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Protocols
Figure 1 summarizes a generalized image processing work flow in Xmipp and how each of the developed protocols fits in there. CPU-intesive protocols that allow parallel execution (via MPI) are indicated in orange, the rest in yellow. Note that the output from one protocol can often be used as the input for the next, such that the protocols may guide the user through the entire image processing workflow.
| /protocol_diagram.jpg |
| Figure 1: 3DEM work flow diagram |
The table below provides links to more extensive documentation, providing for each protocol:
- a brief description
- test input data
- corresponding output data
- screen shoots
| protocol name | description |
|---|---|
| PreprocessMicrographs | Starting from digitized micrographs in TIFF format, the user may pre-process these (convert them to RAW format, down-sample, estimate contrast transfer function (CTF) parameters, and correct CTF phases in the micrographs) |
| ManualParticleSelection | Launch a graphical program for manual particle picking (both for single micrographs and tilt pairs) |
| PreprocessParticles | Pre-process the individual particles (windowing, background normalization and particle sorting) |
| RotationalSpectraClassification | 2D Image classification based on differences in rotational symmetry |
| ML2DClassification | Reference-free 2D image alignment and classification using maximum-likelihood multi-reference refinemen |
| KerdenSOMClassification | 2D image classification based on kerdenSOM |
| RandomConicalTilt | 3D reconstruction using random conical tilt |
| ML3DClassification | 3D angular refinement and reconstruction using multi-reference maximum likelihood refinement |
| ProjectionMatchingRefinement | 3D angular refinement and reconstruction using projection matching complemented with a re-alignment of each of the classes at every iteration. It can handle defocus groups |
| Multi-resolutionRefinement | 3D angular refinement and reconstruction based on a combination of multi-resolution wavelet refinement and continuous angular assignments, and allows correction of CTF amplitudes through iterative data refinement |
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G40P.tar.gz- test data for 3D reconstruction by random conical tilt (Nunez-Ramirez R, Robledo Y, Mesa P, Ayora S, Alonso JC, Carazo JM, Donate LE. Quaternary polymorphism of replicative helicaseG40P: structural mapping and domain rearrangement., J Mol Biol. 2006 Apr 7;357(4):1063-76. )
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ribosome.tar.gz- test data 3D processing other than random conical tilt. This is synthetic data generated after the 3D reconstruction appeared in Scheres SH, Gao H, Valle M, Herman GT, Eggermont PP, Frank J, Carazo JM. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat Methods. 2007 Jan;4(1):27-9.