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Integrated Protocols
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By Packages
- xmipp3 (58 protocols)
- scipion (56 protocols)
- spider (12 protocols)
- relion (9 protocols)
- eman2 (5 protocols)
- grigoriefflab (5 protocols)
- pytom_scipion (3 protocols)
- bsoft (2 protocols)
- appion (1 protocols)
- emxlib (1 protocols)
- resmap (1 protocols)
- simple (1 protocols)
- igbmc (1 protocols)
- cryoem_scipion (1 protocols)
- atsas (1 protocols)
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scipion - ProtImport: Base class for other all Import protocols.
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scipion - import averages: Protocol to import a set of averages to the project
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scipion - import ctf: Common protocol to import a set of ctfs into the project
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scipion - import coordinates: Protocol to import a set of coordinates
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scipion - ProtImportFiles: Base class for other Import protocols.
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scipion - None: Common protocol to import a set of images into the project
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scipion - import mask: Class for import masks from existing files.
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scipion - import micrographs: Protocol to import a set of micrographs to the project
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scipion - import tilted micrographs: Protocol to import untilted-tilted pairs of micrographs in the project
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scipion - import movies: Protocol to import a set of movies (from direct detector cameras) to the project
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scipion - import particles: Protocol to import a set of particles to the project
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scipion - import pdb volumes: Protocol to import a set of pdb volumes to the project
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scipion - import volumes: Protocol to import a set of volumes to the project
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pytom_scipion - import: Import a particle list of subtomograms
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scipion - ctf assign: This protocol assign a CTF estimation to a particular
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grigoriefflab - ctffind: Estimates CTF on a set of micrographs
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scipion - ProtCTFMicrographs: Base class for all protocols that estimates the CTF
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scipion - ProtExtractMovieParticles: Extract a set of Particles from each frame of a set of Movies.
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xmipp3 - movie alignment: Aligns movies, from direct detectors cameras, into micrographs.
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scipion - ProtProcessMovies: Protocol base for processing movies from direct detectors cameras.
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grigoriefflab - Summovie: Summovie is used to align the frames of movies recorded
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grigoriefflab - Unblur: Unblur is used to align the frames of movies recorded
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xmipp3 - ctf discrepancy: Protocol to estimate the agreement between different estimation of the CTF
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xmipp3 - ctf estimation: Protocol to estimate CTF on a set of micrographs using Xmipp 3.1
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xmipp3 - movie extract particles: Extract a set of Particles from each frame of a set of Movies.
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xmipp3 - preprocess micrographs: Protocol to preprocess a set of micrographs in the project. You can crop borders, remove bad pixels, etc.
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bsoft - bfilter: Wrapper around bfilter program.
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bsoft - particle picking: Protocol to pick particles in a set of micrographs using bsoft
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appion - dogpicker: Protocol to pick particles in a set of micrographs using appion dogpicker
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eman2 - boxer: Protocol to pick particles in a set of micrographs using eman
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scipion - extract coordinates: Extract the coordinates information from a set of particles.
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scipion - ProtExtractMovieParticles: Extract a set of Particles from each frame of a set of Movies.
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scipion - ProtFilterParticles: Base class for filters on particles of type ProtPreprocessParticles
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igbmc - auto-picking: gEMpicker is a template-based cryo-EM particle picking program that use
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scipion - import coordinates: Protocol to import a set of coordinates
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scipion - ProtMaskParticles: This is the base for the branch of mask,
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scipion - ProtOperateParticles: Base class for operations on particles of type ProtPreprocessParticles
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scipion - ProtProcessParticles: This class will serve as a base for all protocol
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relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking
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relion - auto-picking (step 1): This Relion protocol uses 2D class averages as templates to run the auto-picking
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relion - particle polishing: Reconstruct a volume using Relion from a given set of particles.
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relion - preprocess particles: Wrapper to Relion preprocess program.
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eman2 - sparx gaussian picker: Protocol to pick particles automatically in a set of micrographs using sparx gaussian picker
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spider - filter particles: Apply Fourier filters to an image or volume
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xmipp3 - auto-picking (step 2): Protocol to pick particles automatically in a set of micrographs using previous training
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xmipp3 - break symmetry: Classify particles according their similarity to the others in order to detect outliers.
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xmipp3 - assignment tiltpair: From two sets of points (tilted and untilted) the protocol determines the affine transformation between
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xmipp3 - ctf_correct_wiener2d: Perform CTF correction by Wiener filtering.
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xmipp3 - consensus picking: Protocol to estimate the agreement between different particle picking algorithms. The protocol
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xmipp3 - crop/resize particles: Crop or resize a set of particles
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xmipp3 - denoise particles: Remove particles noise by filtering them. This filtering process is based on a projection over a basis created from some averages (extracted from classes). This filtering is not intended for processing particles. The huge filtering they will be passed through is known to remove part of the signal
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xmipp3 - movie extract particles: Extract a set of Particles from each frame of a set of Movies.
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xmipp3 - extract particles: Protocol to extract particles from a set of coordinates
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xmipp3 - extract particle pairs: Protocol to extract particles from a set of tilted pairs coordinates
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xmipp3 - filter particles: Apply Fourier filters to a set of particles
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xmipp3 - calculator2D: Apply an operation to two sets of particles
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xmipp3 - apply 2d mask: Apply mask to a set of particles
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xmipp3 - manual-picking (step 1): Xmipp protocol to pick particles in a set of micrographs
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xmipp3 - tilt pairs particle picking: Xmipp protocol to pick particles in a set of micrographs
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xmipp3 - preprocess particles: Preprocess a set of particles. You can remove dust, normalize, apply threshold, etc
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xmipp3 - screen particles: Classify particles according their similarity to the others in order to detect outliers.
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scipion - ProtAlign2D: This class will serve as a base for all protocols that align a set of 2D images.
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scipion - alignment assign: Assign a the alignment calculated for a set of particles to another set.
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scipion - classes consensus: Compare two SetOfClasses
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scipion - ProtCreateMask2D: For those protocols who create mask as output.
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relion - 2D classification: Wrapper to Relion 2D - class averages program.
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spider - align apsr: Reference-free alignment shift and rotational alignment of an image series.
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spider - align pairwise: Reference-free alignment shift and rotational alignment of an image series.
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spider - SpiderProtClassify: Base for Spider classification protocols
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spider - classify diday: Diday’s method, using 'CL CLA'
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spider - classify kmeans: Diday’s method, using 'CL CLA'
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spider - classify ward: Ward’s method, using 'CL HC'
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spider - custom mask: This step creates a custom mask.
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xmipp3 - apply alignment 2d: Apply alignment parameters and produce a new set of images.
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xmipp3 - cl2d: Classifies a set of images using a clustering algorithm
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xmipp3 - align with cl2d: Aligns a set of particles using the CL2D algorithm.
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xmipp3 - create 2d mask: Create a 2D mask.
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xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM)
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xmipp3 - ml2d: Perform (multi-reference) 2D-alignment using
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xmipp3 - projection outliers: Compares a set of classes or averages with the corresponding projections of a reference volume
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xmipp3 - rotational spectra: Protocol to compute the rotational spectrum of the given particles.
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xmipp3 - screen classes: Compares a set of classes or averages with the corresponding projections of a reference volume
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atsas - convert PDB to SAXS curve: Protocol for converting a PDB file (true atoms or pseudoatoms) into a SAXS curve.
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eman2 - initial model: This Protocol wraps e2initialmodel.py Eman2 program which
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eman2 - reconstruct: This Protocol wraps e2make3d.py Eman2 program.
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eman2 - refine easy: This Protocol wraps e2refine_easy.py Eman2 program.
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scipion - ProtAlignVolume: Protocol base for Align volumes protocols
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pytom_scipion - autofocus: Subtomogram averaging using pytom autofocus
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cryoem_scipion - pseudoatoms: Produces one or several initial volumes using cryoem pseudoatoms
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scipion - ProtFilterVolumes: This is the base for the branch of filters,
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grigoriefflab - frealign: Protocol to refine a 3D map using Frealign. The algorithms implemented
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grigoriefflab - frealign classify: Protocol to classify 3D using Frealign. Frealign employs
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pytom_scipion - frm 3d align: Subtomogram averaging using pytom autofocus
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scipion - ProtInitialVolume: Protocol base for Initial volumes protocols
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scipion - ProtMaskVolumes: This is the base for the branch of mask,
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scipion - ProtOperateVolumes: This is the base for the branch of filters,
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scipion - ProtPreprocessVolumes: This class will serve as a base for all protocol
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simple - prime: Produces one or several initial volumes using simple prime
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relion - 3D classification: Protocol to classify 3D using Relion. Relion employs an empirical
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relion - post-processing: Reconstruct a volume using Relion from a given set of particles.
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relion - reconstruct: Reconstruct a volume using Relion from a given set of particles.
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relion - 3D auto-refine: Protocol to refine a 3D map using Relion. Relion employs an empirical
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resmap - local resolution: ResMap is software tool for computing the local resolution of 3D
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spider - reconstruct fourier: Simple reconstruction protocol using Fourier back projection.
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spider - refinement: Iterative reference-based refinement of orientations
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xmipp3 - align volume: Aligns a set of volumes using cross correlation
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xmipp3 - align volume web: Aligns a set of volumes using cross correlation.
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xmipp3 - nma alignment: Protocol for flexible angular alignment.
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xmipp3 - cltomo: Averages a set of subtomograms taking into account the missing edge
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xmipp3 - convert a PDB: Covert a PDB file to a volume.
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xmipp3 - convert to pseudoatoms: Converts an EM volume into pseudoatoms
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xmipp3 - create 3d mask: Create a 3D mask.
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xmipp3 - crop/resize volumes: Crop or resize a set of volumes
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xmipp3 - nma dimred: This protocol will take the images with NMA deformations
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xmipp3 - filter volumes: Apply Fourier filters to a set of volumes
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xmipp3 - helical symmetry: Estimate helical parameters and symmetrize.
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xmipp3 - calculator3D: Apply an operation to two sets of volumes
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xmipp3 - apply 3d mask: Apply mask to a volume
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xmipp3 - multireference_aligneability: Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles.
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xmipp3 - preprocess volumes: Protocol for Xmipp-based preprocess for volumes
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xmipp3 - projection matching: 3D reconstruction and classification using multireference projection matching
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xmipp3 - random conical tilt: Creates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm
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xmipp3 - ransac: Computes an initial 3d model from a set of projections/classes
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xmipp3 - reconstruct fourier: Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles.
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xmipp3 - highres: This is a 3D refinement protocol whose main input is a volume and a set of particles.
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xmipp3 - reconstruct significant: This algorithm addresses the initial volume problem in SPA
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xmipp3 - resolution 3D: Computes resolution by several methods
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xmipp3 - split volume: Split volume in two
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xmipp3 - validate_nontilt: Ranks a set of volumes according to their alignment reliability obtained from a clusterability test.
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xmipp3 - validate tilt: Validates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm
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xmipp3 - calculate strain: Compare two states of a volume to analyze the local strains and rotations
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xmipp3 - nma cluster: Protocol executed when a cluster is created
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xmipp3 - movie alignment: Aligns movies, from direct detectors cameras, into micrographs.
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xmipp3 - auto-picking (step 2): Protocol to pick particles automatically in a set of micrographs using previous training
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xmipp3 - align volume: Aligns a set of volumes using cross correlation
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xmipp3 - align volume web: Aligns a set of volumes using cross correlation.
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xmipp3 - nma alignment: Protocol for flexible angular alignment.
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xmipp3 - break symmetry: Classify particles according their similarity to the others in order to detect outliers.
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xmipp3 - apply alignment 2d: Apply alignment parameters and produce a new set of images.
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xmipp3 - assignment tiltpair: From two sets of points (tilted and untilted) the protocol determines the affine transformation between
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xmipp3 - cl2d: Classifies a set of images using a clustering algorithm
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xmipp3 - align with cl2d: Aligns a set of particles using the CL2D algorithm.
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xmipp3 - cltomo: Averages a set of subtomograms taking into account the missing edge
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xmipp3 - ctf_correct_wiener2d: Perform CTF correction by Wiener filtering.
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xmipp3 - ctf discrepancy: Protocol to estimate the agreement between different estimation of the CTF
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xmipp3 - ctf estimation: Protocol to estimate CTF on a set of micrographs using Xmipp 3.1
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xmipp3 - consensus picking: Protocol to estimate the agreement between different particle picking algorithms. The protocol
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xmipp3 - convert a PDB: Covert a PDB file to a volume.
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xmipp3 - convert to pseudoatoms: Converts an EM volume into pseudoatoms
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xmipp3 - create 2d mask: Create a 2D mask.
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xmipp3 - create 3d mask: Create a 3D mask.
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xmipp3 - crop/resize particles: Crop or resize a set of particles
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xmipp3 - crop/resize volumes: Crop or resize a set of volumes
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xmipp3 - denoise particles: Remove particles noise by filtering them. This filtering process is based on a projection over a basis created from some averages (extracted from classes). This filtering is not intended for processing particles. The huge filtering they will be passed through is known to remove part of the signal
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xmipp3 - nma dimred: This protocol will take the images with NMA deformations
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xmipp3 - movie extract particles: Extract a set of Particles from each frame of a set of Movies.
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xmipp3 - extract particles: Protocol to extract particles from a set of coordinates
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xmipp3 - extract particle pairs: Protocol to extract particles from a set of tilted pairs coordinates
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xmipp3 - filter particles: Apply Fourier filters to a set of particles
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xmipp3 - filter volumes: Apply Fourier filters to a set of volumes
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xmipp3 - helical symmetry: Estimate helical parameters and symmetrize.
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xmipp3 - calculator2D: Apply an operation to two sets of particles
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xmipp3 - calculator3D: Apply an operation to two sets of volumes
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xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM)
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xmipp3 - ml2d: Perform (multi-reference) 2D-alignment using
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xmipp3 - apply 2d mask: Apply mask to a set of particles
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xmipp3 - apply 3d mask: Apply mask to a volume
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xmipp3 - multireference_aligneability: Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles.
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xmipp3 - nma analysis: Flexible angular alignment using normal modes
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xmipp3 - manual-picking (step 1): Xmipp protocol to pick particles in a set of micrographs
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xmipp3 - tilt pairs particle picking: Xmipp protocol to pick particles in a set of micrographs
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xmipp3 - preprocess micrographs: Protocol to preprocess a set of micrographs in the project. You can crop borders, remove bad pixels, etc.
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xmipp3 - preprocess particles: Preprocess a set of particles. You can remove dust, normalize, apply threshold, etc
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xmipp3 - preprocess volumes: Protocol for Xmipp-based preprocess for volumes
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xmipp3 - projection matching: 3D reconstruction and classification using multireference projection matching
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xmipp3 - projection outliers: Compares a set of classes or averages with the corresponding projections of a reference volume
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xmipp3 - random conical tilt: Creates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm
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xmipp3 - ransac: Computes an initial 3d model from a set of projections/classes
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xmipp3 - reconstruct fourier: Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles.
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xmipp3 - highres: This is a 3D refinement protocol whose main input is a volume and a set of particles.
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xmipp3 - reconstruct significant: This algorithm addresses the initial volume problem in SPA
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xmipp3 - resolution 3D: Computes resolution by several methods
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xmipp3 - rotational spectra: Protocol to compute the rotational spectrum of the given particles.
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xmipp3 - screen classes: Compares a set of classes or averages with the corresponding projections of a reference volume
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xmipp3 - screen particles: Classify particles according their similarity to the others in order to detect outliers.
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xmipp3 - split volume: Split volume in two
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xmipp3 - validate_nontilt: Ranks a set of volumes according to their alignment reliability obtained from a clusterability test.
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xmipp3 - validate tilt: Validates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm
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xmipp3 - calculate strain: Compare two states of a volume to analyze the local strains and rotations
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scipion - BatchProtocol: Base class to all protocols that are launched
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scipion - EMProtocol: Base class to all EM protocols.
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scipion - ProtAlign2D: This class will serve as a base for all protocols that align a set of 2D images.
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scipion - ProtAlignVolume: Protocol base for Align volumes protocols
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scipion - alignment assign: Assign a the alignment calculated for a set of particles to another set.
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scipion - ctf assign: This protocol assign a CTF estimation to a particular
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scipion - ProtCTFMicrographs: Base class for all protocols that estimates the CTF
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scipion - classes consensus: Compare two SetOfClasses
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scipion - ProtCreateMask2D: For those protocols who create mask as output.
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scipion - extract coordinates: Extract the coordinates information from a set of particles.
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scipion - ProtExtractMovieParticles: Extract a set of Particles from each frame of a set of Movies.
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scipion - ProtFilterParticles: Base class for filters on particles of type ProtPreprocessParticles
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scipion - ProtFilterVolumes: This is the base for the branch of filters,
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scipion - ProtImport: Base class for other all Import protocols.
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scipion - import averages: Protocol to import a set of averages to the project
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scipion - import ctf: Common protocol to import a set of ctfs into the project
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scipion - import coordinates: Protocol to import a set of coordinates
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scipion - ProtImportFiles: Base class for other Import protocols.
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scipion - None: Common protocol to import a set of images into the project
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scipion - import mask: Class for import masks from existing files.
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scipion - import micrographs: Protocol to import a set of micrographs to the project
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scipion - import tilted micrographs: Protocol to import untilted-tilted pairs of micrographs in the project
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scipion - import movies: Protocol to import a set of movies (from direct detector cameras) to the project
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scipion - import particles: Protocol to import a set of particles to the project
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scipion - import pdb volumes: Protocol to import a set of pdb volumes to the project
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scipion - import volumes: Protocol to import a set of volumes to the project
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scipion - ProtInitialVolume: Protocol base for Initial volumes protocols
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scipion - ProtMaskParticles: This is the base for the branch of mask,
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scipion - ProtMaskVolumes: This is the base for the branch of mask,
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scipion - ProtOperateParticles: Base class for operations on particles of type ProtPreprocessParticles
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scipion - ProtOperateVolumes: This is the base for the branch of filters,
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scipion - ProtPreprocessVolumes: This class will serve as a base for all protocol
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scipion - ProtProcessMovies: Protocol base for processing movies from direct detectors cameras.
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scipion - ProtProcessParticles: This class will serve as a base for all protocol
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scipion - ProtSets: Base class for all protocols related to subsets.
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scipion - split sets: Protocol to split a set in two or more subsets.
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scipion - subset: Create a set with the elements of an original set that are also
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scipion - parallel test: A parallel test protocol.
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scipion - union sets: Protocol to join two or more sets of images.
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scipion - create subset: Create subsets from the GUI.
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scipion - Protocol: The Protocol is a higher type of Step.
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spider - align apsr: Reference-free alignment shift and rotational alignment of an image series.
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spider - align pairwise: Reference-free alignment shift and rotational alignment of an image series.
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spider - capca: Correspondence Analysis (CA) or Principal Component Analysis (PCA).
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spider - SpiderProtClassify: Base for Spider classification protocols
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spider - classify diday: Diday’s method, using 'CL CLA'
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spider - classify kmeans: Diday’s method, using 'CL CLA'
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spider - classify ward: Ward’s method, using 'CL HC'
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spider - custom mask: This step creates a custom mask.
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spider - filter particles: Apply Fourier filters to an image or volume
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spider - reconstruct fourier: Simple reconstruction protocol using Fourier back projection.
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spider - refinement: Iterative reference-based refinement of orientations
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spider - SpiderProtocol: Sub-class of EMProtocol to group some common Spider utils.
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relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking
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relion - auto-picking (step 1): This Relion protocol uses 2D class averages as templates to run the auto-picking
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relion - 2D classification: Wrapper to Relion 2D - class averages program.
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relion - 3D classification: Protocol to classify 3D using Relion. Relion employs an empirical
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relion - particle polishing: Reconstruct a volume using Relion from a given set of particles.
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relion - post-processing: Reconstruct a volume using Relion from a given set of particles.
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relion - preprocess particles: Wrapper to Relion preprocess program.
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relion - reconstruct: Reconstruct a volume using Relion from a given set of particles.
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relion - 3D auto-refine: Protocol to refine a 3D map using Relion. Relion employs an empirical
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eman2 - boxer: Protocol to pick particles in a set of micrographs using eman
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eman2 - initial model: This Protocol wraps e2initialmodel.py Eman2 program which
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eman2 - reconstruct: This Protocol wraps e2make3d.py Eman2 program.
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eman2 - refine easy: This Protocol wraps e2refine_easy.py Eman2 program.
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eman2 - sparx gaussian picker: Protocol to pick particles automatically in a set of micrographs using sparx gaussian picker
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grigoriefflab - ctffind: Estimates CTF on a set of micrographs
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grigoriefflab - frealign: Protocol to refine a 3D map using Frealign. The algorithms implemented
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grigoriefflab - frealign classify: Protocol to classify 3D using Frealign. Frealign employs
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grigoriefflab - Summovie: Summovie is used to align the frames of movies recorded
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grigoriefflab - Unblur: Unblur is used to align the frames of movies recorded
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pytom_scipion - autofocus: Subtomogram averaging using pytom autofocus
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pytom_scipion - frm 3d align: Subtomogram averaging using pytom autofocus
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pytom_scipion - import: Import a particle list of subtomograms
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bsoft - bfilter: Wrapper around bfilter program.
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bsoft - particle picking: Protocol to pick particles in a set of micrographs using bsoft
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appion - dogpicker: Protocol to pick particles in a set of micrographs using appion dogpicker
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emxlib - emx export: Export micrographs, coordinates or particles to EMX format.
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resmap - local resolution: ResMap is software tool for computing the local resolution of 3D
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simple - prime: Produces one or several initial volumes using simple prime
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igbmc - auto-picking: gEMpicker is a template-based cryo-EM particle picking program that use
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cryoem_scipion - pseudoatoms: Produces one or several initial volumes using cryoem pseudoatoms
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atsas - convert PDB to SAXS curve: Protocol for converting a PDB file (true atoms or pseudoatoms) into a SAXS curve.
Scipion v1.0.0 (15 Jan 2016)
>>>>> python /home/josem/work/development/workspace/scipion/pyworkflow/apps/pw_protocol_list.py "--with-doc" "--asciidoc"