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== EMAN 2.2 == = EMAN2 Release Notes =
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Please note that while there is an experimental EMAN 2.2 binary download for Linux, we are designing a new binary installation framework at the moment, so there isn't a proper stable 2.2 release just yet. We will update this page (and elsewhere) when things have stabilized. If you are anxious to play with 2.2, at present the best strategy is to compile from source directly from GitHub. There is an all new strategy for building from source on the Mac, which is quite straightforward (unlike the old method), and standard methods should still work on Linux. == Changes in the 2.91 release include ==

=== EMAN2 changes ===

 * Full PPPT subtomogram averaging pipeline capable of near-atomic resolution
  * Numerous improvements for in-situ subtomogram averaging
  * New dedicated deep-learning tomography particle picker
  * Simultaneous (visual) picking of multiple macromolecular species
  * New options for tilt series alignment in tricky cases
 * Data compression support for both CryoEM and CryoET
  * Native HDF5 mechanism
  * lossless or lossy with user-selectable bit count
  * Files still readable by Chimera
  * No quality/resolution loss
  * Typical 10-20x size reduction, dramatically improves disk I/O and network transfer
 * Extensive work on e2boxer
  * improved deep learning picker
  * Fixed problems with reference-based and local pickers
  * Added simple inline instructions
 * Deep learning GMM for single particle variability studies (e2gmm.py, see arxiv paper, experimental)
 * New local resolution and filtration based on mFSC (Penczek), for SPA and SPT (iterative)
 * New visualization options for volume stacks
 * Support for EER format & oversampling (counting-mode Falcon 4 images)
 * Colored isosurfaces functioning, and automatic local resolution display when computed
 * Speed improvements for image I/O operations
 * Better integration with Numpy and Jupyter image object data sharing (advanced users)
 * Improved option for x/y/z projections in e2display
 * Drag and drop support for rearranging images in tiled image display
 * Python 3 based (finally!)

== Changes in the 2.31 release include ==

=== EMAN2 changes ===

 * General changes:
  * New browser options for display of stacks of 3-D volumes
  * RCTboxer works properly again
  * Fixed a problem reading A/pix from FEI-style MRC files
  * New Processor for bit-compression of image files (makes images more compressible)
 * PPPT Subtomogram averaging:
  * Automatic CTF based handedness checking for tomograms
  * Focused refinement https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_more#Focused_refinement
  * Better parallelism
  * Slightly improved tilt series alignment (resolution improvement)

=== SPHIRE 1.3 changes ===

 * Support for processing helical specimens
 * AutoSPHIRE - automatic refinement tool
 * Integration of crYOLO
 * Cinderella for 2D class selection


== Changes in the 2.3 release include ==

 * A complete CryoET pipeline from tilt series through subnanometer resolution hybrid subtomogram averaging
  * fiducial-less fully automated tilt series alignment (also works with fiducials)
  * rapid tiled Fourier reconstruction
  * full tilt/geometry aware CTF correction
  * multi class 3-D particle picker with new ties to deep-learning annotation
  * SGD automatic initial model generation
  * traditional 3-D subtomogram averaging
  * per-particle per-tilt hybrid subtomogram/single particle reconstruction to subnanometer resolution
 * A new switchable filter in e2boxer making it dramatically easier to distinguish particles in images
 * New improvements to bispectral classification for 2-D unsupervised classification and 3-D refinement
 * Focused classification in 3-D refinement available from the workflow interface
 * Improvements to e2extractsubparticles as an alternative to focused classification
 * Upgrade from Qt4 to Qt5 as part of the process of transitioning to Python3 over the next year
 * Many minor bugfixes


== 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)

EMAN2 Release Notes

Changes in the 2.91 release include

EMAN2 changes

  • Full PPPT subtomogram averaging pipeline capable of near-atomic resolution
    • Numerous improvements for in-situ subtomogram averaging
    • New dedicated deep-learning tomography particle picker
    • Simultaneous (visual) picking of multiple macromolecular species
    • New options for tilt series alignment in tricky cases
  • Data compression support for both CryoEM and CryoET
    • Native HDF5 mechanism
    • lossless or lossy with user-selectable bit count
    • Files still readable by Chimera
    • No quality/resolution loss
    • Typical 10-20x size reduction, dramatically improves disk I/O and network transfer
  • Extensive work on e2boxer
    • improved deep learning picker
    • Fixed problems with reference-based and local pickers
    • Added simple inline instructions
  • Deep learning GMM for single particle variability studies (e2gmm.py, see arxiv paper, experimental)
  • New local resolution and filtration based on mFSC (Penczek), for SPA and SPT (iterative)
  • New visualization options for volume stacks
  • Support for EER format & oversampling (counting-mode Falcon 4 images)

  • Colored isosurfaces functioning, and automatic local resolution display when computed
  • Speed improvements for image I/O operations
  • Better integration with Numpy and Jupyter image object data sharing (advanced users)
  • Improved option for x/y/z projections in e2display
  • Drag and drop support for rearranging images in tiled image display
  • Python 3 based (finally!)

Changes in the 2.31 release include

EMAN2 changes

  • General changes:
    • New browser options for display of stacks of 3-D volumes
    • RCTboxer works properly again
    • Fixed a problem reading A/pix from FEI-style MRC files
    • New Processor for bit-compression of image files (makes images more compressible)
  • PPPT Subtomogram averaging:

SPHIRE 1.3 changes

  • Support for processing helical specimens
  • AutoSPHIRE - automatic refinement tool
  • Integration of crYOLO
  • Cinderella for 2D class selection

Changes in the 2.3 release include

  • A complete CryoET pipeline from tilt series through subnanometer resolution hybrid subtomogram averaging
    • fiducial-less fully automated tilt series alignment (also works with fiducials)
    • rapid tiled Fourier reconstruction
    • full tilt/geometry aware CTF correction
    • multi class 3-D particle picker with new ties to deep-learning annotation
    • SGD automatic initial model generation
    • traditional 3-D subtomogram averaging
    • per-particle per-tilt hybrid subtomogram/single particle reconstruction to subnanometer resolution
  • A new switchable filter in e2boxer making it dramatically easier to distinguish particles in images
  • New improvements to bispectral classification for 2-D unsupervised classification and 3-D refinement
  • Focused classification in 3-D refinement available from the workflow interface
  • Improvements to e2extractsubparticles as an alternative to focused classification
  • Upgrade from Qt4 to Qt5 as part of the process of transitioning to Python3 over the next year
  • Many minor bugfixes

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)

EMAN2/Eman22Release (last edited 2021-03-31 03:45:14 by SteveLudtke)