EMAN2.9/SPHIRE1.4/SPARX

Release Date

2021-02-10

Summary

PLEASE USE the 2.91 bugfix release instead!

We are pleased to announce a new major release of EMAN2/SPARX/SPHIRE. The largest change in this version is the switch from Python2 to Python3, though this will have little impact on typical end-users. The new tomography pipeline in EMAN2 has been significantly improved since its initial release, and other significant new tools have been added as well. Data compression is now a standard part of the package for both CryoEM and CryoET data processing pipelines, providing dramatic reductions in disk usage and transfer times with no reduction in quality. The compressed HDF files in EMAN2 can still be opened in Chimera for visualization. There are also many additional changes and improvements throughout the system, summarized below.

• Documentation: eman2.org
• For assistance: Google Group
• For confidential assistance or for users without Google access: sludtke@bcm.edu

Note: The _huge installers are for machines without network access. Normally the installer will download appropriate dependencies at install-time.

Description

EMAN2, SPARX and SPHIRE are jointly distributed scientific image processing software packages designed primarily for the CryoEM and CryoET communities. Please visit http://eman2.org for more information. It is possible to perform complete CryoEM single particle reconstructions as well as CryoET subtomogram averaging to near-atomic resolution using only the tools in this package. There are additional tools for analysis of compositional and conformational variability, generic image processing, format conversions and 2D/3D visualization.

Version changes

The complete list of changes would be quite extensive. Here is a partial list of major changes:

• Numerous improvements for in-situ subtomogram averaging
  • Full PPPT subtomogram averaging pipeline capable of near-atomic resolution
  • 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)
• Speed improvements for image I/O operations
• Better integration with Numpy and Jupyter image object data sharing (advanced users)
• Python 3 based (finally!)

Known Bugs (2.91 bugfix planned)

• Some programs may generate folders such as spt_1 instead of spt_01, which may cause other issues