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| = EMAN2.2 Release Notes= | = EMAN2.2 Release Notes = == Changes in the 2.21a release include == * Fix bug causing "missing SNR" problem during refinement in specific situations * Testing support for bispectrum based class-averaging and 3-D refinement. ~10-50x faster. Better 2-D class averages * Better support for GPU in Neural Network tomogram segmentation and particle picking * Direct support for phase plates in CTF correction with adjustable phase slider and autofitting (first version, room for improvement). Issues with astigmatism in this version. * Better GUI display of CTF and Astigmatism * e2symsearch3d bugs fixed * Many subtomogram averaging bugs fixed. New pipeline under development. * Many improvements to e2evalrefine for particle and class-average assessment == Changes from EMAN 2.12 -> EMAN 2.2 == |
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| * Optional tophat filter (similar to Relion post processing), side chains often look even better than Relion | * Optional tophat filter (similar to Relion post processing), side chains often (but not always) look even better than Relion/CryoSparc |
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| * Including multi-model refinement with or without alignment, masked particle subtraction, 2-D and 3-D Deep Learning approaches | * Including multi-model refinement with or without alignment, masked particle subtraction, 2-D and 3-D Deep Learning approaches (experimental) |
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| * Easy and fast refinement at progressive resolutions | * Easy and fast refinement at progressive resolutions within a single project * Phase plate CTF correction * Supports phase shifts covering full 360 degree range, with explicit 'phase' slider * No automatic fitting of phase shift in this version (next minor release) |
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| * New localweight averager (experimental) * excludes "bad" parts of individual particles (overlaps, contamination, etc.) * New 2-D registration algorithm * scales well with box size * more accurate going into "refine" alignment (in many cases refine can be skipped) |
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| * Integrates SciPy, Theano, PyLearn and other toolkits * GitHub * Source code is now managed via a public GitHub repository (cryoem/eman2) |
* Integrates !SciPy, Theano, !PyLearn and other toolkits * New installers, with better OpenMPI/Pydusa support * !GitHub * Source code is now managed via a public !GitHub repository (cryoem/eman2) |
EMAN2.2 Release Notes
Changes in the 2.21a release include
- Fix bug causing "missing SNR" problem during refinement in specific situations
- Testing support for bispectrum based class-averaging and 3-D refinement. ~10-50x faster. Better 2-D class averages
- Better support for GPU in Neural Network tomogram segmentation and particle picking
- Direct support for phase plates in CTF correction with adjustable phase slider and autofitting (first version, room for improvement). Issues with astigmatism in this version.
- Better GUI display of CTF and Astigmatism
- e2symsearch3d bugs fixed
- Many subtomogram averaging bugs fixed. New pipeline under development.
- Many improvements to e2evalrefine for particle and class-average assessment
Changes from EMAN 2.12 -> EMAN 2.2
Single Particle Analysis
- Many, deep improvements to refinement
- Substantial refinement changes and new filtering techniques
- Optional tophat filter (similar to Relion post processing), side chains often (but not always) look even better than Relion/CryoSparc
- Local resolution and filtration
- can be enabled in refinement to provide local detail appropriate to local resolution
- Several new methods for conformational/compositional heterogeneity
- Including multi-model refinement with or without alignment, masked particle subtraction, 2-D and 3-D Deep Learning approaches (experimental)
- New bad particle identification strategy
- Proven to produce better maps in several projects!
- Automatic CTF
- Used to be several manual steps. Entire process now automated.
- Easy and fast refinement at progressive resolutions within a single project
- Phase plate CTF correction
- Supports phase shifts covering full 360 degree range, with explicit 'phase' slider
- No automatic fitting of phase shift in this version (next minor release)
- New e2boxer (particle picker)
- Fixes the problems with the old particle picker
- New (optional) neural network picker for difficult projects
- Stochastic Gradient Descent initial model generator (experimental)
- Automatic magnification anisotropy correction tool
- Post-processing program which corrects for the common microscope anisotropy problem on FEI scopes
- Automatic, does not require additional data collection
- New direct detector movie aligner
- All new program. Competitive with other alignment programs in quality
- Workflow for handling movies in EMAN2 projects
- New localweight averager (experimental)
- excludes "bad" parts of individual particles (overlaps, contamination, etc.)
- New 2-D registration algorithm
- scales well with box size
- more accurate going into "refine" alignment (in many cases refine can be skipped)
Subtomogram Averaging
- New subtomogram averaging tools
- New pipelines for subtomogram averaging and classification
- Up to 20x faster 3-D alignments,
- now practical to study 10,000 300x300x300 particles on a single workstation
- New automatic missing wedge identification/compensation in alignment/averaging
Tomogram Segmentation
- Workflow for semi-automatic tomogram annotation/segmentation
- Uses convolutional neural network technology with user guided training of features.
Overall Changes
- Anaconda Python based distribution
Integrates SciPy, Theano, PyLearn and other toolkits
- New installers, with better OpenMPI/Pydusa support
GitHub
Source code is now managed via a public GitHub repository (cryoem/eman2)
- Windows 10/7 64 bit
- Initial support, poorly tested, but available for the first time (EMAN2 only, SPARX/SPHIRE do not support this platform)