setting + the value when the column is on will change the EHT immediately. This + should report as continuously variable but not all values will be achievable so + writers should expect differences between CurrentValue and + LastSetValue. Unit: "V" + + + + + The distance from the lower lens to the expected + tightest convergence point of the beam. Unit: "m" + + + + + + The stigmation value in the (scan rotation zero) column + X direction. Should be unitless on range [-1..1]. + + + + + The stigmation value in the (scan rotation zero) column + Y direction. Should be on unitless range [-1..1]. + + + + + The full swing deflection of a scan perpendicular to + the optical axis. This is not necessarily the image width or height. + If the scanner is using the full range in X, it would be the image width, but + this is not known to the column. A value of 300um means the beam is + deflected +/-150um from the optical axis by a full range scan in the X or Y + direction. Settings on other interfaces (tilt correction) may cause + the deflection amplitude in Y to be less than in X. Unit: "m" + + + + + + The shift FROM the center of the optical axis TO the + center of the image in the (scan rotated) IMAGE X axis direction. + Note: this definition means that if a feature in the center of the image does + not shift as scan rotation is varied, then the beam shift values + reported will change as the scan is rotated (as in SmartSEM Jan 2019). + Unit: "m" + + + + + The shift FROM the center of the optical axis TO the + center of the image in the (scan rotated) IMAGE Y axis direction. + Note: this definition means that if a feature in the center of the image does + not shift as scan rotation is varied, then the beam shift values + reported will change as the scan is rotated (as in SmartSEM Jan 2019). + Unit: "m" + + + + + The angle FROM the microscope reference +X axis + direction TO the image +X axis direction around the microscope + reference +Z axis by the right-hand rule. When scan rotation is changed, the + feature in the center of the image should rotate but not translate, + even if beam shift is set (as in SmartSEM Jan 2019). A + positive rotation causes the image of the surface of a perpendicular sample to + rotate clockwise, meaning that the features in the image are moving + counterclockwise. Unit: "Degree" + + + + + Is the beam currently blanked?. May be disabled based + on column state. + + + + + The liner voltage (for FESem). Unit: "V" + + + + + + The condenser lens voltage (for FIB). Unit: + "V" + + + + + The objective lens voltage (for FIB). Unit: + "V" + + + + + - The numerical aperture of the condenser. + The stage used to acquire the image using an electron + microscope. - - + + + + + + An identifier to uniquely identify this Stage. + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + The stage type, such as eucentric or cartesian. + Values: UnknownStage - The stage type is unknown. This + should not occur in a well configured system. CartesianStage - + The stage is a cartesian stage with Z, X, Y, T, R stacking order. + EucentricStage - The stage is an eucentric stage with Z, T, X, Y, M, R + stacking order. + + + + + + + + + + + + The position of the stage in the microscope reference X + direction. The positive direction is oriented EAST. The values will + be calibrated to be correct in scale, and the zero position will place the + center of the dovetail mount under the optical axis. Unit: + "m" + + + + + The position of the sample stage in the microscope + reference Y direction when the tilt is zero. In a Eucentric Type + stage, the Y axis direction is rotated around the X axis by the tilt value. + The positive direction is oriented NORTH at a tilt of zero. The values will be + calibrated to be correct in scale, and the zero position will place + the center of the dovetail mount under the optical axis at a tilt of + zero. Unit: "m" + + + + + The position of the sample stage in the microscope + reference Z direction. The positive direction is oriented UP. The + values will be calibrated to be correct in scale, and the zero position will be + the DOWN limit of travel. Unit: "m" + + + + + The rotation of the sample stage around the microscope + reference Z direction when the tilt is zero. The rotation axis is + tilted around the X axis by the tilt value. The positive direction is determined + by the right-hand rule and the stage positive Z direction. The stage + value reported must follow this convention. The value will be + calibrated to be correct in scale, and the zero position will be calibrated to + be the position that places the dovetail in the upright orientation + (backstop to the left, threads for the transfer rod on the right) in + a scan rotation zero image. Unit: "Degree" + + + + + The rotation of the sample stage around the stage X + axis. The positive direction is determined by the right-hand rule and + the stage positive X direction. The stage value reported must follow this + convention. The values will be calibrated to be correct in scale, and + the zero position will place the dovetail surface perpendicular to the + microscope Z reference direction. Unit: "Degree" + + + + + + The position of the sample stage in the microscope + reference Z direction. In Eucentric Type stages, the M axis is + rotated around the positive X axis by the tilt value. The positive direction is + oriented UP. The values will be calibrated to be correct in scale, + and the zero position will be the DOWN limit of travel. In + relation to Z and M, two calibration values are required.The first is the + distance from the tilt axis to the lens when Z is at the lowest + travel. This is similar to the current lens to flat value. The second is the + distance from the dovetail flat to the tilt axis when M is at the + lowest travel. With these two calibrations, it should be possible to + place a sample at tilt eucentric and at a specific working distance if the + dovetail flat to sample surface measurement is known. Unit: + "m" + + + + + The information whether tilt correction is on. + + + + + + The stage tilt correction angle. Unit: + "Degree" + + + + + - The ratio between two active channels. + The particle beam scan generator used to acquire the image + using an electron microscope. - - - - - - An identifier to uniquely identify this channel. - - - - - A name for the channel that is suitable to be presented to the user. - - - - - - - - - The type of an online calculation where the channel is the destination. - - The following values are possible: - - NoOnlineCalculation - The data channel receives raw scan data. - OnlineRatio - (S1+C1)/(S2+C2)*C3+C4 - OnlineSubtraction - (S1*C1-S2*C3)/C2+C4 - OnlineSubtractionRatio - (S1-S2*C1)/(S1+S2*C2)*C3+C4 - OnlineHillFunction - C3*(C4/C5)*(S1-C1)/(C2-S2) - OnlineReferenceRatio - (S1-S2+C1)/(S2-C2)*C3+C4 - OnlineLinearUnmixing - The Linear Unmixing processing. - - The operands and constants are: - - S1 - Source1 - S2 - Source2 - C1 - RatioConstant1 - C2 - RatioConstant2 - C3 - RatioConstant3 - C4 - RatioConstant4 - C5 - RatioConstant5 - - - - - - - - - - - - - - - - - - Contains the constant C1 for online ratio calculations. - [unit:none] - - - - - - - Contains the constant C2 for online ratio calculations. - [unit:none] - - - - - - - Contains the constant C3 for online ratio calculations. - [unit:none] - - - - - - - Contains the constant C4 for online ratio calculations. - [unit:none] - - - - - - - Contains the constant C5 for online ratio calculations. - [unit:none] - - - - - - - Contains the constant C6 for online ratio calculations. - [unit:none] - - - - - - - Specifies the source operands S1 for an online calculation. - - - - - - - - - - - - Specifies the source operands S2 for an online calculation. - - - - - - - - - - - - - - - - The time it takes the laser to sweep through the distance that corresponds to one pixel. - Also known as PixelDwellTime. - [unit:s] - - - - - - - The time it takes the laser to sweep through the distance that corresponds to one line. - [unit:s] - - - - - - - The time it takes the laser to sweep through the area of a frame. - [unit:s] - - - - - - - The scan can be performed more than once and for the resulting image, each pixel value is gained by - averaging the different scanning results for this pixel. - The Averaging element says how often the scanning was done. - - - - - - - The scanning mode for the channel. - For the moment, all channels of an LSM image are acquired with the same scanning mode. - That means, all channels are supposed to have the same value here. - - Line and spot scans in time series aggregate their image data in sub-blocks for performance reasons. An - sub-block contains one or more time points of the experiment. See document DS_ZISRAW-FileFormate for - further details. - - A spline scan is a specific kind of line scan and is marked with the value "Line". - - - - - - - - - - - - - - - - - The rotation angle of the scan coordinates relative to the microscope coordinates in degrees. This value is used for rotated scans. - [unit:degrees] - Note: The subblock metadata contains a corresponding element (name: RoiRotation). - Ensure to keep the values synchronized if possible. - - - - - - - X-scanner-offset of the center of the scanned image relative to the center for the maximum possible scan field. - [unit:microns] - Note: The subblock metadata contains a corresponding element (name: RoiCenterOffsetX). - Ensure to keep the values synchronized if possible. - - - - - - - Y-scanner-offset of the center of the scanned image relative to the center for the maximum possible scan field. - [unit:microns] - Note: The subblock metadata contains a corresponding element (name: RoiCenterOffsetY). - Ensure to keep the values synchronized if possible. - - - - - - - Defines whether a bidirectional or unidirectional scan was employed. - - - - - - - - - - - - - The x-scanner zoom factor. - [unit:none] - - - - - - - The y-scanner zoom factor. - [unit:none] - - - - - - - The z-scanner zoom factor. - [unit:none] - This value is currently not used. - - - - - - The CropOffset is a relict, it is not used. For sample offset, see elements SampleOffsetX and SampleOffsetY. - - - - - - The attenuation of the laser in percentage (valid range: [0, 1]). - The laser intensity is then gained via '1 - LaserAttenuatorMeas'. - - This element is not supported by ZEN any more. Use DimensionChannel/LightSourcesSettings/LightSourceSettings/Attenuation instead. - - - - - - Stores the DichroicId of a Main Beam Splitter Vis. The details of this dichroic can be found under Instrument/Dichroics - - - - - Stores the DichroicId of a Main Beam Splitter InVis. The details of this dichroic can be found under Instrument/Dichroics. - - - - - Stores the DichroicId of a Secondary Beam Splitter. The details of this dichroic can be found under Instrument/Dichroics. - - - - - - A boolean indicating whether laser blanking is active. - - - - - - - The attenuation of the laser bleaching in percentage (valid range: [0, 1]). - The 'intensity' is then gained via '1 - LaserAttenuatorBleach'. - - - - - - - Depending on the value, only every n-th line is scanned. - The lines in between are interpolated. - Note: LineStep is only relevant if ScanningMode is Frame. - LineStep is fixed for AiryScan acquisition (1 for standard AiryScan, 4 for Fast AiryScan). - - - - - - - Informal parameter to characterize the scan-speed. This parameter has no defined unit, it is used in ZEN-UI to control the scan-speed. - It ranges from 1 (slow) to 16 (very fast). - Note: The available maximum scan speed depends on the Frame Size and zoom factor. - - - - - - - - - - - - - The method used for averaging. - Note: AveragingMethod is only relevant if Averaging is defined and greater than 1. - - - - - - - - - - - - - - The mode used for averaging. - If the value is Frame, the calculation of the average is based on individual full frames. - If the value is Line, the calculation of the average is based upon individual lines, which are acquired sequentially before moving on. - Note: AveragingMode is only relevant if Averaging is defined and greater than 1 and if the ScanningMode is Frame. - - - - - - - - - - - - - - The state of the laser attenuator. - If the laser attenuator is off, the full laser intensity range can be used. - If the laser attenuator is on, only low intensity emission is possible (the attenuation is depending on the laser wavelength). - Note: Only some LSM systems are equipped with a laser attenuator. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This holds the setting applied to a detector as well as a reference to the detector. - The ID is the detector used in this case. - - - - - - Refers to an instance of InstrumentDetector in Information/Instrument/Detectors. - - - - - Represents the number of pixels that are combined to form larger pixels. - - - - - - - - - - Specifies the behavior of the shutter. This field is only to be expected with CCD/CMOS detectors. - - - - - - - - - - - - - The "DetectorMode" property specifies if the detector has been used in - photon counting or integration mode during acquisition. - - - - - - - - - - - - - - The PhotonConversionFactor (PCF) allows to recalculate the number of detected photons out of the grey values. - PCF is defined as the number of photons at scale maximum (1.). In order to get the number of photons per gray scale value (digit) - it should be normalized (divided) to the maximum gray value (U16->65535). - Potential dependencies: gain (EMGain, Master Gain, digital Gain / Bitshift), Averaging Mode. [units:none] - - - - - - The Gain of the detector. [units:none] - - - - - - The digital gain of the detector. Can be applied additionally to the ('electronical') detector gain. [units:none] - - - - - - The digital Offset for the detector. [units:none] - - - - - - The Voltage of the detector. volts[V] - - - - - - The speed at which the detector can read out the pixels. - Unit of ReadOutRate is MBytes per second (1MByte=1,000,000 bytes!). - - - - - - - The brightness and contrast correction for stacks and z-scans was active - during acquisition and is defined by sets of variable values for AOTF power, - PMT gain and detector amplifier gain and offset for the positions of the focus drive. - - - - - - - The maximum possible pixel value that the camera can acquire. - If the bit depth can be changed for the detector, this value is different for different bit depths. - - - - - - - The pixel accuracy. This is a normalized value calculated as (1.0 / possible number of values). - - - - - - - The pixel scale factor. This typically coincides with the camera pixel maximum. - If not defined, it can be derived from the normalized pixel accuracy by: pixel scale factor = (1.0 / pixel accuracy) - 1. - - - - - - - The processing mode of the camera (concerning H (=phase) dimension). - This is of interest when using ApoTome: The camera can either send raw images (containing phase dimension), - or it can process the raw images such that the resulting image does not contain an H index any more. - - - - - - - No phase images were acquired at all. - - - - - Phase images were acquired and processed to a Widefield image internally. - - - - - Phase images were acquired and internally processed to get an optical section. - - - - - Phase images were acquired, no internal processing. - - - - - - - - - - - Indicating whether the FocusRoi is available. - - - - - - - - - - - The photon conversion factor is calculated using internal camera parameters photon conversion coefficient and photon factor offset. - Both values are relevant for optimizing the SMLM processing. - - - - - - - The photon conversion coefficient allows to recalculate the number of detected photons out of the grey values. - - - - - - - The photon factor offset allows to recalculate the number of detected photons out of the grey values. - The offset describes the noise in a dark image. - - - - - - - - - This holds a list of image processing operation which take place on the images - acquired from the camera before the image is stored in the document. - - - - - - - - - - This identifies the image processing operation which occurs on the image from the detector. - The list is expected to be extended (e.g. shading correction would fit in here). - - - - - - - - - - Information about the HDR processing. - - - - - - - A HDR-image is composed by a couple of images with different brightness. This is a list of (dimensionless) numbers which describe - the brightness of the images (that make up the sequence used to compose the HDR-image). The brightness of each image is given as the ratio - brightness_of_image(n) / brightness_of_image(1). The brightness of the first image is therefore always 1, and it is to be included in the list - (the list must therefore always start with the value 1). - So, the number of images (that make up the HDR-sequence) is equal to the number of elements. - By definition, each element must be greater or equal zero. If a negative number is given, it has the meaning "unknown". - - - - + + + + + + An identifier to uniquely identify this Scan + component. + + + + + Use of this field is deprecated. The canonical place + for a human-readable name is Manufacturer.Model. + + + + + + The scan type. Values: Raster + Serpentine DoubleSerpentine BidirectionalLineMill + UnidirectionalLineMill UnidirectionalLineScan Other + + - + + + + + + + + + - - - - - - - In this node more specicialized parameters for the employed method of HDR-processing may be given. - - - - - - - - - In this node more specialized parameters for the employed method of HDR-processing may be given. - - - - - - - - - - The specialized parameters for HDR-processing in case of LSM. - - - - - - - - - - - - - - - - - - - - - - - The "effective" numerical aperture of the lighthsheet optics. - - - - - Describes the characteristic of the light sheet. - - - - - - - - - - - - - - - - A reference to a cylindrical lens listed under "Instruments". - If this entry is not present, it means "no cylindrical lens" present. If one wants - to describe the situation "a cylindrical lens is present, but I do not know anything - about its parameters", then you have to create an empty cylindrical-lens-entry under - "Instruments" (empty means: no parameters are given). - - - - - - - - The parameters which describe the operation of the resonance scanner. - - - - - - - The parameters which describe the operation of the galvo scanner. - - - - - - - - - - - The "effective" numerical aperture of the detection lightpath (in case of SPIM). - Note: this field has been superseded by DimensionChannel/EffectiveNA, consider using this new field. - - - - - - - - - - - - - - - - - - - - - - - - This holds the settings defining the analyzer and polarizer - angle used for polarization images. The angles are defined in - degrees. - - - - - - - The type of the polarization. - xPol: Linear polarization used for crossed polarization. Remark: The polarizer and analyzer angles define the direction of the respective polarization. - cPol: Circular polarization. Remark: Polarizer and analyzer angles are not applicable in case of circular polarization. - pPol: Linear polarization used for pleochroismus polarization. Remark: The polarizer angle defines the direction of the linear polarization. Analyzer angle is not applicable in this case. - - - - - - - - - - - - - - The angle is defined by the angle of the matching analyzer which - is in crossed rotation compared to the polarizer. - The actual polarizing angle of the polarizer is 90° - PolarizerAngle. - The angle is defined in degrees and within a range of 0° to 90°. - It is only NaN when ChannelPolarizingSettings was not initialized or - a polarizer was present but the angle is unknown. - - - - - - - The angle defines an incidence angle at which light - with particular polarization is perfectly transmitted through a - transparent filter. - The angle is defined in degrees and within a range of 0° to 90°. - It is only NaN when ChannelPolarizingSettings was not initialized or - an analyzer was present but the angle is unknown. - The axis for this angle should be matching for different kinds - of microscopes. Same results can be expected. - - - - - - - - - This holds the settings defining the settings - for TIE images. - - - - - - - The slice distance. - - - - - - - Pseudo Contrast type for the TIE contrast. There are currently two possible image outputs from the TIE image processing function: - a) TIEPhaseContrast (-->PseudoPhaseContrast): a pseudo phase contrast image - b) TIEReliefContrast (-->PseudoDIC): a pseudo differential interference contrast image. - - - - - - - - - - - - - - - This holds the setting applied to a SIM device as well as a reference to the SIM device. - - - - - - Refers to an instance of InstrumentSIMDevice in Information/Instrument/SIMDevices. - - - - - - The grating period (i.e. the distance of the maxima of the grating which has been used - to acquire the data of the channel) in pixel units. - Crucial for SIM processing. - - - - - - - The grating rotation in degrees. - Normally, this value would be 0 or 90 degree. - - - - - - - A descriptive text about the grid that was used for the acquisition. - Typically, this should include the position number, the number of lines and some additional information. - E.g. used for Vivatome. - - - - - - - The name of the reflector/filter set that is used in the SIM device. (E.g. VivaTome2 contains a particular reflector.) - For additional information about wavelenghts, see the element FilterSet. - - - - - - - Refers to an instance of InstrumentFilterSet in Information/Instrument/FilterSets (reference by ID). - The referenced filter set contains wavelength information about the filters that are applied in the reflector/filter set of the SIM device - (see also Reflector element which contains the name of the reflector/filter set). - - - - - - - In the Elyra setting, three diffracted beams of the order -1, 0 and +1 are interfered - to produce five orders in the interference pattern. - The “DiffractionEfficiency” corresponds to the amplitude of the diffraction orders: - DiffractionEfficiency1 is for the “-1” diffraction order. - Normally, the amplitude of the “-1” diffraction order is equal to the amplitude of the “1” diffraction order. - - - - - - - In the Elyra setting, three diffracted beams of the order -1, 0 and +1 are interfered - to produce five orders in the interference pattern. - The “DiffractionEfficiency” corresponds to the amplitude of the diffraction orders: - DiffractionEfficiency2 is for the “0” diffraction order. - - - - - - - In the Elyra setting, three diffracted beams of the order -1, 0 and +1 are interfered - to produce five orders in the interference pattern. - The “DiffractionEfficiency” corresponds to the amplitude of the diffraction orders: - DiffractionEfficiency3 is for the “1” diffraction order. - Normally, the amplitude of the “-1” diffraction order is equal to the amplitude of the “1” diffraction order. - - - - - - - - - - This holds the setting applied to a lattice SIM device. - - - - - - The display name of the grating. - - - - - - The time a lattice SIM acquisition needs to acquire one frame. [Unit: milliseconds - ms] - - - - - - - - - This holds the settings applied to an Airyscan system. - - - - - - - AiryScan Draft - - The Airy-scan mode. Possible values are "SuperResolution", "VirtualPinhole" and "MultiBeam". - - - - - - AiryScan Draft - - The Airy-mode is Super-Resolution. - - - - - - AiryScan Draft - - The Airy-mode is "Virtual-Pinhole". + + + + The dwell time that will be used for the image + acquisition. The clock interval can be reflected in the datapoint + SmallestIncrement value. Scan speed-based systems should take the + last set value, configure to the closest scan speed in log(time) space and + reflect the dwell time of the selected scan speed in the current + value. Be sure to check the SmallestIncrement for dwell time. It is + not continuously variable. Unit: "s" + + + + + The number of times to scan a line at the selected + dwell time before the scan progresses to the next line in the frame. + LineAverages = 1 means a line will be scanned once. LineAverages = 2 + means a line will be scanned twice. LineAverages = 0 is invalid. - - - - - AiryScan Draft - - The Airy-mode is "Multi-Beam" aka FAST. + + + + + An acquisition is made of a number of frames, were only + every Nth line in each frame is scanned, where N is the Interlacing. + With Interlacing = 1, it is a conventional scan. With Interlacing = 2, + the acquisition is scanned in 2 frames. In the first frame, the 1st, + 3rd, 5th… lines are scanned. In the second frame, the 2nd, 4th, 6th… + lines are scanned. With Interlacing = 3, in the first frame, the 1st, + 4th, 7th… lines are scanned. . The pixel data in the MMF + should update with the partial scan data as the scan progresses. - - - - - AiryScan Draft - - TODO: What exactly does this mean? We have results from an Airy-scan-detector, but this scan - has had no "clearly definied purpose" (not SuperResolution, not VirtualPinhole and not MultiBeam)? - Or does it mean that not the Airy-scan-detector-array was used? Please provide a description - or remove - this entry. + + + + + An acquisition is made of a number of full frames, and + the resulting image is the average of all the frames. In live + acquisition the provided pixel data is a rolling average and is updated on a + line/block basis as the acquisition progresses. FrameAverages = 1 + means the frame is scanned once. FrameAverages = 2 means the frame is + scanned twice. FrameAverages = 0 is invalid. . + In a single acquisition, the pixel data is provided on a line/block basis as the + acquisition progresses. I.e., the user sees a live image that is + continuously updating will the acquisition is progressing. - - - - - - + + + + + + + + + + Camera pixel size [nm]. + + + + + + + + + + + + + + + + + + + + + + + Camera sensor size in pixels. + + + + + + + + + + Mean focal length of the MLA [m] + + + + + + Diameter of the respective microlens [m] + + + + + + Micro lense aperture magnification. + + + + + + Angle of the camera center with respect to the + micro lens array in radians. + + + + + Dark offset of the camera, value in pixel + intensity. + + + + + Coefficients for the dispersion formula. + + + + + + + + + + + + + + + + + + + + + + + Roi cutting x + offset to the nominal lens position [pixel]. + + + + + + Roi cutting x + offset to the nominal lens position [pixel]. + + + + + + Defocus of + the Microlens [m] signed i.e. (actual-nominal) focal + length. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Specifies at which event a + track switch has been performed. Possible values are: + Line - after each scan line Frame - + after each frame FrameFast - after each frame + without movement of slow hardware and ZStack + - after each z stack. The value is the same + for all tracks in a recording. + + + + + + + + + + + + + + The switch order of the tracks. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This associates a timestamp to each t-coordinate. + The data must not be confused with the "acquisition time" of a + camera frame. It has just the meaning of "some representative + and informative" timestamp which is associated with each t-coordinate. + For a simple timelapse document this might be the real acquisition time, but + for a tiled image there is no simple "acquisition time for an + x-y-plane". In addition, we make no promises if this corresponds + to the "real acquisition time" or the interval which was + specified when setting up the experiment (=theoretical interval vs real + interval). The basic idea is: we have one absolute point in + time (given by the StartTime field) which acts as a reference + point in time. Then we give the relative time to this reference for t=0, + t=1 and so on. Note that specifying the reference point is optional - if it + is not given then we just have time offsets for each + t-coordinate. Remarks: - Specifying just the + StartTime but not the TimeStamps is quite pointless, although it + is not forbidden. - If there are less offsets given than there + are t-coordinates in the documents it means "no timestamp + available" for the surplus t-coordinates. - If there are more + offsets given, they are simply ignored. [Unit: Seconds] Time + Stamps: For each index in a time series acquisition, a time + stamp can be stored in a list. I.e. the number of time stamps + equals Information/Image/SizeT. (Time stamps must not be mixed + up with the subblock/slice-specific acquisition time! E.g. in + case of an image with SizeT = 10 and SizeZ = 20, there are 10 time stamps, + but 200 different acquisition time items.) In most LSM cases, + there will be a large number of time stamps and then the time stamps will be + stored in an attachment. Yet, for a small number of time stamps, + they can be stored within this xml data. + + + + + + Reference point in time + (optional), as round trip format string. + + + + + + Definition of the offsets for + each T Index. This may be given as + start+offset or as an explicit list [unit:s]. + + + + + + + + + + This associates a spatial point for each Z Index. + The data must not be confused with the "focus position" of a + camera frame. It has just the meaning of "some representative + and informative" position which is associated with each z-index. + The offsets may be positive or negative. They could also be not monotone - + although this would be an unusual experiment. The + position of Z=0 is StartZPosition + Start (in case of ZInterval) or Start + + ZOffsetList[0]. This approach avoids ambiguities when + StartZPosition is not given. [unit:micrometers] + + + + + + + The shear definition of the + z-axis with respect to x-y. + + + + + + No shear present, + the z-axis is strictly orthogonal to x-y planes + (e.g. µSPIM fully de-skewed or standard z-stack). + + + + + + The image data in + z-direction is sheared and rotated about the x axis + by 60 degrees (e.g. µSPIM raw data). + + + + + + The image data in + z-direction is pixel interpolated x-shear corrected + and rotated about the x axis by 60 degrees (e.g. + de-sheared µSPIM raw data). + + + + + + The image data in + z-direction is integer x-shear corrected by the + bounds and rotated about the x axis by 60 degrees + (e.g. roughly de-sheared µSPIM raw data). + + + + + + + + + Specifies the chirality of the + coordinate system defined by - X axis in a + subblock, from left to right - Y axis in a + subblock, from top to bottom (-> origin in the top-left corner) + - Z axis given by Z-index This chirality is + used when arranging the z-slices spatially according to their + Z-index. It is recommended to ensure that the + chirality (and the order of the z-slices) is unchanged + when arranging the z-slices according to their associated + distances (as given by ../Dimensions/Z/Positions). + + + + + + + The + coordinate-system is orientated left-handed. + + + + + + The + coordinate-system is orientated right-handed. + + + + + + The orientation of + the coordinate-system is undefined or not known. + This is the default to be assumed if this field is + not present. + + + + + + + + THIS IS AN EXPERIMENTAL + DEFINITION! We define the z-axis to be + collinear with the optical axis. On this axis the z-coordinates + of the focal plane are measured, and their distances are found + in the Z-labels (defined under + ../Dimensions/Z/Positions) and the FocusPosition-field found in + subblock-metadata. The direction of the axis + may either be “from specimen to objective” or “from objective to + specimen”. In this coordinate system the + specimen is at a fixed position. Note that the origin of the + coordinate system is _not_ defined here. + Possible values are: FromSpecimenToObjective, + FromObjectiveToSpecimen and undefined. + Undefined is the default (and to be assumed if this element is + not present). Note that the coordinate system + defined here is different to the one defined with + "XYZHandedness". + + + + + + The z-axis is + pointing from specimen to objective. + + + + + + The z-axis is + pointing from objective to specimen. + + + + + + The direction of + the z-axis is undefined/not known. + This is the default to be assumed if this field is + not present. + + + + + + + + Description of mode of + operation of the Z-Drive. "Continuous" means that + the z-drive did not stop while acquiring the image. "Step" means + that the Z-drive did not move during the + acquisition of the image. Used for SPIM. + + + + + + + + + + + + In Continuous-mode, this + specifies the speed of the z-drive. Used for + SPIM. [unit:µm/s]. + + + + + Absolute reference position + [unit=µm]. Typically the absolute center position of the Z + stack. + + + + + Definition of the offsets for + each Z index relative to StartPosition. These offsets may + be given as Start + i * Increment or as an explicit list + [unit=µm]. + + + + + + + + + + This associates a rotation angle to each R index. + [unit: degrees] + + + + + + Reference position + [unit=degrees]. + + + + + Definition of the angles (for + each R index). + + + + + + + + + + This associates a phase to each H index. [unit: + none] Used in SIM acquisitions where the data is recorded from + various illumination grating phase shifts. If a channel in this + document is marked as an Airy-scan image (by Channel/ChannelType), then + the H-dimension has a different meaning - then the H-dimension is used to + label the images from the different fibers of an + Airy-scan-detector-array. + + + + + + Reference position [unit=µm]. + + + + + + Definition of the phase offsets + for each H index. This may be given as an + explicit list or as start+offset [unit=none]. + + + + + + + + + + + This associates an illumination direction to each + I index. Values: e.g. from left=0, from right=1. [unit: none] + + + + + + + Reference position [unit=µm]. + + + + + + Definition of the illumination + values for each I index. [unit: none] + + + + + + + + + + + This associates a rotation angle to each V index. + This dimension is used with SPIM-acquisitions, where it denotes + the rotation of the specimen [unit: degrees] + + + + + + + Directional vector specifying + the axis of rotation. We have three numbers + which give the components in (physical) x-, y- and z-direction + (in a left-handed coordinate-system). + The scaling used for the numbers is arbitrary (since only the + direction is what matters), however the + scaling must be the same for x-y- and z-direction. + A rotation around the y-axis corresponds to "0 1 0", rotation + around the x-axis corresponds to "1 0 0". For + the time being, only these two values are expected. + If this parameter is not given, we default to "rotation around + y-axis ("0 1 0"). + + + + + + + + + + + + + Tentative definition: Position + of the "center of the image" in stage coordinates, + given as three doubles for the X-,Y- and Z-position. [unit:µm] + + + + + + + + + + + + + + Reference position + [unit=degrees]. + + + + + Definition of the angles (for + each V-index). + + + + + + + + + + Regions from Tiles Acquisition. + + + + + + + + + + + + + + + + + + + Mosaic Tiles. + + + + + + Reference position for X + dimension [unit=µm]. + + + + + Reference position for Y + dimension [unit=µm]. + + + + + Tile offset in X [unit: + micrometers] + + + + + Tile offset in Y [unit: + micrometers] + + + + + + + + + + This element contains information about the + "X-dimension". + + + + + + The stage orientation for the + axis. Possible values: 1, -1. Undefined: 0 or all other values. + + + + + + + + + + This element contains information about the + "Y-dimension". + + + + + + The stage orientation for the + axis. Possible values: 1, -1. Undefined: 0 or all other values. + + + + + + + + + + + + + + Information about pyramid for this scene. + + + + + + The unique identifier of the corresponding region + (tile region or single tile region). + + + + + An optional hint string to be specified with the + scene. + + + + + + + + + + + + + + The array name if the scene was acquired from a + single position which is part of an array. + + + + + The category which is optionally specified for + the scene/region. + + + + + The contour center position (X and Y) of the + scene/region in absolute stage coordinates (µm). This specifies the center + position of the bounding box. Note the string representation of + the center position: value for X and Y are separated by comma, e.g. + "-8000.2,6000.5". + + + + + The contour size of the scene/region in absolute + stage coordinates (µm). This specifies the bounding box size of the contour + which was defined to setup the region. It makes only sense for + extended regions, e.g. tile regions with more than one tile. + + + + + + + + + + + + + + + Shape definition from which this scene/region is + part of. This is relevant if the region was setup from an + underlying sample carrier, e.g. a multiwell. + + + + + + + + + + + + + + + + If the region is rectangular, this is the column + number of tiles in the region. This parameter only makes sense + if the tiling is like a checkerboard. + + + + + If the region is rectangular, this is the row + number of tiles in the region. This parameter only makes sense + if the tiling is like a checkerboard. + + + + + + The "Positions" define a list of all stage + positions for acquired tiles. This list might not be complete. + For example, if the number of positions is too large, it might + only contain the first acquired position. + + + + + + + + + + + The zero based scene index which corresponds to the + StartS immage coordinate. + + + + + + + + + + + Specifies whether the pyramid is complete. It it + is marked as sane, then we assume that the whole scene is + covered by the pyramid _and_ that all pyramid-layers are present + and have the correct content. If this element is not present, we + assume that the pyramid is broken (and it might not be leveraged + in some cases). + + + + + The number of pyramid layers. Counting starts + with the layer above the original resolution layer. + + + + + + A boolean describing whether the tiles provide a + minimal coverage. + + + + + The factor by which consecutive pyramid layers + have been shrunken. + + + + + Specifies the method that was used for minifying + the pyramid tiles. + + + + + + + + + + + + + + + + + + + + + + + + + + Format: "X1,Y1 X2,Y2 .. Xn,Yn" + + + + + + + + + The X, Y and Z attributes are the real hardware device + positions (stage and focus). [unit: micrometers] + + + + + + + The TheM attribute defines the corresponding M index + for this position. It is numbered from 0 and corresponds to the + StartM-index of the subblocks of this image document. NOTE: + If there is a TheM defined, the stage position refers to the center of the tile + with index=TheM. If there is no TheM defined, then the stage position + refers to the center of the complete scene. + + + + + + + There must be at least one element per channel in the Image, + even for a single-plane image. Information about how each channel was + acquired is stored here. + + + + + + + + AiryScan Draft + This field (in a sense) has the highest + precedence when determining/assigning the microscopy method how + a channel was acquired. Usually, the AcquisitionMode-field is + used to give an indication which microscopy method was used. But if this + field "ChannelType" is present, it has higher precedence - i. e. + it should be checked first. + + + + + + This channel represents a heightmap. + Note that additional restrictions apply when declaring a channel + as heightmap. Some of the restrictions are: a + corresponding "TopographyDataItem"-structure has to be present, + the channel must be of pixel-type Gray32Float. + For details see DS_TopoImageExtensions.docx. + + + + + + + + + + + AiryScan Draft + This channel contains a + processed (combined) super-resolution from an + Airy-scan-acquisition in draft quality - for + preview purposes. TODO: - Do we find this one + for all Airy-Scan-types or only for Super-Resolution? + - Do we need to distinguish between super-resolution and virtual + pinhole and multibeam? + + + + + AiryScan Draft + This channel contains the + images of all sensors in the Airy-Scan-sensor- + array. The scan is intended to give a higher-resolution image. + This also implies that an H-dimension is present in this + document, and that (in this document) the + H-dimension is used to label the images + captured from the different sensors in the + Airy-Scan-sensor-array. Note that this value + is used for all types of Airy-Scan (currently, this is + Super-Resolution, Virtual-Pinhole and Multibeam). + Note: this value "AiryScanRawSr" is deprecated, use + "AiryScanRaw" instead. + + + + + AiryScan Draft + This channel contains the + images of all sensors in the Airy-Scan-sensor- + array. The scan is intended to give a higher-resolution image. + This also implies that an H-dimension is present in this + document, and that (in this document) the + H-dimension is used to label the images + captured from the different sensors in the + Airy-Scan-sensor-array. Note that this value + is used for all types of Airy-Scan (currently, this is + Super-Resolution, Virtual-Pinhole and Multibeam). + Note: this value is synonymous to "AiryScanRawSr", this one is + the recommended one. + + + + + AiryScan Draft + This channel contains the + (processed) super-resolution image (typically processed + from a raw image of ChannelType=AiryScanRaw, all the different + H-dimension images have been condensed into a + resolution-enhanced image). + + + + + AiryScan Draft + This channel contains the + (processed) "virtual pinhole" image (typically processed + from a raw image of ChannelType=AiryScanRaw, all the different + H-dimension images have been condensed into a + "virtual-pinhole" image). TODO - find better + wording... + + + + + AiryScan Draft + This channel contains the + (processed) "multi-beam" image (typically processed + from a raw image of ChannelType=AiryScanRaw, all the different + H-dimension images have been condensed into a + "multi-beam" image). TODO - find better + wording... + + + + + AiryScan Draft + This channel contains the + Sheppard-sum created from 4 fiber-rings. TODO: + add explanation... + + + + + This channel contains the + stereoscopic image data of a Lightfield 4D (LF4D) camera. + The camera captures the view of a specimen from 37 different + perspectives which then can be processed to obtain a z-stack. + + + + + + This channel contains the + result of an online unmixing acquisition with a laser-scanning + microscope. (i.e. Online-Fingerprinting) + + + + + + + + + + + + + This channel may contain NaN values - used to + determine if IP functions can work with this type of images. + + + + + + + AcquisitionMode describes the type of microscopy + performed for each channel. Possible modes: + WideField LaserScanningConfocalMicroscopy - CLSM or LSCM + SpinningDiskConfocal SlitScanConfocal + StructuredIllumination SingleMoleculeImaging + TotalInternalReflection FluorescenceLifetime + SpectralImaging FluorescenceCorrelationSpectroscopy + NearFieldScanningOpticalMicroscopy - NSOM + SecondHarmonicGenerationImaging - Second harmonic imaging microscopy + (SHIM) PALM - photo-activated + localization microscopy, photo-activation localization microscopy + STORM - stochastic optical reconstruction + microscopy STED - stimulated + emission depletion TIRF - total + internal reflection fluorescence (TIRFM) FSM + - Fluorescence speckle microscopy LCM + - Laser capture microdissection SPIM + - Selective Plane Illumination SEM + - Scanning Electron Microscopy FIB + - Focus Ion Beam FIB-SEM - Focus Ion + Beam - Scanning Electron Microscopy AngularIllumination + - Angular illumination, uses bright field illumination via LED Matrix + LatticeLightsheet - Lattice lightsheet + StructuredIlluminationSr - Structured Illumination with super + resolution (Elyra, Lattice SIM) LightField + - Light field microscope (LFM) based on micro lens array Other + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The method of illumination used to capture the + channel. Possible values: Transmitted + Epifluorescence Oblique NonLinear Other + "Epifluorescence" in this context just describes the fact that the objective + is used to bring the fluorescence inducing light ("the + illumination") to the specimen (in contrast to transmitted illumination + e.g.). This does not neccessarily require that we do a + fluorescence acquisition. + + + + + + + + + + + + + + + + ContrastMethod describes the technique used to + achieve contrast for each channel. Possible values: + Brightfield Phase DIC - + Differential Interference Contrast HoffmanModulation - + Hoffman Modulation Contrast (HMC) ObliqueIllumination + PolarizedLight - Polarization Microscopy Darkfield + Fluorescence MultiPhotonFluorescence - multi-photon excitation + was employed TIE - Transport Of Intensity + Equation Other + + + + + + + + + + + + + + + + + + + + + + + An identifier to uniquely identify this lookup + table. + + + + + + + Illumination Wavelength as either a single Peak + or a list of Ranges. This characterizes the light used for + illuminating the specimen. More specific, it is about the light + that actually hits the specimen, not the light as it leaves the light + source. + + + + + Detection Wavelength as either a single Peak or a + list of Ranges. This characterizes the part of the spectrum for + which the detector used for this channel is actually sensitive for. + It gives in any case the "net result" - it does not matter what technique is + used to limit the detection range. + + + + + Wavelength of excitation for this channel in + nanometers. This characterizes the fluorochrome - the + fluorochrome one was interested in this channel. It has just an + informative meaning - it is not meant to characterize the fluorochrome in + depth, that is what the DyeId is meant for. [units:nanometers]. + + + + + + Wavelength of emission for this particular + channel, in nanometres[nm]. This information refers to the + fluorochrome. + + + + + Gives the "effective numerical aperture" of the + optical imaging used for acquiring this channel. The "effective NA" may + include other circumstances than merely the NA of the objective + lens, so the two are not necessarily interchangeable. + + + + + + The dye id which is unique within the original dye + database. + + + + + The id (Guid) of the original database this dye is taken + from. + + + + + The optional PinholeSize element allows + specifying adjustable pinhole diameters for confocal microscopes. + The Pinhole is track specific. I.e. channels of the same track need to have + the same value here. [units:micrometers]. + + + + + + The size of the pinhole in units of the airy + disc. Since this value cannot (easily) be derived from the above + PinholeSize (in micrometers), the rule is that we store this + value separately. [units:none]. + + + + + The geometry of the pinhole, either circular or + rectangular. + + + + + + + + + + + + + The Fluor element is used for fluorescence + images. This is the name of the fluorophor used to produce this + channel [plain text string]. This element is just for + informative purposes. The fluorochrome is far better identified by the + DyeId. However - if you do not have a DyeId at hand, you may use this field + in order to give at least an informative string. + + + + + + The NDfilter element is used to specify the + combined effect of any neutral density filters used. + [units:optical density expressed as a PercentFraction] + + + + + + The PockelCellSetting used for this channel. + This is the amount the polarization of the beam is rotated by. [units:none] + + + + + + The original color of the channel (the color that + was defined by the dye or the user before the acquisition). + + + + + + Exposure time used to acquire this channel for + informative purposes. The value may be given as a single number + or a range. Examples: "4000" "89944" "887-1100" "100-1000" + This element gives just an informative value for the exposure time used to + acquire this channel. It must not be understood to have the + meaning of "exposure time is constant for all pictures in this channel". + If the exposure time is not constant, then a range may be given here. + If it does not apply at all (e. g. because no CCD-camera or similar was used + as detector), leave it out. [units:nanoseconds]. + + + + + + + + + + + The depth of focus [unit: micrometers]. + There are several formulas how to evaluate the depth of focus. + The following one is used for images acquired on ZENblue: depth + of focus = 2 * n * w / (objectiveNA)^2. where: n = + ImmersionRefractiveIndex, w = emission wavelength, objectiveNA = numerical + aperture of objective lens. + + + + + The thickness of the section (e.g. for SIM + acquisition). [unit: micrometers]. + + + + + + + + + + + Refers to an instance of InstrumentFilterSet in + Information/Instrument/FilterSets. + + + + + Same as element 'FilterSetRef', this is the + legacy-element-name (and here for backwards-compatibility reasons). This + element should not be written. If both elements are present, + then 'FilterSetRef' takes precedence. + + + + + Here we find information how the laser operated when scanning + the field. + + + + + + Here we find information about the details of the + illumination for a SPIM-acquisition. This element is only + expected to be present if AcquisitionMode=SPIM. + + + + + + + Here we find information about the details of the + detection lightpath for a SPIM-acquisition. This element is only + expected to be present if AcquisitionMode=SPIM. + + + + + + + Information about the details of a SIM + acquisition. This element is only expected to be present if + AcquisitionMode=StructuredIllumination. + + + + + + Information about the details of a lattice SIM + acquisition. This element is only expected to be present if + AcquisitionMode=StructuredIllumination and the device is a + lattice device. + + + + + + Information about the details of a polarizing. + This element is only expected to be present if polarizing filter was used. + + + + + + + Information about the details of the Transport Of + Intensity Equation. This element is only expected to be present + if TIE was used. + + + + + Information about the details of a Airyscan + acquisition. + + + + + + The name of the reflector which was used for this + channel. + + + + + + The condenser contrast that was used for this + channel. + + + + + + The numerical aperture of the condenser. + + + + + + + + + + The ratio between two active channels. + + + + + + + An identifier to uniquely identify this + channel. + + + + + A name for the channel that is suitable to be presented to the + user. + + + + + + + + The type of an online calculation where the + channel is the destination. The following values are possible: + NoOnlineCalculation - The data channel receives raw scan data. + OnlineRatio - (S1+C1)/(S2+C2)*C3+C4 OnlineSubtraction + - (S1*C1-S2*C3)/C2+C4 OnlineSubtractionRatio - + (S1-S2*C1)/(S1+S2*C2)*C3+C4 OnlineHillFunction - + C3*(C4/C5)*(S1-C1)/(C2-S2) OnlineReferenceRatio - + (S1-S2+C1)/(S2-C2)*C3+C4 OnlineLinearUnmixing - The Linear + Unmixing processing. The operands and constants are: + S1 - Source1 S2 - Source2 C1 - RatioConstant1 + C2 - RatioConstant2 C3 - RatioConstant3 C4 - + RatioConstant4 C5 - RatioConstant5 + + + + + + + + + + + + + + + + Contains the constant C1 for online ratio + calculations. [unit:none] + + + + + Contains the constant C2 for online ratio + calculations. [unit:none] + + + + + Contains the constant C3 for online ratio + calculations. [unit:none] + + + + + Contains the constant C4 for online ratio + calculations. [unit:none] + + + + + Contains the constant C5 for online ratio + calculations. [unit:none] + + + + + Contains the constant C6 for online ratio + calculations. [unit:none] + + + + + Specifies the source operands S1 for an online + calculation. + + + + + + + + + + Specifies the source operands S2 for an online + calculation. + + + + + + + + + + + + + + The time it takes the laser to sweep through the + distance that corresponds to one pixel. Also known as + PixelDwellTime. [unit:s] + + + + + The time it takes the laser to sweep through the + distance that corresponds to one line. [unit:s] + + + + + + The time it takes the laser to sweep through the + area of a frame. [unit:s] + + + + + The scan can be performed more than once and for + the resulting image, each pixel value is gained by averaging the + different scanning results for this pixel. The Averaging element + says how often the scanning was done. + + + + + The scanning mode for the channel. + For the moment, all channels of an LSM image are acquired with the same + scanning mode. That means, all channels are supposed to have the + same value here. Line and spot scans in time series aggregate + their image data in sub-blocks for performance reasons. An + sub-block contains one or more time points of the experiment. See document + DS_ZISRAW-FileFormate for further details. A spline + scan is a specific kind of line scan and is marked with the value "Line". + + + + + + + + + + + + + + + + The rotation angle of the scan coordinates + relative to the microscope coordinates in degrees. This value is used for + rotated scans. [unit:degrees] Note: The subblock + metadata contains a corresponding element (name: RoiRotation). + Ensure to keep the values synchronized if possible. + + + + + + X-scanner-offset of the center of the scanned + image relative to the center for the maximum possible scan field. + [unit:microns] Note: The subblock metadata contains a + corresponding element (name: RoiCenterOffsetX). Ensure to keep + the values synchronized if possible. + + + + + Y-scanner-offset of the center of the scanned + image relative to the center for the maximum possible scan field. + [unit:microns] Note: The subblock metadata contains a + corresponding element (name: RoiCenterOffsetY). Ensure to keep + the values synchronized if possible. + + + + + Defines whether a bidirectional or unidirectional + scan was employed. + + + + + + + + + + + The x-scanner zoom factor. + [unit:none] + + + + + The y-scanner zoom factor. + [unit:none] + + + + + The z-scanner zoom factor. + [unit:none] This value is currently not used. + + + + + + The CropOffset is a relict, it is not used. For sample offset, + see elements SampleOffsetX and SampleOffsetY. + + + + + + The attenuation of the laser in percentage (valid + range: [0, 1]). The laser intensity is then gained via '1 - + LaserAttenuatorMeas'. - This element is not supported by ZEN any + more. Use + DimensionChannel/LightSourcesSettings/LightSourceSettings/Attenuation + instead. + + + + + Stores the DichroicId of a Main Beam Splitter Vis. The details + of this dichroic can be found under Instrument/Dichroics + + + + + Stores the DichroicId of a Main Beam Splitter InVis. The + details of this dichroic can be found under + Instrument/Dichroics. + + + + + Stores the DichroicId of a Secondary Beam Splitter. The + details of this dichroic can be found under + Instrument/Dichroics. + + + + + + A boolean indicating whether laser blanking is + active. + + + + + + The attenuation of the laser bleaching in + percentage (valid range: [0, 1]). The 'intensity' is then gained + via '1 - LaserAttenuatorBleach'. + + + + + + Depending on the value, only every n-th line is + scanned. The lines in between are interpolated. + Note: LineStep is only relevant if ScanningMode is Frame. + LineStep is fixed for AiryScan acquisition (1 for standard AiryScan, 4 for + Fast AiryScan). + + + + + + Informal parameter to characterize the + scan-speed. This parameter has no defined unit, it is used in ZEN-UI to + control the scan-speed. It ranges from 1 (slow) to 16 (very + fast). Note: The available maximum scan speed depends on the + Frame Size and zoom factor. + + + + + + + + + + + + The method used for averaging. Note: + AveragingMethod is only relevant if Averaging is defined and greater than 1. + + + + + + + + + + + + + + The mode used for averaging. If the + value is Frame, the calculation of the average is based on individual full + frames. If the value is Line, the calculation of the average is + based upon individual lines, which are acquired sequentially before moving + on. Note: AveragingMode is only relevant if Averaging is defined + and greater than 1 and if the ScanningMode is Frame. + + + + + + + + + + + + + + The state of the laser attenuator. If + the laser attenuator is off, the full laser intensity range can be used. + If the laser attenuator is on, only low intensity emission is possible (the + attenuation is depending on the laser wavelength). Note: Only + some LSM systems are equipped with a laser attenuator. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - AiryScan Draft - - Parameters specific for the Airy-scan mode "MultiBeam" are found here. This element is only - to be expected if Mode=MultiBeam. - - - - - - - - - - - - - - - Fast AiryScan Draft - - Parameters specific to the airy-scan mode "FastAiryScan". - - - - - - - AiryScan Draft - - Assuming that the shape of the illumination spot is a line, this is a (2D) directional vector describing - the orientation and the length of the line. - The vector is given in "units of pixels" (in the resulting image) in a coordinate system where the origin - is at the upper left corner. - The norm of this vector (usually) gives the parallelization factor. - - - - - - - - - - - - - - AiryScan Draft - - Assuming that the shape of the illumination spot is a line, this is a (2D) directional vector describing - the orientation and the length of the line (as found on the specimen). The vector is given in units of µm. - - - - - - - - - - - - - - AiryScan Draft - - In the case a subset of 32 Airyscan detector elements is acquired (as in FAST), specifies the active detector elements - (aka fibers, 1 to 32). + This holds the setting applied to a detector as well as a + reference to the detector. The ID is the detector used in this case. - - - - - - - - - - - AiryScan Draft - - This gives the numerical aperture in x-direction for the illumination lightpath. - TODO: check explanation - - - - - - AiryScan Draft - - This gives the numerical aperture in y-direction for the illumination lightpath. - TODO: check explanation - - - - - - - - - - This ID refers to an instance of InstrumentLightSource in Information/Instrument/LightSources. - - - - The Wavelength of the light source. Unit: nanometres[nm] - - - - - - The attenuation of the light source [units:none] - A fraction, as a value from 0.0 to 1.0. - A value of 0.0 means "no attenuation", and 1.0 means "all light was blocked". - So, the attenuation equals: 1 - light_intensity_after_attenuation / light_intensity_before_attentuation. - - - - - - - The transmission of the light source [units:none] - A fraction, as a value from 0.0 to 1.0. - A value of 0.0 means "no transmission", and 1.0 means "all light is transmitted". - Transmission = 1 - attenuation - - - - - - - An information string about the intensity of the light source. - The intensity might be set in percent or in Volt; the unit is part of the string value. - Note: to get the exact numerical intensity value, use the Attenuation element to calculate the intensity - (normalized_intensity = 1 - attenuation). - - - - - - - The duration of the flashing light in milliseconds. - This value refers to the Intensity value, i.e. the light source had the intensity of the Intensity value for the duration of the Duration value. - - - - - - - This parameter gives the TIRF-angle (in degrees). - It is only to be expected if "LightSource" is referencing a light-source - of type "TIRF", otherwise it may be considered noise. - - - - - - - This parameter gives the depth of penetration (in µm) of the TIRF-laserbeam. - It is only to be expected if "LightSource" is referencing a light-source - of type "TIRF", otherwise it may be considered noise. - If value == 99999, it means infinity (=Epi). - - - - - - - This parameter gives the calibration state of the TIRF device for this channel. - It is only to be expected if "LightSource" is referencing a light-source - of type "TIRF", otherwise it may be considered noise. - - - - - - - This parameter gives the tunable information about the LightSource (LaserLine). - True means the LaserLine is tunable otherwise false. - - - - - - - - - - - - - - - - - - - Lists filters and dichroic which are used for the particular channel. - - - - - - The Filters placed in the Excitation light path. - This ID refers to an instance of InstrumentFilter in Information/Instrument/Filters. - - - - - - This ID refers to an instance of InstrumentDichroic in Information/Instrument/Dichroics. - - - + + + + Refers to an instance of InstrumentDetector in + Information/Instrument/Detectors. + + + + + Represents the number of pixels that are combined to form + larger pixels. + + + + + + + + + + + Specifies the behavior of the shutter. This field is only to + be expected with CCD/CMOS detectors. + + + + + + + + + + + + + The "DetectorMode" property specifies if the + detector has been used in photon counting or integration mode + during acquisition. + + + + + + + + + + + + The PhotonConversionFactor (PCF) allows to + recalculate the number of detected photons out of the grey values. + PCF is defined as the number of photons at scale maximum (1.). In order to + get the number of photons per gray scale value (digit) it should + be normalized (divided) to the maximum gray value (U16->65535). + Potential dependencies: gain (EMGain, Master Gain, digital Gain / Bitshift), + Averaging Mode. [units:none] + + + + + The Gain of the detector. [units:none] + + + + + The digital gain of the detector. Can be applied + additionally to the ('electronical') detector gain. [units:none] + + + + + + The digital Offset for the detector. + [units:none] + + + + + + The Voltage of the detector. volts[V] + + + + + The speed at which the detector can read out the + pixels. Unit of ReadOutRate is MBytes per second + (1MByte=1,000,000 bytes!). + + + + + The brightness and contrast correction for stacks + and z-scans was active during acquisition and is defined by sets + of variable values for AOTF power, PMT gain and detector + amplifier gain and offset for the positions of the focus drive. + + + + + + The maximum possible pixel value that the camera + can acquire. If the bit depth can be changed for the detector, + this value is different for different bit depths. + + + + + + The pixel accuracy. This is a normalized value + calculated as (1.0 / possible number of values). + + + + + + The pixel scale factor. This typically coincides + with the camera pixel maximum. If not defined, it can be derived + from the normalized pixel accuracy by: pixel scale factor = (1.0 / pixel + accuracy) - 1. + + + + + + The processing mode of the camera (concerning H + (=phase) dimension). This is of interest when using ApoTome: The + camera can either send raw images (containing phase dimension), + or it can process the raw images such that the resulting image does not + contain an H index any more. + + + + + + No phase images were acquired at + all. + + + + + Phase images were acquired and processed to a + Widefield image internally. + + + + + Phase images were acquired and internally + processed to get an optical section. + + + + + Phase images were acquired, no internal + processing. + + + + + + + + + + Indicating whether the FocusRoi is available. + + + + + + + + + - - The Filters placed in the Emission light path. - This ID refers to an instance of InstrumentFilter in Information/Instrument/Filters. - + The photon conversion factor is calculated using internal + camera parameters photon conversion coefficient and photon factor offset. + Both values are relevant for optimizing the SMLM processing. + - - - - - - - Description of the spectrum. - - - + + + + The photon conversion coefficient allows to + recalculate the number of detected photons out of the grey values. + + + + + + The photon factor offset allows to recalculate + the number of detected photons out of the grey values. The + offset describes the noise in a dark image. + + + + + + - - The spectrum is characterized by giving the wavelength of the (single) peak [unit:nm]. - + This holds a list of image processing operation which take + place on the images acquired from the camera before the image is stored in + the document. - - + + + + + - - The spectrum is characterized by single peaks or start-end intervals in a - textual form [units=nm]. - The numbers may be given with a decimal point (e.g. "42" or "42.484") - Valid examples: "430.45,440-,500" "440,460,490" "480.85-490,510,530" - "400-" means: "400-infinity" - + This identifies the image processing operation which occurs + on the image from the detector. The list is expected to be extended (e.g. + shading correction would fit in here). - - - - - - - - - - - Each track holds a collection of all channels that it contains. The channels are referenced by Id. - - - - - - - - - - - - - - An identifier to uniquely identify this track. - - - - - - The name of the track as specified by the user. - - - - - - - Each lambda stack holds a collection of all (lambda) channels that it contains. The channels are referenced by Id. - - - - - - - - - - - - - - An identifier to uniquely identify this Lambda Stack. - - - - - - - The positions in most of the dimensions may be given in three ways: as start+offset, - as a list of doubles in XML or as a link to a BLOB somewhere in the document. - - - - - + + + + + - - The offsets specified as an explicit list. The first value corresponds - to Index=0, the next to t=1 and so on. [unit is the base unit for this dimension] - + Information about the HDR processing. + - - - - - - - - - - - - - - - - - - - - - - - - - - This lists the parameters associated with each V-index. We have the offset (=the angle of rotation), - and (optionally and just for informative purposes) the start of the Z-stack, the Z-spacing and X- and Y-coordinates. - "Informative" means: if these parameters are given, then it can be assumed that - the Z-coordinates obey the formation rule: Z(z_index,v_index) = ZStart(v_index) + ZSpacing(v_index) * z_index, - and it can be assumed that all images with v_index=const have the same x- and y-position. - Nevertheless - even if these parameters are given here, we still need to give - the corresponding description in Dimensions/Z. - - - - + + + + A HDR-image is composed by a couple of images + with different brightness. This is a list of (dimensionless) numbers which + describe the brightness of the images (that make up the sequence + used to compose the HDR-image). The brightness of each image is given as the + ratio brightness_of_image(n) / brightness_of_image(1). The + brightness of the first image is therefore always 1, and it is to be + included in the list (the list must therefore always start with + the value 1). So, the number of images (that make up the + HDR-sequence) is equal to the number of elements. By definition, + each element must be greater or equal zero. If a negative number is given, + it has the meaning "unknown". + + + + + + + + + + + + In this node more specicialized parameters for + the employed method of HDR-processing may be given. + + + + + + - - The offset to the angle. [unit=degree] - + In this node more specialized parameters for the employed + method of HDR-processing may be given. - - + + + + + - - The z-start-position. [unit=µm] - NOTE: This is just a promise, the truth is what you find under Dimension/Z - or (an even deeper truth) in the subblock-metadata. - + The specialized parameters for HDR-processing in case of LSM. + - - + + + + + + + + + + + + + + + + + + + + + + + The "effective" numerical aperture of the lighthsheet + optics. + + + + + Describes the characteristic of the light + sheet. + + + + + + + + + + + + + + + + A reference to a cylindrical lens listed under + "Instruments". If this entry is not present, it means "no + cylindrical lens" present. If one wants to describe the + situation "a cylindrical lens is present, but I do not know anything + about its parameters", then you have to create an empty + cylindrical-lens-entry under "Instruments" (empty means: no + parameters are given). + + + + + + The parameters which describe the operation of + the resonance scanner. + + + + + The parameters which describe the operation of + the galvo scanner. + + + + + + + + + The "effective" numerical aperture of the + detection lightpath (in case of SPIM). Note: this field has been + superseded by DimensionChannel/EffectiveNA, consider using this new field. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - The z-start-position. [unit=µm] - NOTE: This is just a promise, the truth is what you find under Dimension/Z - or (an even deeper truth) in the subblock-metadata. - + This holds the settings defining the analyzer and polarizer + angle used for polarization images. The angles are defined in degrees. + - - + + + + The type of the polarization. xPol: + Linear polarization used for crossed polarization. Remark: The polarizer and + analyzer angles define the direction of the respective polarization. + cPol: Circular polarization. Remark: Polarizer and analyzer angles are not + applicable in case of circular polarization. pPol: Linear + polarization used for pleochroismus polarization. Remark: The polarizer + angle defines the direction of the linear polarization. Analyzer angle is + not applicable in this case. + + + + + + + + + + + + The angle is defined by the angle of the matching + analyzer which is in crossed rotation compared to the polarizer. + The actual polarizing angle of the polarizer is 90° - PolarizerAngle. + The angle is defined in degrees and within a range of 0° to 90°. + It is only NaN when ChannelPolarizingSettings was not initialized or + a polarizer was present but the angle is unknown. + + + + + + The angle defines an incidence angle at which + light with particular polarization is perfectly transmitted + through a transparent filter. The angle is defined + in degrees and within a range of 0° to 90°. It is only NaN when + ChannelPolarizingSettings was not initialized or an analyzer was + present but the angle is unknown. The axis for this angle should + be matching for different kinds of microscopes. Same results can + be expected. + + + + + + + + + This holds the settings defining the settings for TIE + images. + + + + + The slice distance. + + + + + Pseudo Contrast type for the TIE contrast. There + are currently two possible image outputs from the TIE image processing + function: a) TIEPhaseContrast (-->PseudoPhaseContrast): a pseudo + phase contrast image b) TIEReliefContrast (-->PseudoDIC): a + pseudo differential interference contrast image. + + + + + + + + + + + + + + + + This holds the setting applied to a SIM device as well as a + reference to the SIM device. + + + + + Refers to an instance of InstrumentSIMDevice in + Information/Instrument/SIMDevices. + + + + + The grating period (i.e. the distance of the + maxima of the grating which has been used to acquire the data of + the channel) in pixel units. Crucial for SIM processing. + + + + + + The grating rotation in degrees. + Normally, this value would be 0 or 90 degree. + + + + + A descriptive text about the grid that was used + for the acquisition. Typically, this should include the position + number, the number of lines and some additional information. + E.g. used for Vivatome. + + + + + The name of the reflector/filter set that is used + in the SIM device. (E.g. VivaTome2 contains a particular reflector.) + For additional information about wavelenghts, see the element FilterSet. + + + + + + Refers to an instance of InstrumentFilterSet in + Information/Instrument/FilterSets (reference by ID). The + referenced filter set contains wavelength information about the filters that + are applied in the reflector/filter set of the SIM device (see + also Reflector element which contains the name of the reflector/filter set). + + + + + + In the Elyra setting, three diffracted beams of + the order -1, 0 and +1 are interfered to produce five orders in + the interference pattern. The “DiffractionEfficiency” + corresponds to the amplitude of the diffraction orders: + DiffractionEfficiency1 is for the “-1” diffraction order. + Normally, the amplitude of the “-1” diffraction order is equal to the + amplitude of the “1” diffraction order. + + + + + In the Elyra setting, three diffracted beams of + the order -1, 0 and +1 are interfered to produce five orders in + the interference pattern. The “DiffractionEfficiency” + corresponds to the amplitude of the diffraction orders: + DiffractionEfficiency2 is for the “0” diffraction order. + + + + + + In the Elyra setting, three diffracted beams of + the order -1, 0 and +1 are interfered to produce five orders in + the interference pattern. The “DiffractionEfficiency” + corresponds to the amplitude of the diffraction orders: + DiffractionEfficiency3 is for the “1” diffraction order. + Normally, the amplitude of the “-1” diffraction order is equal to the + amplitude of the “1” diffraction order. + + + + + + + - - The number of Z-Slices (how many "Z's" you will find for this V-index). - NOTE: This is just a promise. - + This holds the setting applied to a lattice SIM device. + - - + + + + The track detection mode of an Elyra acquisition. + Lattice SIM: Structured Illumination Microscopy acquisition. SIM + Apotome: Apotome acquisition. SMLM: Single Molecule Localization + Microscopy acquisition. Laser Widefield: Laser illuminated + Widefield acquisition. + + + + + + + + + + + + + The used track switching mode. + Channels Fast: Track switching without hardware movement. + Channels: Track switching with hardware movement. Sequential C: + Only happens on SMLM tracks with time series. Slow multi-track with track + switching after certain time points. + + + + + + + + + + + + The display name of the grating. + + + + + The time a lattice SIM acquisition needs to + acquire one frame. [Unit: milliseconds - ms] + + + + + The number of cycles of a sequential-c time + series of an SMLM track. The total amount of time series cycles + will be cycle number x sequence size. + + + + + The size of the sequence of a sequential-c time + series of an SMLM track. The total amount of time series cycles + will be cycle number x sequence size. + + + + + The mode of the Total Internal Reflection + Fluorescence (TIRF) Microscopy illumination of an SMLM track. + Unknown: Unknown illumination. Epi: Neutral position used for + SIM, Apotome and Laser Widefield. HiLo: HiLo optical sectioning + illumination. Tirf: Total Internal Reflection Fluorescence + illumination. + + + + + + + + + + + + + The angle of the Total Internal Reflection + Fluorescence (TIRF) Microscopy illumination of an SMLM track. + [unit: degrees] + + + + + - - The x-coordinate [unit=µm]. - NOTE: This gives an offset to the StartX-coordinate in the subblock-metadata. - + This holds the settings applied to an Airyscan system. + - - + + + + + AiryScan Draft + The Airy-scan mode. Possible values are + "SuperResolution", "VirtualPinhole" and "MultiBeam". + + + + + + AiryScan Draft + The Airy-mode is + Super-Resolution. + + + + + AiryScan Draft + The Airy-mode is + "Virtual-Pinhole". + + + + + AiryScan Draft + The Airy-mode is "Multi-Beam" + aka FAST. + + + + + AiryScan Draft + TODO: What exactly does this + mean? We have results from an Airy-scan-detector, but this scan + has had no "clearly definied purpose" (not SuperResolution, not + VirtualPinhole and not MultiBeam)? Or does it + mean that not the Airy-scan-detector-array was used? Please + provide a description - or remove this entry. + + + + + + + + + AiryScan Draft + Parameters specific for the Airy-scan mode + "MultiBeam" are found here. This element is only to be expected + if Mode=MultiBeam. + + + + + + + + + + + + - - The y-coordinate [unit=µm]. - NOTE: This gives an offset to the StartY-coordinate in the subblock-metadata. - + Fast AiryScan Draft + Parameters specific to the airy-scan mode "FastAiryScan". + - - - - - - - - The positions in most of the dimensions may be given in three ways: as start+offset, - as a list of doubles in XML or as a link to a BLOB somewhere in the - document (the latter is not yet implemented!). - - - - - + + + + + AiryScan Draft + Assuming that the shape of the illumination + spot is a line, this is a (2D) directional vector describing + the orientation and the length of the line. The vector is + given in "units of pixels" (in the resulting image) in a coordinate + system where the origin is at the upper left corner. + The norm of this vector (usually) gives the parallelization factor. + + + + + + + + + + + + + + AiryScan Draft + Assuming that the shape of the illumination + spot is a line, this is a (2D) directional vector describing + the orientation and the length of the line (as found on the specimen). + The vector is given in units of µm. + + + + + + + + + + + + + AiryScan Draft + In the case a subset of 32 Airyscan + detector elements is acquired (as in FAST), specifies the active + detector elements (aka fibers, 1 to 32). + + + + + + + + + + + + AiryScan Draft + This gives the numerical aperture in x-direction + for the illumination lightpath. TODO: check explanation + + + + + + AiryScan Draft + This gives the numerical aperture in y-direction + for the illumination lightpath. TODO: check explanation + + + + + + + + + + This ID refers to an instance of InstrumentLightSource in + Information/Instrument/LightSources. + + + + + The Wavelength of the light source. Unit: + nanometres[nm] + + + + + The attenuation of the light source [units:none] + A fraction, as a value from 0.0 to 1.0. A value of 0.0 means "no + attenuation", and 1.0 means "all light was blocked". So, the + attenuation equals: 1 - light_intensity_after_attenuation / + light_intensity_before_attentuation. + + + + + The transmission of the light source [units:none] + A fraction, as a value from 0.0 to 1.0. A value of 0.0 means "no + transmission", and 1.0 means "all light is transmitted". + Transmission = 1 - attenuation + + + + + An information string about the intensity of the + light source. The intensity might be set in percent or in Volt; + the unit is part of the string value. Note: to get the exact + numerical intensity value, use the Attenuation element to calculate the + intensity (normalized_intensity = 1 - attenuation). + + + + + + The duration of the flashing light in + milliseconds. This value refers to the Intensity value, i.e. the + light source had the intensity of the Intensity value for the duration of + the Duration value. + + + + + This parameter gives the TIRF-angle (in degrees). + It is only to be expected if "LightSource" is referencing a light-source + of type "TIRF", otherwise it may be considered noise. + + + + + + + This parameter gives the depth of penetration (in + µm) of the TIRF-laserbeam. It is only to be expected if + "LightSource" is referencing a light-source of type "TIRF", + otherwise it may be considered noise. If value == 99999, it + means infinity (=Epi). + + + + + This parameter gives the calibration state of the + TIRF device for this channel. It is only to be expected if + "LightSource" is referencing a light-source of type "TIRF", + otherwise it may be considered noise. + + + + + This parameter gives the tunable information + about the LightSource (LaserLine). True means the LaserLine is + tunable otherwise false. + + + + + + + + + + + + + + + + + + + Lists filters and dichroic which are used for the particular + channel. + + + + + The Filters placed in the Excitation light path. + This ID refers to an instance of InstrumentFilter in + Information/Instrument/Filters. + + + + + This ID refers to an instance of InstrumentDichroic in + Information/Instrument/Dichroics. + + + + + The Filters placed in the Emission light path. + This ID refers to an instance of InstrumentFilter in + Information/Instrument/Filters. + + + + + + - - The offsets specified as an explicit list. The first value corresponds - to Index=0, the next to t=1 and so on. [unit is the base unit for this dimension] - + Description of the spectrum. - - - - - - - - The offset specified as start+increment. If Start is given but not Increment - this means that all dimension indices have the same offset (same as Increment=0), - if Increment is given but not Start then the offset for index=0 defaults to 0. - - - - + + + + The spectrum is characterized by giving the + wavelength of the (single) peak [unit:nm]. + + + + + The spectrum is characterized by single peaks or + start-end intervals in a textual form [units=nm]. + The numbers may be given with a decimal point (e.g. "42" or "42.484") + Valid examples: "430.45,440-,500" "440,460,490" "480.85-490,510,530" + "400-" means: "400-infinity" + + + + + + + + + + + - - The offset for the first coordinate. [unit=see where this type is used] - + Each track holds a collection of all channels that it contains. The + channels are referenced by Id. - - + + + + + + + + + + + + + An identifier to uniquely identify this track. + + + + + The name of the track as specified by the user. + + + + + - - The increment for consecutive coordinates. [unit=see where this type is used] - + Each lambda stack holds a collection of all (lambda) channels that it + contains. The channels are referenced by Id. - - - - - - - The offsets specified as an explicit list. The first value corresponds - to the first coordinate and so on. - - - - + + + + + + + + + + + + + An identifier to uniquely identify this Lambda + Stack. + + + + + + + + The positions in most of the dimensions may be given in three + ways: as start+offset, as a list of doubles in XML or as a link to a BLOB + somewhere in the document. + + + + + + The offsets specified as an explicit list. The + first value corresponds to Index=0, the next to t=1 and so on. + [unit is the base unit for this dimension] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This lists the parameters associated with each V-index. We + have the offset (=the angle of rotation), and (optionally and just for + informative purposes) the start of the Z-stack, the Z-spacing and X- and + Y-coordinates. "Informative" means: if these parameters are given, then it + can be assumed that the Z-coordinates obey the formation rule: + Z(z_index,v_index) = ZStart(v_index) + ZSpacing(v_index) * z_index, and it + can be assumed that all images with v_index=const have the same x- and y-position. + Nevertheless - even if these parameters are given here, we still need to give + the corresponding description in Dimensions/Z. + + + + + The offset to the angle. [unit=degree] + + + + + + The z-start-position. [unit=µm] NOTE: + This is just a promise, the truth is what you find under Dimension/Z + or (an even deeper truth) in the subblock-metadata. + + + + + + The z-start-position. [unit=µm] NOTE: + This is just a promise, the truth is what you find under Dimension/Z + or (an even deeper truth) in the subblock-metadata. + + + + + + The number of Z-Slices (how many "Z's" you will + find for this V-index). NOTE: This is just a promise. + + + + + + The x-coordinate [unit=µm]. NOTE: + This gives an offset to the StartX-coordinate in the subblock-metadata. + + + + + + The y-coordinate [unit=µm]. NOTE: + This gives an offset to the StartY-coordinate in the subblock-metadata. + + + + + + + + - - The list of offsets. [unit=specified where this type is used] - + The positions in most of the dimensions may be given in three + ways: as start+offset, as a list of doubles in XML or as a link to a BLOB + somewhere in the document (the latter is not yet implemented!). + - - - - - - - - - - The time offset are given in a binary data block somewhere else in the document. - - - - + + + + + The offsets specified as an explicit list. The + first value corresponds to Index=0, the next to t=1 and so on. + [unit is the base unit for this dimension] + + + + + + + + + The offset specified as start+increment. If Start is given + but not Increment this means that all dimension indices have the same offset + (same as Increment=0), if Increment is given but not Start then the offset + for index=0 defaults to 0. + + + + + The offset for the first coordinate. [unit=see + where this type is used] + + + + + The increment for consecutive coordinates. + [unit=see where this type is used] + + + + + + + + The offsets specified as an explicit list. The first value + corresponds to the first coordinate and so on. + + + + + The list of offsets. [unit=specified where this + type is used] + + + + + + + + + + + The time offset are given in a binary data block somewhere + else in the document. + + + + + This string refers to a BLOB in the document file + which contains the offsets in some binary form. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A bit flag for the enumeration: + Visible = 0 ElementsNoCreate = 1 ElementsNoMove = 2 + ElementsNoResize = 4 ElementsNoRemove = 8 + ElementsNoSelect = 16 ElementsNoAttributeChange = 32 + NoPersist = 64 + + + + + + + + + + + + + + Defines the graphic layer usage. By default, the + layer is used for annotation and interactive measurement (Annotation). + AutoFocus, The layer for automatic focus ROI elements. + Acquisition, The layer for acquisition ROI elements. + AcquisitionHistory, The layer for acquisition history. + Selection, The layer for selection ROI elements. Annotation, The + layer for annotation/interactive measure elements. AutoMeasure, + The layer for automatic measure elements. Preview, The layer for + preview/background elements of IP or others. Group, The layer + for grouping elements. For Lsms the follwoing graphic layer + usages are defined. Annotation, The layer for 2D display. + Acquisition, The layer for the scan ROIs. Linescan, The layer + for the overlay with the line scan selection line or Bezier curve. + TopoProfile, The layer for the overlay in topography profile display. + TopoIsoline, The layer for the topography display with the profile selection + line. MeanOfRois, The layer for the ROIs used during a scan in + “Mean of ROIs” mode. + + + + + The "CoordinateUnitX" property specifies the unit + in which the x-coordinate of the drawing element is specified. + + + + + + The "CoordinateUnitY" property specifies the unit + in which the y-coordinate of the drawing element is specified. + + + + + + The "CoordinateUnitZ" property specifies the unit + in which the z-coordinate of the drawing element is specified. + + + + + + + + Defines the opacity when the layer is + inactive. + + + + + Defines the opacity when the layer is + active. + + + + + + + + - - This string refers to a BLOB in the document file which contains the offsets - in some binary form. - + Filled rectangle for display of the currently used color + palette. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - - - - + + + + + + + + + + + + + - - - - - - + + + + + - - A bit flag for the enumeration: - Visible = 0 - ElementsNoCreate = 1 - ElementsNoMove = 2 - ElementsNoResize = 4 - ElementsNoRemove = 8 - ElementsNoSelect = 16 - ElementsNoAttributeChange = 32 - NoPersist = 64 - + A cross with one horizontal and one vertical line and a + circle where the center is the crosspoint of the two lines. + - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - Defines the graphic layer usage. By default, the layer is used for annotation and interactive measurement (Annotation). - AutoFocus, The layer for automatic focus ROI elements. - Acquisition, The layer for acquisition ROI elements. - AcquisitionHistory, The layer for acquisition history. - Selection, The layer for selection ROI elements. - Annotation, The layer for annotation/interactive measure elements. - AutoMeasure, The layer for automatic measure elements. - Preview, The layer for preview/background elements of IP or others. - Group, The layer for grouping elements. - - For Lsms the follwoing graphic layer usages are defined. - Annotation, The layer for 2D display. - Acquisition, The layer for the scan ROIs. - Linescan, The layer for the overlay with the line scan selection line or Bezier curve. - TopoProfile, The layer for the overlay in topography profile display. - TopoIsoline, The layer for the topography display with the profile selection line. - MeanOfRois, The layer for the ROIs used during a scan in “Mean of ROIs” mode. - + A rectangle in x, y, z-space. - - + + + + + + + + + + + + + + + + + + + + - - The "CoordinateUnitX" property specifies the unit in which the x-coordinate of the drawing element is specified. - + An ellipse in x, y, z-space. - - + + + + + + + + + + + + + + + + + + + + - - The "CoordinateUnitY" property specifies the unit in which the y-coordinate of the drawing element is specified. - + A circle in x, y, z-space. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Defines the line for the radius if it is required for + interaction and is displayed. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Format: "X1,Y1 X2,Y2 .. Xn,Yn" + + + + + - - The "CoordinateUnitZ" property specifies the unit in which the z-coordinate of the drawing element is specified. - + This element can be created by use of a set of points and a + caliper that defines the local coordinate system. - - - - + + + + + + + + + + + + + + Defines the + delta X which is the X-coordinate of the end point + of the normal line. + + + + + + Defines the + delta Y which is the Y-coordinate of the end point + of the normal line. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Defines the opacity when the layer is inactive. + A caliper can be created by using a base line and the + endpoint of the normal line. - - + + + + + + + + + + + Defines the delta X which is + the X-coordinate of the end point of the normal line. + + + + + + Defines the delta Y which is + the Y-coordinate of the end point of the normal line. + + + + + + + + + + - Defines the opacity when the layer is active. + A multiple caliper can be created by using a base line and + the end points of each normal line. - - - - - - - - - - Filled rectangle for display of the currently used color palette. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cross with one horizontal and one vertical line and a circle where the center is the crosspoint of the two lines. - - - - - - - - - - - - - - - - - - - - - - - A rectangle in x, y, z-space. - - - - - - - - - - - - - - - - - - - - - - - - - An ellipse in x, y, z-space. - - - - - - - - - - - - - - - - - - - - - - - - - A circle in x, y, z-space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + Specifies a collection of + distances. The distances are the end points of the normal lines. + + + + + + + Specifies a + distance. The distance is the end point of one + normal line. + + + + + + + + Defines the delta X which is the X-coordinate of + the end point of one normal line. + + + + + + + Defines the delta Y which is the Y-coordinate of + the end point of one normal line. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Defines the line for the radius if it is required for interaction and is displayed. + This element consists of a grid and multiple circles and a + cross. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Format: "X1,Y1,Z1 X2,Y2,Z2 .. + Xn,Yn,Zn" + + + + + + + + + + + + + + + + + + + - Format: "X1,Y1 X2,Y2 .. Xn,Yn" + Common attributes for graphic elements. + - - - - - - - This element can be created by use of a set of points and a caliper that defines the local coordinate system. - - - - - - - - - - - - - - - - - Defines the delta X which is the X-coordinate of the end point of the normal line. - - - - - - - Defines the delta Y which is the Y-coordinate of the end point of the normal line. - - - - - + + + + + + Specifies the text or visual representation of this + element. + + + + + The rotation angle of this element. Unit: + degrees. + + + + + Size of the mouse catch area for activation of a drawing + element with a mouse click. The value is used for new generated drawing + elements in the LSM program. + + + + + The character set used for the elements + text. + + + + + + + + + + + + + + + + + + + + + + + + + + + If "true" the drawing element was completely + edited. + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + + + + + + - - + + + - - - - - - - - - - - - - - A caliper can be created by using a base line and the endpoint of the normal line. - - - - - - - - - - - - - - Defines the delta X which is the X-coordinate of the end point of the normal line. - - + - - - - Defines the delta Y which is the Y-coordinate of the end point of the normal line. - - + + + + + + + + + + - - - - - - - - - - A multiple caliper can be created by using a base line and the end points of each normal line. - - - - - - - - - - - - - - Specifies a collection of distances. The distances are the end points of the normal lines. - - - - - - - - Specifies a distance. The distance is the end point of one normal line. - - - - - - - - Defines the delta X which is the X-coordinate of the end point of one normal line. - - - - - - - Defines the delta Y which is the Y-coordinate of the end point of one normal line. - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This element consists of a grid and multiple circles and a cross. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + - - - - - - - - - - - - - - - - - - Format: "X1,Y1,Z1 X2,Y2,Z2 .. Xn,Yn,Zn" - + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - Common attributes for graphic elements. - - - - - - - - Specifies the text or visual representation of this element. - - - - - The rotation angle of this element. Unit: degrees. - - - - - Size of the mouse catch area for activation of a drawing element with a mouse click. The value is used for new generated drawing elements in the LSM program. - - - - - The character set used for the elements text. - - - - - - - - - - - - - - - - - - - - - - - - - - - If "true" the drawing element was completely edited. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bit flag for the enumeration: - Visible = 0x80000000 - Acquisition = 0x0001 - Bleach = 0x0002 - Analysis = 0x0004 - Background = 0x0010 - Reference = 0x0020 - Group1 = 0x0040 - Group2 = 0x0080 - Group3 = 0x0100 - - - - - - - A boolean indicating whether the measure can be enabled. - - - - - - - - - Text collection for the additional text. E.g. annotations, label and custom text. - - - - - - - - - - - Specifies the posibility to move the absolute or the relative position. - - - - - Specifies if the text align with the properties horizontal and vertical alignment. - - - - - - The text can contain following wildcards: - [m] measurement, [a] annotation, [i] displayId, [n] name, [t:TagName], .. - The wildcards are replaced by the required graphicElement properties. - - - - - - - - Specify the top left position of the text. The position is set in absolute image coordinate. Format: "X1,Y1" or "X1,Y1,Z1" - - - - - - Specify the rotation of the text. - - + + + + + + + + + + - - - - - - - - - - - - - - Specify the type of text position. The relevants of the other attributes depends on this type. - - - - - - - - - - - - - - - - - - - - - - Defines the selected features (measurements) information about the graphic element. - - - - - - - - Specifies the information about the selected Feature. - - - - - The name of the feature. - - - - - The localized name to be displayed with the feature. - - - - - The display unit of the feature. - - - + + + + + + + A bit flag for the enumeration: + Visible = 0x80000000 Acquisition = 0x0001 Bleach = + 0x0002 Analysis = 0x0004 Background = 0x0010 + Reference = 0x0020 Group1 = 0x0040 Group2 = 0x0080 + Group3 = 0x0100 + + + + + A boolean indicating whether the measure can be + enabled. + + + + + + - - Defines the method and if required some properties for the feature. The available features are defined in a configuration file. - Eg. Features.FibreLength - Features.Area - Features.Radius - Features.Angle - Features.DistanceX - Features.DistanceY - For simple measurements, the (default) name defines the measurement method. - For complex measurements, the Expression value is required. - + Text collection for the additional text. E.g. annotations, + label and custom text. - - + + + + + + + + + Specifies the posibility to move the absolute or + the relative position. + + + + + Specifies if the text align with the properties + horizontal and vertical alignment. + + + + + The text can contain following + wildcards: [m] measurement, [a] annotation, + [i] displayId, [n] name, [t:TagName], .. The + wildcards are replaced by the required graphicElement + properties. + + + + + + + + Specify the top left position of the text. The + position is set in absolute image coordinate. Format: "X1,Y1" or + "X1,Y1,Z1" + + + + + Specify the rotation of the + text. + + + + + + + + + + + + + + + Specify the type of text position. + The relevants of the other attributes depends on this type. + + + + + + + + + + + + + + + + + + + + + - Indicates if the feature is displayed or not. + Defines the selected features (measurements) information about the + graphic element. - - + + + + + + - Indicates if the feature is user defined or not. + Specifies the information about the selected + Feature. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + The name of the feature. + + + + + The localized name to be displayed with the + feature. + + + + + The display unit of the feature. + + + + + Defines the method and if required some + properties for the feature. The available features are defined in a + configuration file. Eg. Features.FibreLength + Features.Area Features.Radius Features.Angle + Features.DistanceX Features.DistanceY For simple + measurements, the (default) name defines the measurement method. + For complex measurements, the Expression value is required. + + + + + + Indicates if the feature is displayed or + not. + + + + + Indicates if the feature is user defined or + not. + + + + + + - - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - + - - - - - - + + - + - - - - - - + + - + - - - - - - + + + + + + + + + + + - - - - - - - - - - - - + - - - - - - - - - - - - + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An identifier to uniquely identify this track. - - - - - - - - - - - - - - - The start time when the event occurred [s]. - - - - - The duration of the event [s]. - - - - - The bounds associated with this event. - - - - - - - - Information about how this event was triggered. - - - - - - - - - - - - - - - A boolean indicating whether the timeline element is enabled for annotations which - are typically shown in the image as special text graphic elements. - - - - - - - An identifier to uniquely identify this timeline-element. - - - - - - Event description. Information about what happened. - - - - - - - - - - - - - - - - - - - Laser intensity in range of [0..100]. - - - - - Laser wavelength in [nm]. - - - - - - - - - - - - - - - - The unit of the 'Value' elements depends on the sensor type, e.g. Celsius for temperature channels. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Information about a FRAP/Bleaching event. - - - - - - - - - - - - - - - - Information about an event marker created by user interaction. - - - - - - - - - - - - - - - Information about a hardware setting event, applied by user interaction. - - - - - - - - - - - - - - - Record current incubation values. - - - - - - - - Record current Linkam heating stage values. - - - - - - - - - Information about a focus action event and its result. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Information about an event marker, created by changes of experiment execution. - - - - - - - - - - - - - - - - - - - - - - Information about an event marker, created by changes of a digital input port. - - - - - - - - - - - - - - - - Information about an event marker, created by changes of a time series interval. Interval time is provided in [ms]. - - - - - - - - Information about an immersion event. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Contains user settings that are set in a specific image viewer can be persisted in order to restore them when opening a document in this specific viewer. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PixelType for the entire image is for informative purpose only. - In Dimensions/Channels/Channel each Channel has its own PixelType which might be different - from the other channels' pixel types. - - - - - - - Valid bits per pixel of a pixel component. - ComponentBitCount for the entire image is for informative purpose only. In Dimensions/Channels/Channel each Channel has its own ComponentBitCount element. - If not specified or 0, the component bit count is derived from the pixel type. - Normally, this value is used with 16 bit images only to indicate the maximum possible valid bits - of the sensor, e.g. 12 defines a 12 bit camera. - - - - - - - - The acquisition date of the Image. - The element contains a string in the ISO 8601 dateTime format (i.e. 1988-04-07T18:39:09) - - - - - - - The duration of the image acquisition. [unit: ms] - In case of Pollux, the acquisition duration includes the focus surface evaluation as well as the tiles scan duration. - - - - - - - This is an informative text specifying a compression method which is used (at subblock-level) when - writing the CZI-document. Note that conceptually, the compression method (and it parametrization) is - per subblock, so there is no such thing as a "compression method of the CZI-document". The compression - state of each subblock may be different, and it is by no means guaranteed that all subblocks are using - the same method or the same parameters. - So, this field is meant to give a best effort, global characterization of the compression method used in - this document. By its nature, no precise technical assumptions should be based on the content of this field - alone. - Use members of the CompressionMethods type for string content, e.g. "Jpg" or "JpgXr". - - - - - - - The original encoding quality (10..100) used when the file was initially saved with compression. - Note that this element is mostly present on legacy CZI files. Please refer to the - OriginalCompressionParameters element when saving the CZI. The encoding quality can be part of it. - - - - - - - This is an informative text specifying the compression parameters which were used (at subblock-level) the - first time the CZI-document was written. Note that conceptually, the compression parameters are - per subblock, so there is no such thing as "compression parameters of the CZI-document". The compression - state of each subblock may be different, and it is by no means guaranteed that all subblocks are using - the same method or the same parameters. - So, this field is meant to give a best effort, global characterization of the compression parameters used in - this document. By its nature, no precise technical assumptions should be based on the content of this field - alone. - The format should be key-value pairs, while each pair is separated with ',' and keys and values are - separated with ':', e.g. 'Lossless: False, Quality: 77'. - - - - - - - This is an informative text specifying the compression parameters which were used (at subblock-level) the - last time the CZI-document was written. Note that conceptually, the compression parameters are - per subblock, so there is no such thing as "compression parameters of the CZI-document". The compression - state of each subblock may be different, and it is by no means guaranteed that all subblocks are using - the same method or the same parameters. - So, this field is meant to give a best effort, global characterization of the compression parameters used in - this document. By its nature, no precise technical assumptions should be based on the content of this field - alone. - The format should be key-value pairs, while each pair is separated with ',' and keys and values are - separated with ':', e.g. 'Lossless: False, Quality: 77'. - - - - - - - - - - - - - - This element describes the transformation from pixel-coordinate-system into the stage-coordinate-system. - - - - - - - - - - - - - - - - - The Zoom value of the microscope (e.g. in a Stereo microscope). [units:none] - - - - - - - - - - The total magnification present at the eyepiece. [units:none] - This is for informational purpose. - - - - - - - - - Information about the specimen that was used in the acquisition. - - - - - - - The refractive index of the cover glass or the sample carrier bottom. [units:none] - - - - - - - The thickness of the cover glass or the sample carrier bottom. [units:µm] - - - - - - - The offset specifies the distance of the bottom to the contact surface of the microscope stage. - E.g. for multi wells this is typically a skirt which may also be 0 for skirt-less multi wells. For slide holders, - this may be the thickness or the slide holder itself. The bottom offset may be used to calculate - the optimal or working focus position or other optical parameters, e.g. the optimal value for correctable objectives. - [units:µm] - - - - - - - The material of the coverglass or the sample carrier bottom. - - - - - - - - - - - - - The thickness of the embedding media (between coverglass and specimen). - [units:µm] - - - - - - - The refractive index of the embedding media. [units:none] - E.g. necessary for TIRF. - - - - - - - The TIRF refractive index glass describes at the same time the refractive index - of the objective, of the immersion and of the bottom of the petri dish for a TIRF system - (i.e. the refractive indices of these three objects should ideally have the same value). - [units:none] - - - - - - - The diameter of the agar cylinder (for SPIM-acquisitions). - [units:µm] - - - - - - - - - This collection of tube lenses can contain one or two tube lenses, in general. - Two lenses are possible e.g. if the optovar revolver has a Bertrand lens at its current position, while - at the same time the reflector changer has selected an optovar lens as its current element. - Then, both of these lenses are supposed to be contained in this list. - - - - - - - - - - The Session metadata containing the unique SessionId and other information about the session during which the image has been acquired. - The session is a valid state of the instrument enabling to unite a collection of images with a common coordinate system in one logical entity. - A new session is created at application startup and on demand if important instrument parameters change (e.g. automatically or manually triggered calibrations). - - - - - - 4x4 matrix in homogeneous coordinates describing how the session is oriented to the reference coordinate system. [string to be parsed as double values separated by space] - - - - - Holder name. [plain text string] - - - - - Holder ID. [plain text string] - - - - - Correlative Workspace holder ID. [integer] - - - - - The number of sessions already created while running the application. - - - - - The session rotation at start. - - - - - - - GUID to uniquely identify the session. Format: 8-4-4-4-12, IETF RFC4122, e.g. "00000000-0000-0000-0000-000000000000" - - - - - Name to be displayed in user interface elements containg system type and start date and time of session. [plain text string] - - - - - Session creation enum - information about "how and why a new session was created". - - + + + + + + + + + + + + + + + + + + + + + + + + + - - - - No information available about the session-creation. - - - - - - - Use the system specific default transform. No calibration done. Use the knowledge about the system to place image in the session. - - - - - - - The stage has been automatically calibrated and measured a (0,0) position. - - - - - - - The stage has been manually calibrated. The user set a specific position as (0,0) position. - - - - - - - Session has been created after successful ShuttleAndFind calibration. - - - - - - - A new session was created by user-interaction - user forced the creation of a new session. - - - + + + + - - - - - - - This data structure is intended to describe the relation of coordinate - systems used for describing the image and its formation. - Futher information and clarification is to found in - "DS_ZISRAW-FileFormat.doc" ch. 9.5. - - - - - - - This gives the transformation of the pixel-coordinate-system to - the stage-coordinates. - The pixel-coordinate system refers to the pixel-data, and - stage-coordinates refer to the stage of the microscope. The - units of the the stage-coordinate-system are fixed to µm. - - - - - - - Experimental and interim metadata for "describing the rotation of a z-stack, used by the CorrelativeWorkspace". - - - - - - - - - The data describes a spatial rotation of the z-stack. - We describe a rotation of the stack, parametrized by a point (on the axis of rotation), a directional - vector (giving the axis of rotation) and an angle. - The coordinate system where this description is made is a left-handed pixel-coordinate-system, with - X and Y as the "image" and Z is the z-index. - - /\ Z - | - | - | - | - --------------> X - / - / - / - |/_ Y - - The X- and Y-axis are pixel-coordinates of the image, with the top-left corner at x=0 and y=0. "Top-left-corner" - here is defined as the "top-left-corner of the axis-aligned bounding-box of all subblocks" (which may or may not - coincide with the subblock's pixel-coordinate). The z-axis is given by the z-index of the planes. - - - - - - - Gives the coordinates of a point on the axis of rotation. - - - - - - - - - - - - - - - Gives a vector pointing in the axis of rotation. This vector does not need to be normalized. - - - - - - - - - - - - - - - Gives the angle of rotation, in mathematically positive direction, in units of radians. - - - - - - - - - Here we find information which allows to mathematically transform - between a point in pixel-space to the stage-coordinate-system. - We prepare to allow for different parametrizations for this - transformation, although currently only one is defined. - - - - - - - The transformation is parametrized as a defined sequence of - operations, and the scaling-transform is defined implicetely - by the scaling-metadata. - - - - - - - - - The transformation is parametrized by the following operations (in - exactly this order): - (1) scaling, - (2) flipping (mirroring on the vertical/horizontal axis), - (3) rotation and - (4) finally translation. - Only those operations are possible, and the scale is given implicitely - by the document's scale. If the document does not have a scale, then - the transformation is to be considered invalid. - The transformation assumes a pixel-coordinate-system where the - top-left-corner of the axis-aligned-bounding-box of the subblocks - is at (0,0) - note that this might or might not coincide with - the actual subblock's pixel-coordinates. This definition was made in - order to make the parameters of the transformation invariant to a - global shift (of the subblock's pixel-coordinates). - The stage-coordinate-system is assumed to be a Cartesian one. The - unit of measurement of the pixel-coordinate-system is assumed to - be micro-meters (µm). The definitions are to be understood in - the viewpoint of "transforming the object" (as opposed to - "transforming the coordinate-system") - so, the coordinate- - systems keep their meaning. - - - - - - - Gives the angle of rotation (in units of degree). The direction - of the rotation is in mathematical positive direction, which is - defined as the direction in which the - positive x-axis gets mapped onto the positive y-axis in the - shortest way. This definition applies to the pixel-coordinate - system. - - - - - - - Whether to mirror the image along a vertical (X) or horizontal - (Y) line through the middle of the image. - - - - + + + + + + + + + + + + - - Whether to mirror the image along a vertical line through - the middle of the image. - + An identifier to uniquely identify this track. - - + + + + + + + + + + + + + + + The start time when the event occurred [s]. + + + + + The duration of the event [s]. + + + + + The bounds associated with this event. + + + + + + + + Information about how this event was + triggered. + + + + + + + + + + + + + + A boolean indicating whether the timeline element + is enabled for annotations which are typically shown in the + image as special text graphic elements. + + + + - - Whether to mirror the image along a horizontal line - through the middle of the image. - + An identifier to uniquely identify this + timeline-element. - - - - - - - Gives the translation vector (in units of micro-meters). - Translation is defined in the pixel-coordinate-system - (where the top-left-corner of the image is located - at (0,0) before the transformations). - - - - - - - - - - - - - - Name to be displayed in user interface elements. [plain text string] - - - - - First name, sometime called christian name or given name or forename. [plain text string] - - - - - Any other names. [plain text string] - - - - - A person's last name sometimes called surname or family name. [plain text string] - - - - - A person's email address. [valid email address as string] - - - - - - A person's institution. - The organizing structure that people belong to other than groups. A university, or company, etc. - We do not specify a department element, and do not mean for Institution to be used in this way. - We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed location - and of being more recognizable than a group of experimenters. [plain text string] - - - - - - This is the username of the experimenter (in a 'logon' or 'database' sense). [plain text string] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Name of the Image - - - - - - - - User Name defined by the Operating System - - - - - - - Defines the type of the image. If the value is not "Image" or "NULL" a special - viewer is required to display the image. The following sub types are available: - - Image - MeanOfRois - Spectral - Point - Topography - TopoGraphyMask - Kinetic - IcsMap - PalRawData - Pal - PalSumTirfRawData - - - - - - - - Time and date of the creation of the document. - - - - - - - + + + + + Event description. Information about what happened. + + + + + + + + + + + + + + + + + + + Laser intensity in range of [0..100]. + + + + + Laser wavelength in [nm]. + + + + + + + + + + + + + + + + + + The unit of the 'Value' elements depends on the sensor type, + e.g. Celsius for temperature channels. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - The Rating of the image document. Values: 0-5. + Information about a FRAP/Bleaching event. - - - - - - - - + + + + + + + + + + + + + + - Name of the application which created the document. + Information about an event marker created by user + interaction. - - + + + + + + + + + + + + - Version of the application which created the document. + Information about a hardware setting event, applied by user + interaction. - - + + + + + + + + + + + + - - Build identifier of the application which created the document. - The format is not further detailed, it is a free-format string. - + Record current incubation values. - - - - - - - + + + + + - Temperature (°C) + Record current Linkam heating stage values. - - + + + + + + - Air pressure in millibars (mbar) + Information about a focus action event and its + result. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Humidity as a fraction from 0.0 to 1.0. + Information about an event marker, created by changes of experiment + execution. - - + + + + + + + + + + + + + + + + + + + - CO2 as a fraction from 0.0 to 1.0. + Information about an event marker, created by changes of a digital + input port. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Unmixing contains the parameters that have been used to generate the image pixel - data by linear unmixing from an image generated with the spectral imager. - - - - + + + + + + + + + + + + + - - The "Autoscale" property specifies whether or not the results of the - linear unmixing have been auto scaled to maximum intensity. Auto - scaling is always done for the individual result channels separately. - + Information about an event marker, created by changes of a time series + interval. Interval time is provided in [ms]. - - + + + + + - - The "CalculateResiduals" property specifies whether or not an additional - result image channel has been generated where the maximum deviation from - the calculated linear combination of the unmixing results is stored. - The calculation of the residual image is done for each image pixel - individually. The deviation of the acquired spectrum from the linear - combination of the unmixing results is determined for each wavelength - and the maximum of the absolute value of the deviations is determined - and written to the additional result channel. - + Information about an immersion event. - - - - - The "IgnoreNegativeResults" property specifies whether or not a constrained - linear unmixing algorithm has been used. The constrained linear unmixing - algorithm checks for each pixel if unmix results are negative. If so, the - unmixing is recalculated without the spectrum for the dye where the result - was negative. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Contains user settings that are set in a specific + image viewer can be persisted in order to restore them when opening a + document in this specific viewer. + + + + + + + + + + + + + + + + + + + + + + + + + + + + PixelType for the entire image is for informative + purpose only. In Dimensions/Channels/Channel each Channel has + its own PixelType which might be different from the other + channels' pixel types. + + + + + Valid bits per pixel of a pixel component. + ComponentBitCount for the entire image is for informative purpose only. In + Dimensions/Channels/Channel each Channel has its own ComponentBitCount + element. If not specified or 0, the component bit count is + derived from the pixel type. Normally, this value is used with + 16 bit images only to indicate the maximum possible valid bits + of the sensor, e.g. 12 defines a 12 bit camera. + + + + + + + The acquisition date of the Image. + The element contains a string in the ISO 8601 dateTime format (i.e. + 1988-04-07T18:39:09) + + + + + The duration of the image acquisition. [unit: ms] + In case of Pollux, the acquisition duration includes the focus surface + evaluation as well as the tiles scan duration. + + + + + This is an informative text specifying a + compression method which is used (at subblock-level) when + writing the CZI-document. Note that conceptually, the compression method + (and it parametrization) is per subblock, so there is no such + thing as a "compression method of the CZI-document". The compression + state of each subblock may be different, and it is by no means guaranteed + that all subblocks are using the same method or the same + parameters. So, this field is meant to give a best effort, + global characterization of the compression method used in this + document. By its nature, no precise technical assumptions should be based on + the content of this field alone. Use members of the + CompressionMethods type for string content, e.g. "Jpg" or "JpgXr". + + + + + + The original encoding quality (10..100) used when + the file was initially saved with compression. Note that this + element is mostly present on legacy CZI files. Please refer to the + OriginalCompressionParameters element when saving the CZI. The encoding + quality can be part of it. + + + + + This is an informative text specifying the + compression parameters which were used (at subblock-level) the + first time the CZI-document was written. Note that conceptually, the + compression parameters are per subblock, so there is no such + thing as "compression parameters of the CZI-document". The compression + state of each subblock may be different, and it is by no means guaranteed + that all subblocks are using the same method or the same + parameters. So, this field is meant to give a best effort, + global characterization of the compression parameters used in + this document. By its nature, no precise technical assumptions should be + based on the content of this field alone. The format + should be key-value pairs, while each pair is separated with ',' and keys + and values are separated with ':', e.g. 'Lossless: False, + Quality: 77'. + + + + + This is an informative text specifying the + compression parameters which were used (at subblock-level) the + last time the CZI-document was written. Note that conceptually, the + compression parameters are per subblock, so there is no such + thing as "compression parameters of the CZI-document". The compression + state of each subblock may be different, and it is by no means guaranteed + that all subblocks are using the same method or the same + parameters. So, this field is meant to give a best effort, + global characterization of the compression parameters used in + this document. By its nature, no precise technical assumptions should be + based on the content of this field alone. The format + should be key-value pairs, while each pair is separated with ',' and keys + and values are separated with ':', e.g. 'Lossless: False, + Quality: 77'. + + + + + + + + + + + + + + + This element describes the transformation from + pixel-coordinate-system into the stage-coordinate-system. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The Zoom value of the microscope (e.g. in a Stereo + microscope). [units:none] + + + + + + + + + + The total magnification present at the eyepiece. + [units:none] This is for informational purpose. + + + + + + + + + Information about the specimen that was used in the + acquisition. + + + + + The refractive index of the cover glass or the + sample carrier bottom. [units:none] + + + + + The thickness of the cover glass or the sample + carrier bottom. [units:µm] + + + + + The offset specifies the distance of the bottom + to the contact surface of the microscope stage. E.g. for multi + wells this is typically a skirt which may also be 0 for skirt-less multi + wells. For slide holders, this may be the thickness or the slide + holder itself. The bottom offset may be used to calculate the + optimal or working focus position or other optical parameters, e.g. the + optimal value for correctable objectives. [units:µm] + + + + + + The material of the coverglass or the sample carrier + bottom. + + + + + + + + + + + The thickness of the embedding media (between + coverglass and specimen). [units:µm] + + + + + + The refractive index of the embedding media. + [units:none] E.g. necessary for TIRF. + + + + + + + The TIRF refractive index glass describes at the + same time the refractive index of the objective, of the + immersion and of the bottom of the petri dish for a TIRF system + (i.e. the refractive indices of these three objects should ideally have the + same value). [units:none] + + + + + The diameter of the agar cylinder (for + SPIM-acquisitions). [units:µm] + + + + + + + + This collection of tube lenses can contain one or two tube + lenses, in general. Two lenses are possible e.g. if the optovar revolver has + a Bertrand lens at its current position, while at the same time the + reflector changer has selected an optovar lens as its current element. Then, + both of these lenses are supposed to be contained in this list. + - - - - - The "BackgroundSpectrum" property specifies the index of the spectrum in - the unmix spectra array that contains the spectrum of the background. - The background is subtracted from the input spectra for the individual - pixels before the linear unmixing is performed. A spectrum index less than - zero indicates that there is no background spectrum. If a valid spectrum - index is specified the linear umnixing has not generated an image channel - for that spectrum. - + + + + + + + + The Session metadata containing the unique SessionId and + other information about the session during which the image has been acquired. + The session is a valid state of the instrument enabling to unite a collection of + images with a common coordinate system in one logical entity. A new session + is created at application startup and on demand if important instrument parameters + change (e.g. automatically or manually triggered calibrations). + - - - - - "Weighted" option includes a statistical analysis of the signal-related (Poisson-) noise and - weighs the respective contribution to the fitting of the combination of reference spectra to the - experimental data. - + + + + 4x4 matrix in homogeneous coordinates describing how the + session is oriented to the reference coordinate system. [string to be parsed + as double values separated by space] + + + + + Holder name. [plain text string] + + + + + Holder ID. [plain text string] + + + + + Correlative Workspace holder ID. [integer] + + + + + The number of sessions already created while running the + application. + + + + + The session rotation at start. + + + + + + + GUID to uniquely identify the session. Format: 8-4-4-4-12, IETF + RFC4122, e.g. "00000000-0000-0000-0000-000000000000" + + + + + Name to be displayed in user interface elements containg system + type and start date and time of session. [plain text string] + + + + + Session creation enum - information about "how and why a new + session was created". + + + + + + No information available about the + session-creation. + + + + + Use the system specific default transform. + No calibration done. Use the knowledge about the system to place + image in the session. + + + + + The stage has been automatically calibrated + and measured a (0,0) position. + + + + + The stage has been manually calibrated. The + user set a specific position as (0,0) position. + + + + + + Session has been created after successful + ShuttleAndFind calibration. + + + + + A new session was created by + user-interaction - user forced the creation of a new session. + + + + + + + + + + + This data structure is intended to describe the relation of + coordinate systems used for describing the image and its formation. + Futher information and clarification is to found in + "DS_ZISRAW-FileFormat.doc" ch. 9.5. + + + + + This gives the transformation of the + pixel-coordinate-system to the stage-coordinates. + The pixel-coordinate system refers to the pixel-data, and + stage-coordinates refer to the stage of the microscope. The + units of the the stage-coordinate-system are fixed to µm. + + + + + + Experimental and interim metadata for "describing + the rotation of a z-stack, used by the CorrelativeWorkspace". + + + + + + + + + + The data describes a spatial rotation of the z-stack. + We describe a rotation of the stack, parametrized by a point (on the axis of + rotation), a directional vector (giving the axis of rotation) and an angle. + The coordinate system where this description is made is a left-handed + pixel-coordinate-system, with X and Y as the "image" and Z is the z-index. + /\ Z | | | | + --------------> X / / / |/_ Y The + X- and Y-axis are pixel-coordinates of the image, with the top-left corner at x=0 + and y=0. "Top-left-corner" here is defined as the "top-left-corner of the + axis-aligned bounding-box of all subblocks" (which may or may not coincide + with the subblock's pixel-coordinate). The z-axis is given by the z-index of the + planes. + + + + + Gives the coordinates of a point on the axis of + rotation. + + + + + + + + + + + + + Gives a vector pointing in the axis of rotation. + This vector does not need to be normalized. + + + + + + + + + + + + + Gives the angle of rotation, in mathematically + positive direction, in units of radians. + + + + + + + + + Here we find information which allows to mathematically + transform between a point in pixel-space to the stage-coordinate-system. + We prepare to allow for different parametrizations for this transformation, + although currently only one is defined. + + + + + The transformation is parametrized as a defined + sequence of operations, and the scaling-transform is defined + implicetely by the scaling-metadata. + + + + + + + + The transformation is parametrized by the following + operations (in exactly this order): (1) scaling, (2) + flipping (mirroring on the vertical/horizontal axis), (3) rotation and + (4) finally translation. Only those operations are possible, and the scale + is given implicitely by the document's scale. If the document does not have + a scale, then the transformation is to be considered invalid. The + transformation assumes a pixel-coordinate-system where the top-left-corner + of the axis-aligned-bounding-box of the subblocks is at (0,0) - note that + this might or might not coincide with the actual subblock's + pixel-coordinates. This definition was made in order to make the parameters + of the transformation invariant to a global shift (of the subblock's + pixel-coordinates). The stage-coordinate-system is assumed to be a Cartesian + one. The unit of measurement of the pixel-coordinate-system is assumed to + be micro-meters (µm). The definitions are to be understood in the viewpoint + of "transforming the object" (as opposed to "transforming the + coordinate-system") - so, the coordinate- systems keep their meaning. + - - + + + + Gives the angle of rotation (in units of degree). + The direction of the rotation is in mathematical positive + direction, which is defined as the direction in which the + positive x-axis gets mapped onto the positive y-axis in the + shortest way. This definition applies to the pixel-coordinate + system. + + + + + Whether to mirror the image along a vertical (X) + or horizontal (Y) line through the middle of the image. + + + + + + Whether to mirror the image along a + vertical line through the middle of the image. + + + + + + Whether to mirror the image along a + horizontal line through the middle of the image. + + + + + + + + Gives the translation vector (in units of + micro-meters). Translation is defined in the + pixel-coordinate-system (where the top-left-corner of the image + is located at (0,0) before the transformations). + + + + + + + + + + + + + + + Name to be displayed in user interface elements. [plain text + string] + + + + + First name, sometime called christian name or given name or + forename. [plain text string] + + + + + Any other names. [plain text string] + + + + + A person's last name sometimes called surname or family name. + [plain text string] + + + + + A person's email address. [valid email address as + string] + + + + + A person's institution. The + organizing structure that people belong to other than groups. A university, + or company, etc. We do not specify a department element, and do + not mean for Institution to be used in this way. We simply wish + to say XXX at YYY. Where YYY has a better chance of being tied to a + geographically fixed location and of being more recognizable + than a group of experimenters. [plain text string] + + + + + + This is the username of the experimenter (in a 'logon' or + 'database' sense). [plain text string] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Name of the Image + + + + + + User Name defined by the Operating System + + + + + + Defines the type of the image. If the value is not "Image" + or "NULL" a special viewer is required to display the image. The + following sub types are available: Image MeanOfRois Spectral + Point Topography TopoGraphyMask Kinetic IcsMap PalRawData + Pal PalSumTirfRawData PSF EDSMaxIntensity (an EM-specific document + type where the pixel values in different channels represent the abundance of + different chemical elements) + + + + + + Time and date of the creation of the document. + + + + + + + + + The Rating of the image document. Values: + 0-5. + + + + + + + + + + + + Name of the application which created the + document. + + + + + Version of the application which created the + document. + + + + + Build identifier of the application which created + the document. The format is not further detailed, it is a + free-format string. + + + + + + + + + + + Temperature (°C) + + + + + Air pressure in millibars (mbar) + + + + + Humidity as a fraction from 0.0 to 1.0. + + + + + CO2 as a fraction from 0.0 to 1.0. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Unmixing contains the parameters that have been used to + generate the image pixel data by linear unmixing from an image generated + with the spectral imager. + + + + + The "Autoscale" property specifies whether or not + the results of the linear unmixing have been auto scaled to + maximum intensity. Auto scaling is always done for the + individual result channels separately. + + + + + The "CalculateResiduals" property specifies + whether or not an additional result image channel has been + generated where the maximum deviation from the calculated linear + combination of the unmixing results is stored. The calculation + of the residual image is done for each image pixel individually. + The deviation of the acquired spectrum from the linear + combination of the unmixing results is determined for each wavelength + and the maximum of the absolute value of the deviations is determined + and written to the additional result channel. + + + + + The "IgnoreNegativeResults" property specifies + whether or not a constrained linear unmixing algorithm has been + used. The constrained linear unmixing algorithm checks for each + pixel if unmix results are negative. If so, the unmixing is + recalculated without the spectrum for the dye where the result + was negative. + + + + + The "BackgroundSpectrum" property specifies the + index of the spectrum in the unmix spectra array that contains + the spectrum of the background. The background is subtracted + from the input spectra for the individual pixels before the + linear unmixing is performed. A spectrum index less than zero + indicates that there is no background spectrum. If a valid spectrum + index is specified the linear umnixing has not generated an image channel + for that spectrum. + + + + + "Weighted" option includes a statistical analysis + of the signal-related (Poisson-) noise and weighs the respective + contribution to the fitting of the combination of reference spectra to the + experimental data. + + + + + The "ConfidenceIntervals" property specifies if + one additional channel representing relative standard deviation (RSD) is + generated for each unmixed component. It shows the statistical + uncertainty of the pixel intensity in the unmixed channel calculated based + on the (Poisson-) noise of the acquired input-channels. + + + + + + + + + + + + The "Color" + property specifies the color of the channel + corresponding to the spectral component. + + + + + + The + "ComponentName" property specifies the name of the + spectral component that has been used for + linear unmixing. Corresponding spectrum can be + loaded from the spectral database, manualy defined + from the spectral image by the ROI or calculated by + the Automated Component Extraction (ACE). + + + + + + The + "MainBeamSplitter" property specifies the name of + the main beam splitter that + has been used to record the spectrum with the index. + The information is stored to be able to write the + spectra prameters to a + spectra database. + + + + + + The + "Objective" property specifies the name of the + objective that has been used + to record the spectrum. The information is stored to + be able to write back the spectra parameters to a + spectra database. + + + + + + Spectral Data + can be loaded from the spectral database, manualy + defined from the spectral image by the ROI or + calculated by the Automated Component Extraction + (ACE). + + + + + + + + + + The "Intensity" property specifies the intensity + of the spectral channel. + + + + + + + The "Wavelength" specifies the center wavelength + corresponding to the spectral detection channel. + + + + + + + The "StandardDeviation" property sepcifies the + standard deviation of one + intensity in a particular spectrum. + + + + + + + + + + + + The + "Excitations" property provides access the arrays + with the excitation + wavelengths that have been used to record the + spectrum with the index. The + information is stored to be able to write the + spectra parameters to a spectra database. + + + + + + + + + + + + + + + + + + + + The "StructuredIllumination" provides access to the + parameters which are used for resolution enhancement form data of + acquisitions whith structured illumination. + + + + + The "DimensionH" property specifies the number of + phases. + + + + + The "DimensionR" property specifies the number of + rotations. + + + + + The "DimensionC" property specifies the number of + channels. + + + + + The "Phases" property specifies the phase angle + of the grating in structured illumination acquisition with the + specified phase index. + + + + + + + + The "Rotations" properties specifies the rotation + angles of the pixels of the image data with the specified + rotation index. + + + + + + + + + + + + + + The + "ExcitationWavelength" property specifies the + wavelength of the light + which has been used to excite the dye for the + detector that generated the + data for the specified channel. If the wavelength is + 0 the excitation wavelength + is not known. [units:meters]. + + + + + + The + "GratingPeriod" property specifies the distance of + the maxima of the grating + which has been used to acquire the data of the + channel. + + + + + The + "GratingPixels" property specifies the number of + pixels which span the + distance of the maxima of the grating which has been + used to acquire the data of + the channel. + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - The "ConfidenceIntervals" property specifies if one additional channel representing relative standard deviation (RSD) is generated for each unmixed component. - It shows the statistical uncertainty of the pixel intensity in the unmixed channel calculated based on the (Poisson-) noise of the acquired input-channels. - + The "Airyscan" provides access to the parameters which are + used for resolution enhancement with Airyscan acquisition. + - - - - - - - - - - - The "Color" property specifies the color of the channel corresponding to the spectral component. - - - - - - - The "ComponentName" property specifies the name of the spectral component that has been used for - linear unmixing. Corresponding spectrum can be loaded from the spectral database, manualy defined from the spectral image by the ROI or calculated by the Automated Component Extraction (ACE). - - - - - - - The "MainBeamSplitter" property specifies the name of the main beam - splitter that has been used to record the spectrum with the index. The information is stored to be able to write the spectra - prameters to a spectra database. - - - - - - - The "Objective" property specifies the name of the objective that has been - used to record the spectrum. The information is stored to be able to write back the spectra parameters to a spectra database. - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of iterations done during the + reconstruction. [units:none]. + + + + + Alternative criterion to stop iteration process. + Applies if the difference in data fiting quality between the two most recent + iterations is less than the specified value. [units:none]. + + + + + + Pixel sampling of the output image can be + increased by factor 2 for the best resolution. + + + + + + + + + + The factor between used sampling (image + resolution) and widefield Nyquist-Shannon sampling, where sampling is + defined as the (physical) distance between centers of neighboring pixels. + [units:none]. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Iterations determines the number of iterations + during the reconstruction of the Lightfield 4D image. Typical values vary + between 10 and 25 and depend on the signal-to-noise ratio of the sample. + [units:none]. + + + + + TotalVariationDenoising defines the weight of the + total variation regularization during the Lightfield 4D image + reconstruction. [units:none]. + + + + + BackgroundCorrection defines the radius parameter + of the "rolling ball" algorithm, used to subtract the background from the + raw Lightfield 4D image data. Typical values vary between 15 and 35 and + depend on the structure of the imaged sample. [units:pixels]. + + + + + + + + + + + Represents a dataset of calibration values + determined by the user. + + + + + + Effective radius of the + observation spot. + + + + + Average radius of the + observation spot for one detector element. + + + + + + Effective distance between the + detector elements for flow measurements. + + + + + + Ratio between the observation + spot waist in the axial and lateral direction. + + + + + + File name of the calibration + file. + + + + + + + + Effective radius of the observation spot. + + + + + + Average radius of the observation spot for one + detector element. + + + + + Effective distance between the detector elements + for flow measurements. + + + + + Ratio between the observation spot waist in the + axial and lateral direction. + + + + + + + + + + SuperResolutionParameter determines the Wiener + filtering level. Typical values vary between ‐5 and ‐7 and depend on the + signal-to-noise ratio of the sample. [units:none]. + + + + + + Determines if the SuperResolutionParameter is + estimated by the software (automatic mode) or is defined by the user + (manual). [units:none]. + + + + + + + + + + + Resolution enhancement in z can be achieved by + using 3D processing. + + + + + + + + + + + + + Tile-based 3D processing of the large image data + is done to reduce memory usage. + + + + + Number of airyscan detector rings that defines + the size of the virtual pinhole. For example, the value 2,5 means, that 3 + inner rings are selected, the first two rings with the weight "1", and the + third ring with the weight "0.5". [units:none]. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Unique string + identifying the column of the molecule table this + filter operates on, e.g., "Precision" or + "FirstFrame". + + + + + + Boolean that + indicates whether the filter is active and in use. + + + + + + The starting + point of the filter range. Depending on the filter + type it is in nanometer, e.g., for "Precision", or + without units, e.g., "ChiSquare". + + + + + + The end point + of the filter range. Depending on the filter type it + is in nanometer, e.g., for "Precision", or without + units, e.g., "ChiSquare". + + + + + + + + + + + + The starting + point of the filter range for x in nanometer. + + + + + + The end point + of the filter range for x in nanometer. + + + + + + The starting + point of the filter range for y in nanometer. + + + + + + The end point + of the filter range for y in nanometer. + + + + + + Boolean that + indicates whether the filter is active and in use. + + + + + + + + + + + + + + + + + + + Parameter for the SMLM Grouping algorithm + (combine Molecules that appear in more than 1 frame and merge them if they + fullfill some special conditions). + + + + + + Capture radius in nm (Search + radius to combine Molecules that appear in more than 1 frame). + + + + + + Maximum off gap in Number of + Frames (Maximum allowed gap for Molecules that appear in more + than 1 frame) + + + + + Maximum switch-on time in + Number of Frames (maximum permissible switch-on time for + molecules that appear in more than one frame). If molecules + appear in more than MaxOnTime contiguous frames, they are + completely removed. + + + + + + + + Parameter for the SMLM Remove outlier algorithm + (Molecules that do not have a given number of neighbors in a given radius + are removed). + + + + + + Boolean that indicates whether + the remove outlier filter is applied to the data. + + + + + + Radius in nm (Search radius for + finding the molecule neighbors). + + + + + + Minimum number of molecule + neighbours within the radius. + + + + + + + + + Parameter for the live processing settings + (calculation of localized molecules with running acquisition.). + + + + + + + Feature size in pixel used for + the localization. + + + + + Peak quality for the + localization. + + + + + + + + + + + + + Settings of the image correlation + viewer. + + + + + Settings of the image diffusion + viewer. + + + + + Settings of the image flow viewer. + + + + + + + + + + + Value used for the correlation function + representing a value whether the dust filter is activated. + + + + + + Value used for the correlation function + representing a value whether the normalization is activated. + + + + + + Value used for the correlation function + representing a value indicating whether the de-trending filter + is activated. + + + + + Value used for the correlation function + representing a parameter for the dust calculation. + + + + + + Value used for the correlation function + representing a parameter for the detrending calculation. + [units:ms] + + + + + The type of chart which is displayed in the image + correlation viewer. + + + + + + This value represents the + selection of the count rate chart type in the correlation + viewer. + + + + + This value represents the + selection of the residuals chart type in the correlation viewer. + + + + + + + + + The kind of reference image which is displayed in + the image correlation viewer. + + + + + + This value represents the + selection of the pre experiment reference image kind in the + correlation viewer. + + + + + This value represents the + selection of the post experiment reference image kind in the + correlation viewer. + + + + + + + + The Zoom which the user sets and needs to be + synchronized across all three DynamicProfilers viewers. + + + + + - - Spectral Data can be loaded from the spectral database, manualy defined from the spectral image by the ROI or calculated by the Automated Component Extraction (ACE). - + The ViewportOrigin which the user sets and needs to be + synchronized across all three DynamicProfilers + viewers. - - - - - - - - - The "Intensity" property specifies the intensity of the spectral channel. - - - - - - - The "Wavelength" specifies the center wavelength corresponding to the spectral detection channel. - - - - - - - The "StandardDeviation" property sepcifies the standard deviation of one - intensity in a particular spectrum. - - - - - + + + + + + + - - - - - - - The "Excitations" property provides access the arrays with the excitation - wavelengths that have been used to record the spectrum with the index. - The information is stored to be able to write the - spectra parameters to a spectra database. - - - - - - - - - - + + + + + + + + + - - - - - - - - - The "StructuredIllumination" provides access to the parameters which are used for resolution - enhancement form data of acquisitions whith structured illumination. - - - - - - - The "DimensionH" property specifies the number of phases. - - - - - - - The "DimensionR" property specifies the number of rotations. - - - - - - - The "DimensionC" property specifies the number of channels. - - - - - - - The "Phases" property specifies the phase angle of the grating in structured - illumination acquisition with the specified phase index. - - - - - - - - - - The "Rotations" properties specifies the rotation angles of the pixels - of the image data with the specified rotation index. - - - - - - - - - - - - - - - - The "ExcitationWavelength" property specifies the wavelength of the light - which has been used to excite the dye for the detector that generated the - data for the specified channel. If the wavelength is 0 the excitation - wavelength is not known. [units:meters]. - - - - - - - The "GratingPeriod" property specifies the distance of the maxima of the - grating which has been used to acquire the data of the channel. - - - - - - - The "GratingPixels" property specifies the number of pixels which span the - distance of the maxima of the grating which has been used to acquire the - data of the channel. - - - - - - - - - - - - - - - - - - - - + + + + + + + + Value used for the diffusion function + representing a value whether the normalization is activated. + + - - - - - - - - - The "Airyscan" provides access to the parameters which are used for resolution - enhancement with Airyscan acquisition. - - - - - - - - - - - - - - - - - - - - - - - - The factor between used sampling (image resolution) and widefield Nyquist-Shannon sampling, where sampling is defined as the (physical) distance between centers of neighboring pixels. [units:none]. - - - - - - - - - - - - - - - - - - - - - - Represents a dataset of calibration values determined by the user. - - - - - - - - Effective radius of the observation spot. - - + + + Value used for the diffusion function + representing a value whether binning is activated. + + - - - - Average radius of the observation spot for one detector element. - - + + + The type of data displayed in the diagrams and + charts of the image diffusion viewer. + + + + + + This value represents the + selection of inner elements displayed in the Sunset diagram. + + + + + + This value represents the + selection of outer elements displayed in the Sunset diagram. + + + + + - - - - Effective distance between the detector elements for flow measurements. - - + + + The coloring of the diagrams is displayed with + the lookup-table (LUT) defined by the PaletteName. + + - - - - Ratio between the observation spot waist in the axial and lateral direction. - - + + + Value contains settings for each button used in + the diffusion viewer button bar. + - - - - File name of the calibration file. - - + + + + + + + + Value used for the correlation function + representing a value indicating whether the fitted curves are + displayed in the chart. + - - - - - - - Effective radius of the observation spot. - - - - - - - Average radius of the observation spot for one detector element. - - - - - - - Effective distance between the detector elements for flow measurements. - - - - - - - Ratio between the observation spot waist in the axial and lateral direction. - - - - - - - - - - - SuperResolutionParameter determines the Wiener filtering level. Typical values vary between ‐5 and ‐7 and depend on the signal-to-noise ratio of the sample. [units:none]. - - - - - - - Determines if the SuperResolutionParameter is estimated by the software (automatic mode) or is defined by the user (manual). [units:none]. - - - - - - - - - - - - - Resolution enhancement in z can be achieved by using 3D processing. - - - - - - - - - - - - - - - Tile-based 3D processing of the large image data is done to reduce memory usage. - - - - - - - Number of airyscan detector rings that defines the size of the virtual pinhole. For example, the value 2,5 means, that 3 inner rings are selected, the first two rings with the weight "1", and the third ring with the weight "0.5". [units:none]. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + Value contains settings for each button used in + the flow viewer button bar. + - - - - - - - - - - - - - - - - - - Settings of the image correlation viewer. - - - - - - - Settings of the image diffusion viewer. - - - - - - - Settings of the image flow viewer. - - - - - - - - - - - Value used for the correlation function representing a value whether the dust filter is activated. - - - - - - - Value used for the correlation function representing a value whether the normalization is activated. - - - - - - - Value used for the correlation function representing a value indicating whether the de-trending filter - is activated. - - - - - - - Value used for the correlation function representing a parameter for the dust calculation. - - - - - - - Value used for the correlation function representing a parameter for the detrending calculation. - [units:ms] - - - - - - - The type of chart which is displayed in the image correlation viewer. - - - - - - - - This value represents the selection of the count rate chart type in the correlation viewer. - - - - - - - This value represents the selection of the residuals chart type in the correlation viewer. - - - - - - - - - - The kind of reference image which is displayed in the image correlation viewer. - - - - - - - - This value represents the selection of the pre experiment reference image kind in the correlation viewer. - - - - - - - This value represents the selection of the post experiment reference image kind in the correlation viewer. - - - - - - - - - - - - - - Value used for the diffusion function representing a value whether the normalization is activated. - - - - - - - Value used for the diffusion function representing a value whether binning is activated. - - - - - - - The type of data displayed in the diagrams and charts of the image diffusion viewer. - - - - - - - - This value represents the selection of inner elements displayed in the Sunset diagram. - - - - - - - This value represents the selection of outer elements displayed in the Sunset diagram. - - - - - - - - - - The coloring of the diagrams is displayed with the lookup-table (LUT) - defined by the PaletteName. - - - - - - - Value contains settings for each button used in the diffusion viewer button bar. - - - - - - - - - - - Value used for the correlation function representing a value indicating whether the fitted curves - are displayed in the chart. - - - - - - - Value contains settings for each button used in the flow viewer button bar. - - - - - - - - - - - Value used to identify the button by the name of the button. - - - - - - - Value used for the button bar settings representing a value whether the button is selected. - - - - - - - Value used for the button bar settings representing a value which first color is defined. - - - - - - - Value used for the button bar settings representing a value which second color is defined. - - - - - - - - - - - Enumeration for scaling types. They defines different ways for defining scaling information for acquired images. - - - - - - - - Scaling factors calculated by the system based on the current hardware setup and the nominal values of all magnifying components. - - - - - - - Scaling factors generated via interactive user definitions. - - - - - - - Scaling factors calculated based on a measured Scaling with help of the nominal values of the magnifying components. - E.g. when measured scaling values or automatically calculated scaling values are activated and the camera binning is changed, - the new scaling values can be derived from the measured or automatically calculated scaling values. - - - - - - - Scaling factors generated via calibration wizard. - - - - - - - Scaling factors generated via interactive user definitions. The scaling is unused, because of an other scaling for the same hardware configuration. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The physiology view mode. - - - - - - - - - - - - - - - - - Defines whether to follow the acquisition. - - - - - - - Defines whether the timeline view is shown or not. - - - - - - - - - - - The modes of the measurement feature. - - - - - - - - - - - - - - - The background correction mode for physiology. - - - - - - - - - - - - - - - - - - - Units of the Axis. - - - - - - - - - - - - - The time unit for the x axis. - - - - - - - Scaling of the X axis. - - - - - - - - - - - - - - Scaling of the Y axis. - - - - - - - - - - - - - - The maximum value for the x axis. - - - - - - - The minimum value for the x axis. - - - - - - - The maximum for the minimum value of the x axis. - - - - - - - The maximum value for the Y axis. - - - - - - - The minimum value for the Y axis. - - - - - - - The maximum for the minimum value of the left Y axis. - - - - - - - The maximum for the minimum value of the right Y axis. - - - - - - - Tick Settings. - - - - - - - - - - - - - The maximum of the tick settings. - - - - - - - The minimum for the maximum of the tick settings. - - - - - - - The minimum of the tick settings. - - - - - - - The minimum for the minimum of the tick settings. - - - - - - - The maximum for the minimum of the tick settings. - - - - - - - - - - - - - - - - - - - - - - - The element is opaque in this schema, for validation of contained XML refer to HardwareSetting.xsd. - + + + + + + + + Value used to identify the button by the name of + the button. + + + + + Value used for the button bar settings + representing a value whether the button is selected. + + + + + + Value used for the button bar settings + representing a value which first color is defined. + + + + + + Value used for the button bar settings + representing a value which second color is defined. + + + + + + + + + + + + + Enumeration for scaling types. They defines + different ways for defining scaling information for acquired images. + + + + + + + Scaling factors calculated by the + system based on the current hardware setup and the nominal + values of all magnifying components. + + + + + + Scaling factors generated via + interactive user definitions. + + + + + Scaling factors calculated based on a + measured Scaling with help of the nominal values of the + magnifying components. E.g. when measured + scaling values or automatically calculated scaling values are + activated and the camera binning is changed, + the new scaling values can be derived from the measured or + automatically calculated scaling values. + + + + + + Scaling factors generated via + calibration wizard. + + + + + Scaling factors generated via + interactive user definitions. The scaling is unused, because of + an other scaling for the same hardware configuration. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + - - + + + + + + The physiology view mode. + + + + + + + + + + + + + + + + Defines whether to follow the acquisition. + + + + + + Defines whether the timeline view is shown or + not. + + + + + + + + + The modes of the measurement feature. + + + + + + + + + + + + + + The background correction mode for physiology. + + + + + + + + + + + + + + + + + + Units of the Axis. + + + + + + + + + + + The time unit for the x axis. + + + + + + Scaling of the X axis. + + + + + + + + + + + + + Scaling of the Y axis. + + + + + + + + + + + + + The maximum value for the x axis. + + + + + + The minimum value for the x axis. + + + + + + The maximum for the minimum value of the x axis. + + + + + + The maximum value for the Y axis. + + + + + + The minimum value for the Y axis. + + + + + + The maximum for the minimum value of the left Y + axis. + + + + + The maximum for the minimum value of the right Y + axis. + + + + + Tick Settings. + + + + + + + + + + + The maximum of the tick settings. + + + + + + The minimum for the maximum of the tick settings. + + + + + + The minimum of the tick settings. + + + + + + The minimum for the minimum of the tick settings. + + + + + + The maximum for the minimum of the tick settings. + + + + + + + - The element is opaque in this schema, for validation of contained XML refer to Experiment.xsd. + Use this element as the root element for stand-alone image metadata + XML file. - - - - + + + - - + + + + + + + + + + + + + + + + + + + + + + The element is opaque in this schema, for validation of + contained XML refer to HardwareSetting.xsd. + + + + + + + + + + + The element is opaque in this schema, for validation of + contained XML refer to Experiment.xsd. + + + + + + + + + + + The element is opaque in this schema. + + + + + + + + + + + + + + + + + + + + The element is opaque in this schema, for validation of + contained XML refer to HardwareSetting.xsd. + + + + + + + + + + + + - The element is opaque in this schema. + Arbitrary "appliances" may store their data here. - - - - - - - - - - - - - - - - - - The element is opaque in this schema, for validation of contained XML refer to HardwareSetting.xsd. + + + + + + + + + + + + + + + + + + + + An identifier to uniquely identify this application + data. + + + + + + + Contains information about "topography data items", which can + be thought of as a group of channels, where each channel (within this group) + can be attributed as "heightmap" or "texture". NOTES: (1) + The Id of the Appliances node specifying a "topography data item" must be + "Topography:1". Everything else will not be recognized as specifying a + "topography data item". (2) It is _not_ recommended to rely on + Metadata.Information.Document.SubType in order to detect the presence of + "topography data items" in a document. Instead, it is recommended to + actively discover whether this information is present (and if the + document is usable for the respective application). - - - - - - - - - - - - Arbitrary "appliances" may store their data here. - - - - - - - - - - - - - - - - - - An identifier to uniquely identify this application data. - - - - - - - Contains optional advanced information about Height maps and textures. - - - - - - - - - - - - - - - + + + + + + + + + + + This node exists for legacy reasons - its + content is not used. + + + + + + + + + + + + An identifier to uniquely identify this + Topography data. + + + - - - - - - An identifier to uniquely identify this Topography Scaling within a collection. - - - - - - - - - - + + + - - This node exists for legacy reasons - its content is not used. - + Contains optional advanced information about Height maps and + textures. - - - - - - - - - - - - For legacy reasons, all attributes in the attribute grout "SubsetBounds" are - syntactically allowed, but only "StartC" is honored, the remaining are ignored - (and should not be written or used in any way). - - - - - - - - - - - - - - - For legacy reasons, all attributes in the attribute group "SubsetBounds" are - syntactically allowed, but only "StartC" is honored, the remaining are ignored - (and should not be written or used in any way). - - - - - - - - This data structure contains the results of a GrainSize-Measurement by the - product "Hermes". - TODO: please provide a reasonable description - - - - + + + + + + + + + + + + + + + + + + + + An identifier to uniquely identify this Topography Scaling within + a collection. + + + + + + - - This is the measurement result of one plane (=plane is spreading only in X-Y-dimension). The annotations - "TheC", "TheZ" specify to which plane this measurement applies. An attribute (TheC, TheT, TheZ, TheS, TheV) can only be - omitted if the document does not contain this dimension (or, more precise: if the corresponding dimension has a size less than - or equal to 1). If the document e. g. has T-dimension, then "TheT" must be present, otherwise the data is illegal. - Also, it is illegal to have a duplicate plane. - + - - - - - - - TODO: please provide a reasonable description - - - - + + + + This node exists for legacy reasons - its content + is not used. + + + + + + + + + + + + For legacy reasons, all attributes in the attribute + grout "SubsetBounds" are syntactically allowed, but only "StartC" is + honored, the remaining are ignored (and should not be written or used + in any way). + + + + + - - TODO: please provide a reasonable description what this number means. - + - - + + + + + + For legacy reasons, all attributes in the attribute group + "SubsetBounds" are syntactically allowed, but only "StartC" is honored, + the remaining are ignored (and should not be written or used in any + way). + + + + + + + - - TODO: please provide a reasonable description what this number means. - [unit:micrometer] - + This data structure contains the results of a + GrainSize-Measurement by the product "Hermes". TODO: please provide + a reasonable description - - + + + + This is the measurement result of one plane + (=plane is spreading only in X-Y-dimension). The annotations + "TheC", "TheZ" specify to which plane this measurement applies. An attribute + (TheC, TheT, TheZ, TheS, TheV) can only be omitted if the + document does not contain this dimension (or, more precise: if the + corresponding dimension has a size less than or equal to 1). If + the document e. g. has T-dimension, then "TheT" must be present, otherwise + the data is illegal. Also, it is illegal to have a duplicate + plane. + + + + + - - The Chord Pattern contains multiple chord segments. - TODO: please provide a reasonable description - + TODO: please provide a reasonable description + - - - - - - The zoom of the pattern. - TODO: please provide a reasonable description what this number means. - How is "Zoom" defined? Is there a unit associated with this number? - - - - - - - Specifies the standard that was used to perform the measurement. - TODO: please provide a reasonable description - - - - - - - - - + + + + TODO: please provide a reasonable description + what this number means. + - - - - The type of of measuring pattern, can be one of the following: "Combined", "HorizontalLines", "VerticalLines", "XCross", "ConcentricCircles". - TODO: please provide a reasonable description - - - - - - - - - - - + + + TODO: please provide a reasonable description + what this number means. [unit:micrometer] + + - - - - This node contains any number of Line or Circle children. - TODO: please provide a reasonable description - - - - - - - - - A Choord of type Line. - TODO: please provide a reasonable description - - - - - - - - The X1-coordinate for "line-choord". - [unit: pixel] - TODO: please provide a reasonable description - - - - - - - The X2-coordinate for "line-choord". - [unit: pixel] - TODO: please provide a reasonable description - - - - - - - The Y1-coordinate for "line-choord". - [unit: pixel] - TODO: please provide a reasonable description - - - - + + + The Chord Pattern contains multiple chord + segments. TODO: please provide a reasonable description + + + + + - - The Y2-coordinate for "line-choord". - [unit: pixel] - TODO: please provide a reasonable description - + The zoom of the pattern. + TODO: please provide a reasonable description what this number + means. How is "Zoom" defined? Is there a unit + associated with this number? - - + + - - An array of numbers, which specify the intersections points. The list is to be interpreted - as the x-coordinate of an intersection point followed by the y-coordinate of the point. - So, this list must contain an even number of floating-point numbers. - [unit: pixel] - TODO: please provide a reasonable description - + Specifies the standard that was + used to perform the measurement. TODO: please + provide a reasonable description + - - - - - + + + + + - - - - - - - - - - - The X-coordinate of the center of a "circle-choord" - [unit: pixel] - TODO: please provide a reasonable description - - - - - - - The Y-coordinate of the center of a "circle-choord" - [unit: pixel] - TODO: please provide a reasonable description - - - - - - - The radius of a "circle-choord" - [unit: pixel] - TODO: please provide a reasonable description - - - - + + - - An array of numbers, which specify the intersections points. The list is to be interpreted - as the x-coordinate of an intersection point followed by the y-coordinate of the point. - So, this list must contain an even number of floating-point numbers. - [unit: pixel] - TODO: please provide a reasonable description - + The type of of measuring + pattern, can be one of the following: "Combined", + "HorizontalLines", "VerticalLines", "XCross", + "ConcentricCircles". TODO: please provide a + reasonable description - - - - - + + + + + + + - - - - - - - + + + + This node contains any number + of Line or Circle children. TODO: please + provide a reasonable description + + + + + + + + A + Choord of type Line. + TODO: please provide a reasonable description + + + + + + + + The X1-coordinate for "line-choord". + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + The X2-coordinate for "line-choord". + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + The Y1-coordinate for "line-choord". + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + The Y2-coordinate for "line-choord". + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + An array of numbers, which specify the + intersections points. The list is to be + interpreted as the + x-coordinate of an intersection point followed by + the y-coordinate of the point. + So, this list must contain an even number of + floating-point numbers. + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + + + + + + + + + + + + + + The X-coordinate of the center of a + "circle-choord" + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + The Y-coordinate of the center of a + "circle-choord" + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + The radius of a "circle-choord" + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + An array of numbers, which specify the + intersections points. The list is to be + interpreted as the + x-coordinate of an intersection point followed by + the y-coordinate of the point. + So, this list must contain an even number of + floating-point numbers. + [unit: pixel] + TODO: please provide a reasonable description + + + + + + + + + + + + + + + + + + + - - - - - - - - This gives the coordinate of the plane to which this measurement applies. - Note that the specification of the plane must be sufficient which means that - if the document contains e. g. the C-dimension (SizeC greater than 1), then - the C-coordinate MUST be given here. - - - - - - - This gives the coordinate of the plane to which this measurement applies. - Note that the specification of the plane must be sufficient which means that - if the document contains e. g. the T-dimension (SizeT greater than 1), then - the T-coordinate MUST be given here. - - - - - - - This gives the coordinate of the plane to which this measurement applies. - Note that the specification of the plane must be sufficient which means that - if the document contains e. g. the Z-dimension (SizeZ greater than 1), then - the Z-coordinate MUST be given here. - - - - - - - This gives the coordinate of the plane to which this measurement applies. - Note that the specification of the plane must be sufficient which means that - if the document contains e. g. the V-dimension (SizeV greater than 1), then - the V-coordinate MUST be given here. - - - - - - - This gives the coordinate of the plane to which this measurement applies. - Note that the specification of the plane must be sufficient which means that - if the document contains e. g. the S-dimension (SizeS greater than 1), then - the S-coordinate MUST be given here. - - - - - - - + + + + This gives the coordinate of the plane to which this + measurement applies. Note that the specification of the plane must be + sufficient which means that if the document contains e. g. the + C-dimension (SizeC greater than 1), then the C-coordinate MUST be + given here. + + + + + This gives the coordinate of the plane to which this + measurement applies. Note that the specification of the plane must be + sufficient which means that if the document contains e. g. the + T-dimension (SizeT greater than 1), then the T-coordinate MUST be + given here. + + + + + This gives the coordinate of the plane to which this + measurement applies. Note that the specification of the plane must be + sufficient which means that if the document contains e. g. the + Z-dimension (SizeZ greater than 1), then the Z-coordinate MUST be + given here. + + + + + This gives the coordinate of the plane to which this + measurement applies. Note that the specification of the plane must be + sufficient which means that if the document contains e. g. the + V-dimension (SizeV greater than 1), then the V-coordinate MUST be + given here. + + + + + This gives the coordinate of the plane to which this + measurement applies. Note that the specification of the plane must be + sufficient which means that if the document contains e. g. the + S-dimension (SizeS greater than 1), then the S-coordinate MUST be + given here. + + + + + - - Calibration data is not valid without marker data. - For current usage of Shuttle and Find, there must be 3 marker points. There might be more for future applications. - + The ShuttleAndFindData contains the calibration of the marker + points for Shuttle and Find. This data is added to metadata via the + Appliances node (path: Appliances/Appliance/Data/ShuttleAndFindData). NOTE: + Ensure that the Id of the respective Appliance node obeys the following naming + guideline: Id="ShuttleAndFind:*". ('*' generally is an integer but + might be anything.) Hence, algorithms can search for Ids which start with + "ShuttleAndFind:". - - - + + + + + + An identifier to uniquely identify this + ShuttleAndFind data. + + + - - - - - Defines the stage X and stage Y orientation. - If the acquisition is not directed to the image center, the offset to the image center needs to be added to the stage position. - Before adding, the offsets need to be multiplied with the stage orientation values. - Typical values: LM: X=-1, Y=-1. SEM: X=1, Y=-1. - - - - + + + + + + + Calibration data is not valid without marker + data. For current usage of Shuttle and Find, there must be 3 + marker points. There might be more for future applications. + + + + + + + + + + + Defines the stage X and stage Y orientation. + If the acquisition is not directed to the image center, the offset to the + image center needs to be added to the stage position. Before + adding, the offsets need to be multiplied with the stage orientation values. + Typical values: LM: X=-1, Y=-1. SEM: X=1, Y=-1. + + + + + + Stage X axis orientation. Possible values: 1, + -1. + + + + + + + + + + + Stage Y axis orientation. Possible values: 1, + -1. + + + + + + + + + + + + + Defines the type of the microscope with which the image was + created. + + + + + + + + + + + + + + The name of the Shuttle-and-Find holder which was used when + the calibration was created. This field is intended to provide information + only. + + + + + A correlative session defines an acquisition of + images with a calibrated stage. The correlative session + information is used by the correlative workspace extension (CWS). + + + + + + The correlative session id is a + global unique identifier (guid) that identifies a specific + correlative session with defined stage calibration. + + + + + + + + + + + + + + + - Stage X axis orientation. Possible values: 1, -1. + The stage X axis position [unit: micrometers]. - - - - - - - - + + - Stage Y axis orientation. Possible values: 1, -1. + The stage Y axis position [unit: micrometers]. - - - - - - - - - - - - Defines the type of the microscope with which the image was created. - - - - - - - - - - - - - - The name of the Shuttle-and-Find holder which was used when the calibration was created. This field is intended to provide information only. - - - - - - A correlative session defines an acquisition of images with a calibrated stage. - The correlative session information is used by the correlative workspace extension (CWS). - - - - + + - - The correlative session id is a global unique identifier (guid) that identifies a specific - correlative session with defined stage calibration. - + The focus position [unit: micrometers]. - - - - - - - - - - - - - - The stage X axis position [unit: micrometers]. - - - - - The stage Y axis position [unit: micrometers]. - - - - - The focus position [unit: micrometers]. - - - - - An identifier to uniquely identify this calibration point. - - - - - - - The SEM parameters have informational character, e.g. to be displayed as info in applications. - Hence, all parameters are stored as strings, not as numerical values. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Depending on the used SEM system, some specific parameters are set additionally. - - Parameters for system = Evo: - ProbeCurrent, FilamentType, FilamentCurrent, OptiBeamMode, ApertureSelection, - VPAperture, AirWaterMode, StageTemperature, BeamCurrent. - - Parameters for system = Supra, Ultra, Sigma, Merlin or Delta: - ExtractorVoltage, ExtractionCurrent, ApertureNumber, HighCurrentMode. - - Parameters for system = XB, NVision, Neon or Auriga: - FIBVoltage, FIBMode, FIBProbeCurrent, FIBAperture, FIBGISChannel. - - - - - - - The ElectronDose field is a dosage estimate of electrons or rather charge per unit area. The preferred unit to be used here is e/nm^2 (electrons or elementary charge per square nanometer). - - - - - - - - The ApertureSelection field will only be available for older versions. Newer versions store the aperture size in the ApertureSize field under SEMParameters. - - - - - - - - - - - - - - - - - - - - The name of the system. - Possible values: Evo, Supra, Ultra, Sigma, Merlin, Delta, XB, NVision, Neon, Auriga. - - - - - - - - This data contains the initial parameter values for SIM Plugin viewers, as defined by the user for the SIM experiment. - - - - - - - The epsilon for the Spatially Adapted Bleaching Correction (=SABC). [unit: none] - - - - - - - The normalize mode. - - - - - - - - - - - - - + + + + An identifier to uniquely identify this calibration + point. + + + + + - - The name of the processing filter. Also referred to as filter mode. - The filter name actually is redundant with filter harmonics and size. - + The SEMData appliances hold the SEM parameters. + - - - - - - - - - - - - - The filter harmonics for SIM processing. Also referred to as filter component. - + + + + + + + An identifier to uniquely identify this SEM data. + + + + + + + + + The SEM parameters have informational character, e.g. to be + displayed as info in applications. Hence, all parameters are stored as + strings, not as numerical values. + + + + + + + + + + + + + + + + + + + + + + + + + + + + Depending on the used SEM system, some specific parameters + are set additionally. Parameters for system = Evo: ProbeCurrent, + FilamentType, FilamentCurrent, OptiBeamMode, ApertureSelection, VPAperture, + AirWaterMode, StageTemperature, BeamCurrent. Parameters for system = Supra, + Ultra, Sigma, Merlin or Delta: ExtractorVoltage, ExtractionCurrent, + ApertureNumber, HighCurrentMode. Parameters for system = XB, NVision, Neon + or Auriga: FIBVoltage, FIBMode, FIBProbeCurrent, FIBAperture, FIBGISChannel. + - - - - - - - - - - - - - - - - - - - + + + + + The ElectronDose field is a dosage estimate of electrons or + rather charge per unit area. The preferred unit to be used here is e/nm^2 + (electrons or elementary charge per square nanometer). + + + + + + + + The ApertureSelection field will only be available for older + versions. Newer versions store the aperture size in the ApertureSize field + under SEMParameters. + + + + + + + + + + + + + + + + + + + The name of the system. Possible values: Evo, + Supra, Ultra, Sigma, Merlin, Delta, XB, NVision, Neon, Auriga. + + + + + + - - The filter size for SIM processing [unit: none]. - + This data contains the initial parameter values for SIM + Plugin viewers, as defined by the user for the SIM experiment. + - - - - - - Additional information about attachments may be stored here. - - - - - - - - - - - - - - An identifier to uniquely identify this AttachmentInfo data. - The identifier string equals the name of the corresponding attachment. - - - - - - - - Contains information about the Axio Scan profile that was used to acquire the image. - - - - - - - - - Additional information about a Label attachment. - - - + + + + + + + An identifier to uniquely identify this SIM data. + + + + + + + - The angle (in degrees) with which to rotate the label image for GUI display. + This data contains the initial parameter values for SIM + Plugin viewers, as defined by the user for the SIM experiment. + - - + + + + The epsilon for the Spatially Adapted Bleaching + Correction (=SABC). [unit: none] + + + + + + + The normalize mode. + + + + + + + + + + + + + + The name of the processing filter. Also referred + to as filter mode. The filter name actually is redundant with + filter harmonics and size. + + + + + + + + + + + + + The filter harmonics for SIM processing. Also + referred to as filter component. + + + + + + + + + + + + + + + + + + + + + + + The filter size for SIM processing [unit: none]. + + + + + + + - Information about the barcodes contained on this label. + Additional information about attachments may be stored + here. - - - - - - - + + + + + + + + + + + + + An identifier to uniquely identify this AttachmentInfo + data. The identifier string equals the name of the corresponding + attachment. + + + + + - Information about the OCR (Optical Character Recognition) result for this label. + Contains information about the Axio Scan profile that was + used to acquire the image. - - - - - - - - - - - Data to describe a barcode. - - - + + + + + + - The barcode type. + Additional information about a Label attachment. - - + + + + The angle (in degrees) with which to rotate the label image + for GUI display. + + + + + Information about the barcodes contained on this + label. + + + + + + + + + + Information about the OCR (Optical Character Recognition) + result for this label. + + + + + + + + + + + - The content of the barcode. + Data to describe a barcode. - - - - - - An identifier to uniquely identify this barcode. - - - - - - - Data to describe an OCR (Optical Character Recognition) result. - - - + + + + The barcode type. + + + + + The content of the barcode. + + + + + + An identifier to uniquely identify this barcode. + + + + + + - The content of the OCR. + Data to describe an OCR (Optical Character Recognition) + result. - - - - - - An identifier to uniquely identify this OCR data. - - - - - \ No newline at end of file + + + + The content of the OCR. + + + + + + An identifier to uniquely identify this OCR data. + + + + + diff --git a/documentation/version-history.md b/documentation/version-history.md index f7456c8..ecc57c7 100644 --- a/documentation/version-history.md +++ b/documentation/version-history.md @@ -13,3 +13,4 @@ version history {#version_history} 0.5.0 | [20](https://github.com/ZEISS/czicheck/pull/20) | enhance "topographymetadata" checker 0.5.1 | [21](https://github.com/ZEISS/czicheck/pull/21) | add third-party-licenses doc and create public artifacts 0.6.0 | [22](https://github.com/ZEISS/czicheck/pull/22) | enable machine readable output in json and xml format + 0.6.1 | [25](https://github.com/ZEISS/czicheck/pull/25) | update of metadata-schema (including Lf4d) From 872a92d8d46b2c969616e843012b9dc87af8a748 Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 12:12:23 +0100 Subject: [PATCH 2/7] Update MegaLinter workflow and action versions Updated `mega-linter.yml` to use actions/checkout@v4 and actions/upload-artifact@v4. Also upgraded MegaLinter flavor from v6 to v7 for potential improvements and new features. --- .github/workflows/mega-linter.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/mega-linter.yml b/.github/workflows/mega-linter.yml index b7a9fac..19c3f63 100644 --- a/.github/workflows/mega-linter.yml +++ b/.github/workflows/mega-linter.yml @@ -22,14 +22,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout Code - uses: actions/checkout@v3 + uses: actions/checkout@v4 # MegaLinter - name: MegaLinter id: ml # You can override MegaLinter flavor used to have faster performances # More info at https://megalinter.io/flavors/ - uses: oxsecurity/megalinter/flavors/dotnet@v6 + uses: oxsecurity/megalinter/flavors/dotnet@v7 env: # All available variables are described in documentation # https://megalinter.io/configuration/ @@ -38,7 +38,7 @@ jobs: # Upload MegaLinter artifacts - name: Archive production artifacts if: ${{ success() || failure() }} - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: MegaLinter reports path: | From 1642d4448bce7e0a20221376e20a2d675ba0d88b Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 12:13:30 +0100 Subject: [PATCH 3/7] fix link --- documentation/version-history.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation/version-history.md b/documentation/version-history.md index ecc57c7..5427794 100644 --- a/documentation/version-history.md +++ b/documentation/version-history.md @@ -13,4 +13,4 @@ version history {#version_history} 0.5.0 | [20](https://github.com/ZEISS/czicheck/pull/20) | enhance "topographymetadata" checker 0.5.1 | [21](https://github.com/ZEISS/czicheck/pull/21) | add third-party-licenses doc and create public artifacts 0.6.0 | [22](https://github.com/ZEISS/czicheck/pull/22) | enable machine readable output in json and xml format - 0.6.1 | [25](https://github.com/ZEISS/czicheck/pull/25) | update of metadata-schema (including Lf4d) + 0.6.1 | [28](https://github.com/ZEISS/czicheck/pull/28) | update of metadata-schema (including Lf4d) From 0fa44bb7ae94d4733f96a69356eb860214965b2a Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 12:25:09 +0100 Subject: [PATCH 4/7] update version info in "expected results" --- Test/CZICheckSamples/differentpixeltypeinchannel.txt.json | 2 +- Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml | 2 +- Test/CZICheckSamples/duplicate_coordinates.txt.json | 2 +- Test/CZICheckSamples/duplicate_coordinates.txt.xml | 2 +- Test/CZICheckSamples/edf-missing-texture.txt.json | 2 +- Test/CZICheckSamples/edf-missing-texture.txt.xml | 2 +- .../edf-superfluous-missing-channel-subblock.txt.json | 2 +- .../edf-superfluous-missing-channel-subblock.txt.xml | 2 +- Test/CZICheckSamples/edf-superfluous.txt.json | 2 +- Test/CZICheckSamples/edf-superfluous.txt.xml | 2 +- Test/CZICheckSamples/inconsistent_coordinates.txt.json | 2 +- Test/CZICheckSamples/inconsistent_coordinates.txt.xml | 2 +- Test/CZICheckSamples/invalid_componentbitcount.txt.json | 2 +- Test/CZICheckSamples/invalid_componentbitcount.txt.xml | 2 +- .../jpgxrcompressed_inconsistent_pixeltype.txt.json | 2 +- .../jpgxrcompressed_inconsistent_pixeltype.txt.xml | 2 +- .../jpgxrcompressed_inconsistent_size.txt.json | 2 +- .../jpgxrcompressed_inconsistent_size.txt.xml | 2 +- .../layer_0_subblocks_with_no_m_index.txt.json | 2 +- .../layer_0_subblocks_with_no_m_index.txt.xml | 2 +- Test/CZICheckSamples/negative_plane_start_index.txt.json | 2 +- Test/CZICheckSamples/negative_plane_start_index.txt.xml | 2 +- Test/CZICheckSamples/overlapping_scenes.txt.json | 2 +- Test/CZICheckSamples/overlapping_scenes.txt.xml | 2 +- ...xeltype_mismatch_between_metadata_and_subblocks.txt.json | 2 +- ...ixeltype_mismatch_between_metadata_and_subblocks.txt.xml | 2 +- Test/CZICheckSamples/positive_plane_start_index.txt.json | 2 +- Test/CZICheckSamples/positive_plane_start_index.txt.xml | 2 +- Test/CZICheckSamples/sparse_planes.txt.json | 2 +- Test/CZICheckSamples/sparse_planes.txt.xml | 2 +- documentation/usage.md | 6 +++--- 31 files changed, 33 insertions(+), 33 deletions(-) diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json index 6ee322e..7fe900c 100644 --- a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json +++ b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json @@ -112,6 +112,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml index e88c308..2108ae3 100644 --- a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml +++ b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml @@ -99,6 +99,6 @@ WARN CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.json b/Test/CZICheckSamples/duplicate_coordinates.txt.json index de07219..49a075a 100644 --- a/Test/CZICheckSamples/duplicate_coordinates.txt.json +++ b/Test/CZICheckSamples/duplicate_coordinates.txt.json @@ -112,6 +112,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.xml b/Test/CZICheckSamples/duplicate_coordinates.txt.xml index 049fca8..8001554 100644 --- a/Test/CZICheckSamples/duplicate_coordinates.txt.xml +++ b/Test/CZICheckSamples/duplicate_coordinates.txt.xml @@ -99,6 +99,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.json b/Test/CZICheckSamples/edf-missing-texture.txt.json index d30f2aa..a0f77a2 100644 --- a/Test/CZICheckSamples/edf-missing-texture.txt.json +++ b/Test/CZICheckSamples/edf-missing-texture.txt.json @@ -125,6 +125,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.xml b/Test/CZICheckSamples/edf-missing-texture.txt.xml index b004c4b..cf44e50 100644 --- a/Test/CZICheckSamples/edf-missing-texture.txt.xml +++ b/Test/CZICheckSamples/edf-missing-texture.txt.xml @@ -112,6 +112,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json index 52bee5f..1307f41 100644 --- a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json +++ b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json @@ -136,6 +136,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml index 69d3041..4bde44f 100644 --- a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml +++ b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml @@ -123,6 +123,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/edf-superfluous.txt.json b/Test/CZICheckSamples/edf-superfluous.txt.json index ddebc70..bc2d034 100644 --- a/Test/CZICheckSamples/edf-superfluous.txt.json +++ b/Test/CZICheckSamples/edf-superfluous.txt.json @@ -125,6 +125,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/edf-superfluous.txt.xml b/Test/CZICheckSamples/edf-superfluous.txt.xml index e0f13f1..2aafb35 100644 --- a/Test/CZICheckSamples/edf-superfluous.txt.xml +++ b/Test/CZICheckSamples/edf-superfluous.txt.xml @@ -112,6 +112,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.json b/Test/CZICheckSamples/inconsistent_coordinates.txt.json index 79eedde..1d62338 100644 --- a/Test/CZICheckSamples/inconsistent_coordinates.txt.json +++ b/Test/CZICheckSamples/inconsistent_coordinates.txt.json @@ -112,6 +112,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml index 4d84adb..47a526a 100644 --- a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml +++ b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml @@ -99,6 +99,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.json b/Test/CZICheckSamples/invalid_componentbitcount.txt.json index 43d4f44..37eb70e 100644 --- a/Test/CZICheckSamples/invalid_componentbitcount.txt.json +++ b/Test/CZICheckSamples/invalid_componentbitcount.txt.json @@ -94,6 +94,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml index 4fdf47c..1a17a49 100644 --- a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml +++ b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml @@ -81,6 +81,6 @@ WARN CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json index f419f78..b4a8788 100644 --- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json +++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json @@ -100,6 +100,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml index a4e3b2a..54ca471 100644 --- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml +++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml @@ -87,6 +87,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json index 4232440..5c97c19 100644 --- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json +++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json @@ -100,6 +100,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml index 10b4968..eead267 100644 --- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml +++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml @@ -87,6 +87,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json index 986f86f..0d6e8b0 100644 --- a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json +++ b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json @@ -100,6 +100,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml index 1dc51ce..01ff091 100644 --- a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml +++ b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml @@ -87,6 +87,6 @@ WARN CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.json b/Test/CZICheckSamples/negative_plane_start_index.txt.json index 172696b..6e72be6 100644 --- a/Test/CZICheckSamples/negative_plane_start_index.txt.json +++ b/Test/CZICheckSamples/negative_plane_start_index.txt.json @@ -105,6 +105,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.xml b/Test/CZICheckSamples/negative_plane_start_index.txt.xml index 52c0595..b950817 100644 --- a/Test/CZICheckSamples/negative_plane_start_index.txt.xml +++ b/Test/CZICheckSamples/negative_plane_start_index.txt.xml @@ -92,6 +92,6 @@ WARN CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.json b/Test/CZICheckSamples/overlapping_scenes.txt.json index 468e9db..2d7944f 100644 --- a/Test/CZICheckSamples/overlapping_scenes.txt.json +++ b/Test/CZICheckSamples/overlapping_scenes.txt.json @@ -136,6 +136,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.xml b/Test/CZICheckSamples/overlapping_scenes.txt.xml index 0b6725e..01c3f1a 100644 --- a/Test/CZICheckSamples/overlapping_scenes.txt.xml +++ b/Test/CZICheckSamples/overlapping_scenes.txt.xml @@ -123,6 +123,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json index 8050d6e..974ad68 100644 --- a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json +++ b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json @@ -181,6 +181,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml index a01a23c..803c8bd 100644 --- a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml +++ b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml @@ -168,6 +168,6 @@ FAIL CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.json b/Test/CZICheckSamples/positive_plane_start_index.txt.json index 464939b..4d05c32 100644 --- a/Test/CZICheckSamples/positive_plane_start_index.txt.json +++ b/Test/CZICheckSamples/positive_plane_start_index.txt.json @@ -105,6 +105,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.xml b/Test/CZICheckSamples/positive_plane_start_index.txt.xml index 9aad157..86b7206 100644 --- a/Test/CZICheckSamples/positive_plane_start_index.txt.xml +++ b/Test/CZICheckSamples/positive_plane_start_index.txt.xml @@ -92,6 +92,6 @@ WARN CZICheck - 0.6.0 + 0.6.1 diff --git a/Test/CZICheckSamples/sparse_planes.txt.json b/Test/CZICheckSamples/sparse_planes.txt.json index cd883cb..a2a3e24 100644 --- a/Test/CZICheckSamples/sparse_planes.txt.json +++ b/Test/CZICheckSamples/sparse_planes.txt.json @@ -105,6 +105,6 @@ ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } \ No newline at end of file diff --git a/Test/CZICheckSamples/sparse_planes.txt.xml b/Test/CZICheckSamples/sparse_planes.txt.xml index 6f1d771..f26bc89 100644 --- a/Test/CZICheckSamples/sparse_planes.txt.xml +++ b/Test/CZICheckSamples/sparse_planes.txt.xml @@ -92,6 +92,6 @@ WARN CZICheck - 0.6.0 + 0.6.1 diff --git a/documentation/usage.md b/documentation/usage.md index 8e76ed4..a65bfd6 100644 --- a/documentation/usage.md +++ b/documentation/usage.md @@ -6,7 +6,7 @@ Running CZICheck with the `--help` option will print a brief summary of the available options and their usage: ``` -CZICheck version 0.6.0, using libCZI version 0.62.6 +CZICheck version 0.6.1, using libCZI version 0.62.6 Usage: CZICheck [OPTIONS] @@ -170,7 +170,7 @@ See the following example: ], "output_version": { "command": "CZICheck", - "version": "0.6.0" + "version": "0.6.1" } } @@ -243,7 +243,7 @@ See the following example: FAIL CZICheck - 0.6.0 + 0.6.1 From 478d0603b65bb44336a9171d3046842a89f74a31 Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 13:55:49 +0100 Subject: [PATCH 5/7] fix --- Test/CZICheckSamples/edf-missing-texture.txt | 2 +- Test/CZICheckSamples/edf-missing-texture.txt.json | 10 ---------- Test/CZICheckSamples/edf-missing-texture.txt.xml | 10 ---------- 3 files changed, 1 insertion(+), 21 deletions(-) diff --git a/Test/CZICheckSamples/edf-missing-texture.txt b/Test/CZICheckSamples/edf-missing-texture.txt index 98b305b..6c88a44 100644 --- a/Test/CZICheckSamples/edf-missing-texture.txt +++ b/Test/CZICheckSamples/edf-missing-texture.txt @@ -12,7 +12,7 @@ Test "validate the XML-metadata against XSD-schema" : (101,22): no declaration found for element 'RotationCenter' (105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)' (112,21): no declaration found for element 'LookupTables' - <3 more findings omitted> + <1 more finding omitted> FAIL Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK Test "SubBlock-Segments in SubBlockDirectory are valid and valid content" : OK diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.json b/Test/CZICheckSamples/edf-missing-texture.txt.json index a0f77a2..66732f5 100644 --- a/Test/CZICheckSamples/edf-missing-texture.txt.json +++ b/Test/CZICheckSamples/edf-missing-texture.txt.json @@ -76,16 +76,6 @@ "description": "(105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'", "details": "" }, - { - "severity": "FATAL", - "description": "(112,21): no declaration found for element 'LookupTables'", - "details": "" - }, - { - "severity": "FATAL", - "description": "(113,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'", - "details": "" - }, { "severity": "FATAL", "description": "(188,29): attribute 'Id' is not declared for element 'Scaling'", diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.xml b/Test/CZICheckSamples/edf-missing-texture.txt.xml index cf44e50..8521cce 100644 --- a/Test/CZICheckSamples/edf-missing-texture.txt.xml +++ b/Test/CZICheckSamples/edf-missing-texture.txt.xml @@ -65,16 +65,6 @@ (105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'
- - FATAL - (112,21): no declaration found for element 'LookupTables' -
- - - FATAL - (113,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)' -
- FATAL (188,29): attribute 'Id' is not declared for element 'Scaling' From cea4cfc6036945a4658fd3b8dac3f4636be81582 Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 14:51:57 +0100 Subject: [PATCH 6/7] fix expected-results --- Test/CZICheckSamples/edf-missing-texture.txt | 2 +- Test/CZICheckSamples/edf-superfluous.txt | 4 ++-- Test/CZICheckSamples/edf-superfluous.txt.json | 10 ---------- Test/CZICheckSamples/edf-superfluous.txt.xml | 10 ---------- 4 files changed, 3 insertions(+), 23 deletions(-) diff --git a/Test/CZICheckSamples/edf-missing-texture.txt b/Test/CZICheckSamples/edf-missing-texture.txt index 6c88a44..9f41022 100644 --- a/Test/CZICheckSamples/edf-missing-texture.txt +++ b/Test/CZICheckSamples/edf-missing-texture.txt @@ -11,7 +11,7 @@ Test "Basic semantic checks of the XML-metadata" : OK Test "validate the XML-metadata against XSD-schema" : (101,22): no declaration found for element 'RotationCenter' (105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)' - (112,21): no declaration found for element 'LookupTables' + (188,29): attribute 'Id' is not declared for element 'Scaling' <1 more finding omitted> FAIL Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK diff --git a/Test/CZICheckSamples/edf-superfluous.txt b/Test/CZICheckSamples/edf-superfluous.txt index e70ae5a..69c5d56 100644 --- a/Test/CZICheckSamples/edf-superfluous.txt +++ b/Test/CZICheckSamples/edf-superfluous.txt @@ -11,8 +11,8 @@ Test "Basic semantic checks of the XML-metadata" : OK Test "validate the XML-metadata against XSD-schema" : (121,22): no declaration found for element 'RotationCenter' (125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)' - (139,21): no declaration found for element 'LookupTables' - <3 more findings omitted> + (222,29): attribute 'Id' is not declared for element 'Scaling' + <1 more finding omitted> FAIL Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK Test "SubBlock-Segments in SubBlockDirectory are valid and valid content" : OK diff --git a/Test/CZICheckSamples/edf-superfluous.txt.json b/Test/CZICheckSamples/edf-superfluous.txt.json index bc2d034..1a420cd 100644 --- a/Test/CZICheckSamples/edf-superfluous.txt.json +++ b/Test/CZICheckSamples/edf-superfluous.txt.json @@ -76,16 +76,6 @@ "description": "(125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'", "details": "" }, - { - "severity": "FATAL", - "description": "(139,21): no declaration found for element 'LookupTables'", - "details": "" - }, - { - "severity": "FATAL", - "description": "(140,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'", - "details": "" - }, { "severity": "FATAL", "description": "(222,29): attribute 'Id' is not declared for element 'Scaling'", diff --git a/Test/CZICheckSamples/edf-superfluous.txt.xml b/Test/CZICheckSamples/edf-superfluous.txt.xml index 2aafb35..1e866ef 100644 --- a/Test/CZICheckSamples/edf-superfluous.txt.xml +++ b/Test/CZICheckSamples/edf-superfluous.txt.xml @@ -65,16 +65,6 @@ (125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'
- - FATAL - (139,21): no declaration found for element 'LookupTables' -
- - - FATAL - (140,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)' -
- FATAL (222,29): attribute 'Id' is not declared for element 'Scaling' From 21f94bb4711172767692246361302bd839de7732 Mon Sep 17 00:00:00 2001 From: ptahmose Date: Thu, 20 Feb 2025 15:36:51 +0100 Subject: [PATCH 7/7] trigger rebuild --- CZICheck/resultgathererfactory.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/CZICheck/resultgathererfactory.cpp b/CZICheck/resultgathererfactory.cpp index 685ac62..c2cffb5 100644 --- a/CZICheck/resultgathererfactory.cpp +++ b/CZICheck/resultgathererfactory.cpp @@ -23,4 +23,3 @@ std::unique_ptr CreateResultGatherer(const CCmdLineOptions& opt throw std::invalid_argument("Unknown output encoding format"); } } -