ListOfPrograms

List of all Xmipp programs

Note that from Xmipp-2.0 onwards, the names of many Xmipp programs have changed. Click NewNamesProposal to see a table relating the new names with the old ones. For now, both the old and the new names will keep on working (a warning will appear when using an old name). In the next release, the old names will disappear.

By Topic

Micrographs

• TestWiki Testing wiki generation
• Tiff2Raw Converts scanner tiff files to raw format (Obsolete, will be removed in Xmipp 3 .0)
• DenoisingMicrograph Denoising of the raw micrographs
• MicrographDownSample Downsampling of the raw micrographs
• Mark Manual particle picking for single micrographs and tilt pairs
• ParticlePicker Particle picker to generate particle images stacks used on 3D reconstruction.
• TiltPairPicker Tilt Pair Picker matches particle pairs on image pairs.
• Scissor Window-out manually selected particles in single-file Spider format
• Window_micrograph Apply a window to raw micrographsd
• MicrographPhaseFlipping Correct CTF phases (using phase flipping) (similar to ctf_correct_phase but handles microgrphs)

CTF estimation and correction

• Assign_CTF Estimate CTF parameters for a micrograph
• Ctf_create_ctfdat Create a CTFdat file from image selfiles for each micrograph
• IDR_ART Correct CTF amplitudes (using Iterative Data Refinement)
• Correct_Phase Correct CTF phases (using phase flipping)
• Correct_Amplitude2D Correct CTF amplitudes (using Van Cittert's iterations)
• Ctf_group Automatically create CTF groups from a single CTFdat file
• CTF_profile Plot the profile of a CTF
• CTF_viewer Visualize CTF fitting
• Enhance_PSD Enhance power spectral density Thon rings

Selection files, Document files

• OperateMetada Arithmetic operation using metadata columns.
• Append_docfile Concatenate two docfiles
• DocFile_Histogram Computes the histogram of a docfile column
• DocFile_Select_Subset Make a docfile of a subset given in a selfile
• Compare_selfiles Compare two selfiles (overlap, differences etc)
• CpSel Copy images in a selfile to a different location
• Do_SelFile Create a selfile
• RmSel Remove the images in a selfile
• MvSel Move images in a selfile to a different location
• Select_images Select images from a selfile based on a condition in a docfile
• Split_selfile Split selfile in random subsets
• Sel_stats Produces statistics about the images in a selfile
• Subset_selfile Produce random subsets of any size
• Filter_Projections Select projections from a selfile meeting a number of quality criteria

Image header manipulation

Please read the important AlignementParametersNote.

• Header_assign Sets angles, translations and weights to the headers of 2D-images
• Header_extract Gets angles, translations and weights from the headers of 2D-images
• Header_reset Resets the headers of 2D-images, it can be used also for setting tilt series tilt angles
• Header_print Prints header information to the screen

Images

• Align2d 2D-alignment of images
• CenterImage Center images
• Centilt Align tilted images for random conical tilt reconstruction
• Statis Returns the average and standard deviation of a set of images or volumes
• Correlation Calculate correlation coefficient, euclidean distance & mutual information between images
• Denoising Denoise an image or volume
• FindCenter Find center of mass and symmetry elements of an image
• FourierFilter Filter an image or volume
• Visualize_FFT Compute the amplitude or phase of the Fourier Transform of an image or volume
• Applygeo Apply header stored geometric transformation
• Histogram Computes the histogram of an image or volume
• Makespectra Compute rotational spectra
• Mask Apply a mask, create a mask, create a blank image and voxel counting
• MeanShift Filter image by means of the mean-shift algorithm
• XMask Design a mask graphically
• Flip Flip (mirror) an image or volume
• Morphology Apply morphological filters to an image or a volume
• Normalize Normalizes pixel values for images/volumes
• Operate Apply algebraic operations to images or volumes
• RangeAdjust Adjust the grey range
• Resolution Estimate high-resolution limit of a set of images using FRC or DPR
• SeriesRemoveFluctuations Remove flickering in a tilt series
• SSNR Estimate the 3D and volumetric Spectral Signal-to-Noise Ratio
• Reverse_endian Reverses the endian status of the image or volume
• Rotate Rotate an image or a volume
• Scale Scales an image or volume to a new size by interpolation
• Pyramid Image pyramids
• Shift Shift an image or a volume
• Show Visualize images, volumes, sel files, spectras, soms...
• SortByStatistics Sort images based on simple statistics (to identify junk particles)
• Statistics Prints image/volume statistics (avg, stddev, min & max) to the screen
• Threshold Threshold operations (density value conditions, distance conditions and binarization possibility)
• Window Cuts or expands images

Volumes

• Align3D Align two volumes
• Adjust_volume Linear transformation of the gray values of a volume
• Voxels22Blobs Conversion from a voxel volume to a blob volume and viceversa
• Correct_bfactor Sharpen maps through B-factor correction
• CreateProjectionLibrary Create gallery of projections, specially thought for projection matching
• DetectMissingWedge Detect the orientation of the missing wedge in a tomogram
• FindCenter3D Find center of mass and symmetry elements of a volume
• MeanShift Filter volume by means of the mean-shift algorithm
• Project Project a phantom/volume/PDB
• Projection_Real_Shears Project a Xmipp or Spider volume
• ProjectTomography Project a volume for tomography
• Art and Mpi_art 3D algebraic (iterative) reconstruction from projections
• Wbp and Mpi_wbp 3D-Reconstruction using weighted back-projection (arbitrary geometry)
• Fourier and Mpi_fourier 3D-Reconstruction using direct Fourier methods (arbitrary geometry)
• Resolution Estimate high-resolution limit using FRC or DPR between 2 volumes
• Separate_objects Separate connected objects from a binary volume
• Symmetrize Symmetrize a volume
• Segment Segment a volume to a given mass
• ProjectXR Project a volume for X-rays tomography

Classification

• AnalyzeClusters Analyze the compactness of a cluster
• BatchSOM Kohonen Self-Organizing Map using Batch training
• ClassAverages Divide a set of images into a given number of classes
• SortImages Sort a number of classes computed with ClassAverages
• FCMeans Fuzzy C Means
• FKCN Fuzzy Kohonen Clustering Networks
• FSOM Fuzzy Self Organizing Maps
• KCMeans Kernel Probability Density Estimator Clustering algorithm
• KerDenSOM Kernel Density Self Organizing Map
• PCA Principal Components Analysis
• ProjectPCA Project data using PCA
• Sammon Sammon projection algorithm
• SOM Kohonen Self Organizing Maps
• ToPhantom Converts a data file into a phantom description file
• Data2Img Convert data format to images
• ToPDB Converts a data file into a PDB file
• Data2Vol Convert data format to volumes
• Img2Data Convert images to data format
• Vol2Data VConvert data format to volumes
• VolSampler Gets a list of voxel coordinates from a Xmipp volume
• MLalign2D and Mpi_MLalign2D 2D-classification and alignment by maximum-likelihood (ML2D)
• MLrefine3D and Mpi_MLrefine3D 3D-classification and angular assignment by maximum-likelihood (ML3D)
• Mlf_align2dAndmpi_mlf_align2d 2D-classification by maximum-likelihood in Fourier space (MLF2D)
• Mlf_refine3dAndmpi_mlf_refine3d 3D-classification by maximum-likelihood in Fourier space (MLF3D)
• Ml_tomo 3D-classification and alignment of subtomograms or RCT reconstructions by maximum-likelihood
• Tomo_extract_subvolume Extract subvolumes out of (ml_tomo-) aligned subtomograms (e.g. virus vertices)

Angular assignment

• Angular_commonline Provide an initial angular assignment for class averages without any reference volume
• Angular_predict_continuous Continous assignment of Euler angles (by spline interpolation)
• Angular_predict Assigns Euler angles to projection images
• Ang_distribution Makes a picture of the Ewald-sphere and the angular distribution of a projection set
• Angular_distance Computes the distance between two angle sets
• Projection_neighbourhood Group images in defined projection direction neighbourhoods
• Projection_matching and Mpi_projection_matching Projection matching using fast 3D+2D rotational+translational search

Phantoms

• Add_noise Add noise to an image or volume
• PDB2descr Creates a phantom description file from a PDB file
• PDBPhantom Convert a PDB file to a volume
• Create_phantom Create volumes from mathematical description
• Microscope Simulate the effect of the microscope for projections
• Create_micrograph Creates a phantom micrograph
• PhantomTransform Translate, rotate, or scale a Xmipp phantom or a PDB
• PDBPhantom Generate a Xmipp volume from a PDB or MMOL file
• Project Project a phantom/volume/PDB
• ProjectTomography Project a volume for tomography
• Surface Simulates an AFM-like surface
• ProjectXR Project a volume for X-rays tomography
• Transform_Add_noise Add noise to an image or volume

Crystals

• Crystal_angular_projection_matching Assign angles to crystal projections using a reference projection library
• Aph2img Creates images from 2D crystal spots
• CrystalSurface Creation of a lattice in a parabolic surface
• Lattice_vectors Manages lattice vector conversion between MRC and Xmipp
• Deform Deform a volume by a linear transformation defined by a 2x2 matrix
• Unbend Crystal Unbending

Interaction with other programs

• Adapt_for_Spider Several operations to create spider files
• Dm32raw Convert dm3 (digital micrograph) images to raw format (Obsolete, will be removed in Xmipp 3 .0)
• Img2Jpg Convert a Spider image into Jpeg
• Imgconvert Convert between many image formats (Xmipp 3.0)
• Raw22spi Convert raw images to/from spider format. Together with Imagemagick, any image format can be addressed (Obsolete, will be removed in Xmipp 3 .0)
• Spi22ccp4 Convert from/to CCP4/MRC MAP volumes/images (Obsolete, will be removed in Xmipp 3 .0)
• Spi22em Convert from/to EM-format volumes (used in the TOM toolbox)
• Stacks22images Convert from/to spider stacks of images to volumes or set of images
• Tia2raw Convert tia (Tecnai Imaging and Analysis) images to raw format (Obsolete, will be removed in Xmipp 3 .0)
• Vol2Jpg Convert a Spider volume into Jpeg

Tomography

• Angular_align_dual_tilt_series Marker free alignment of two dual single-axis tilt series
• Angular_assign_for_tilt_series Marker free projection alignment for single axis tilt series
• Xray_import Import a tilt series taken by the X-ray microscope
• ProjectXR Project a volume for X-rays tomography
• XrayPsfCreate Precompute the PSF for X-ray tomography