Integrated Protocols

Pablo Conesa edited this page May 28, 2018 · 26 revisions

By Categories

Imports

Micrographs

Particles

2D

  • imagic - msa: Multivariate Statistical Analysis module of IMAGIC.

  • imagic - msa-classify: This classification protocol is a post-processor to the MSA.

  • relion - 2D classification: Wrapper around the Relion 2D classification program

  • scipion - alignment assign: Assigns the alignment calculated for a set of particles to another set

  • scipion - classes consensus: Compares two sets of 2D classes

  • spider - align apsr: Reference-free alignment (both translational and rotational) of an image series. Uses Spider AP SR command

  • spider - align pairwise: Reference-free alignment (both translational and rotational) of an image series. This alignment scheme aligns a pair of images at a time and then averages them. Then, the averages of each of those pairs are aligned and averaged, and then pairs of those pairs, etc. This type of alignment appears to be less random than does 'AP SR', which chooses seed images as alignment references.

  • spider - capca: Executes Correspondence Analysis (CA) or Principal Component Analysis (PCA) on image data using the Spider CA S program

  • spider - classify diday: Performs automatic clustering using Diday’s method and Hierarchical Ascendant Classification (HAC) using Ward’s criterion on factors produced by CA or PCA. Uses the Spider CL CLA program

  • spider - classify kmeans: Performs automatic K-Means clustering and classification on factors produced by CA or PCA. Uses the Spider CL KM program

  • spider - classify ward: Finds clusters of images/elements in factor space (or a selected subspace) by using Diday’s method of moving centers, and applies hierarchical ascendant classification (HAC) (using Ward’s method) to the resulting cluster centers. Uses the Spider CL HC program

  • spider - custom mask: Creates a custom mask using Spider

  • xmipp3 - align with cl2d: Aligns a set of particles using the CL2D algorithm of Xmipp

  • xmipp3 - apply alignment 2d: Applies alignment parameters and produce a new set of images

  • xmipp3 - cl2d: Classifies a set of images using a clustering algorithm to subdivide the original dataset into a given number of classes

  • xmipp3 - create 2d mask: Creates a 2D mask. The mask can be created with a given geometrical shape (Circle, Rectangle, Crown…​) or it can be obtained from operating on a 2D image or a previous mask.

  • xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM) and Fuzzy c-means clustering technique (FCM)

  • xmipp3 - ml2d: Performs a (multi-reference) 2D alignment using a maximum-likelihood target function

  • xmipp3 - rotational spectra: Computes the rotational spectrum of the given particles

  • xmipp3 - screen classes: Compares a set of classes or averages with the corresponding projections of a reference volume

3D

By Packages

xmipp3 (58 protocols)

scipion (20 protocols)

spider (10 protocols)

  • spider - align apsr: Reference-free alignment (both translational and rotational) of an image series. Uses Spider AP SR command

  • spider - align pairwise: Reference-free alignment (both translational and rotational) of an image series. This alignment scheme aligns a pair of images at a time and then averages them. Then, the averages of each of those pairs are aligned and averaged, and then pairs of those pairs, etc. This type of alignment appears to be less random than does 'AP SR', which chooses seed images as alignment references.

  • spider - capca: Executes Correspondence Analysis (CA) or Principal Component Analysis (PCA) on image data using the Spider CA S program

  • spider - classify diday: Performs automatic clustering using Diday’s method and Hierarchical Ascendant Classification (HAC) using Ward’s criterion on factors produced by CA or PCA. Uses the Spider CL CLA program

  • spider - classify kmeans: Performs automatic K-Means clustering and classification on factors produced by CA or PCA. Uses the Spider CL KM program

  • spider - classify ward: Finds clusters of images/elements in factor space (or a selected subspace) by using Diday’s method of moving centers, and applies hierarchical ascendant classification (HAC) (using Ward’s method) to the resulting cluster centers. Uses the Spider CL HC program

  • spider - custom mask: Creates a custom mask using Spider

  • spider - filter particles: Applies Fourier filters to an image or volume using the Spider FQ or FQ NP programs.

  • spider - reconstruct fourier: A simple reconstruction protocol using Fourier back projection. Uses the Spider BP 32F program

  • spider - refinement: Iterative reference-based refinement of particle orientations, based on the Spider AP SHC and AP REF programs (see here the details).

relion (9 protocols)

  • relion - 2D classification: Wrapper around the Relion 2D classification program

  • relion - 3D auto-refine: Refines a 3D map using Relion.

  • relion - 3D classification: Classifies in 3D using Relion.

  • relion - auto-picking (step 1): This Relion protocol uses 2D class averages as templates to run the auto-picking. In this first stage, the auto-picking will be run just in few micrographs to optimize two main parameters: Picking threshold and Minimum inter-particle distance. It will write out so-called FOM maps: two large (micrograph-sized) files per reference.

  • relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking. In this second stage, the protocol reads the FOM maps to optimize the Threshold and Minimum inter-particle distance.

  • relion - particle polishing: Tracks particle movement in movie frames, applies a resolution and dose-dependent weighting scheme for each frame and finally sums them together.

  • relion - post-processing: Relion post-processing protocol for automated masking, overfitting estimation, MTF-correction and B-factor sharpening

  • relion - preprocess particles: Wrapper around the Relion preprocess program

  • relion - reconstruct: Reconstructs a volume from a given set of particles using Relion

eman2 (5 protocols)

grigoriefflab (5 protocols)

imagic (2 protocols)

bsoft (2 protocols)

gctf (1 protocols)

appion (1 protocols)

emxlib (1 protocols)

resmap (1 protocols)

simple (1 protocols)

  • simple - prime: Produces one or several initial volumes using the SIMPLE prime program

igbmc (1 protocols)

  • igbmc - auto-picking: gEMpicker is a GPU-driven template-based particle picking program that uses cross-correlation approach.

cryoem_scipion (1 protocols)

atsas (1 protocols)

gautomatch (1 protocols)


This list was generated with scipion protocols --with-doc --asciidoc command

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