News and Release Notes
a timeline of updates to cryoDRGN
Use commands such as `pip install 'cryodrgn==3.4.3'` (replacing with your preferred version number) to install a specific past version of cryoDRGN!
Release Timeline
09/2025: cryodrgn version v3.5.2 released, with faster backprojection through batched data processing, faster downsampling through I/O threading, and faster reconstruction when using larger default batch sizes
08/2025: cryodrgn version v3.5.1 released, with new
--force-ntiltsto only include particles withxavailable tilts inbackproject_voxel, plotting classes in z-latent-space using scatterplots, and fixing bug with ragged tilt-series inputs to interactive filtering08/2025: cryodrgn version v3.5.0 released, with 1-indexing for output volumes and epochs,
train_decfor reconstruction with an auto-decoder, automaticanalyzeexecuted on the last epoch of training, and a unifiedparse_starcommand04/2025: cryodrgn version v3.4.4 released, with new support for Python 3.12, as well as introducing
--shuffle-seedto fix randomness of batch iteration during training12/2024: cryodrgn version 3.4.3 released, adding a utility
make_moviesfor animations of volumes created by cryoDRGN models, as well improving the interactive filtering interface11/2024: cryodrgn version 3.4.2 released, adding auto mixed-precision training to ab-initio reconstruction for faster training, alongside speedups to
parse_pose_starandanalyze_landscape_full10/2024: cryodrgn version 3.4.1 released, adding support for float16-formatted input .mrcs image stacks and addressing issues with
downsample,filter, and volume evaluation09/2024: cryodrgn version 3.4.0 released, introducing plotting by class labels, support for RELION 3.1, and calculation of phase-randomized Fourier Shell correlations
06/2024: cryodrgn version 3.3.3 released, addressing issues in
backproject,write_star, andfilter05/2024: cryodrgn version 3.3.2 released with improvements and fixes made to several features, including filtering with notebooks, FSC plots in
backproject_voxel, and support for RELION 3.1 inputs inparse_pose_star04/2024: cryodrgn version 3.3.0 released — first non-beta release of cryoDRGN-ET, new command
cryodrgn direct_traversal, improved testing, and cleaned-up Jupyter notebooks03/2024: cryodrgn version 3.2.0-beta released with new commands including
cryodrgn_utils clean,cryodrgn_utils gen_mask, andcryodrgn_utils fsc12/2023: cryodrgn version 3.1.0-beta released with new command
cryodrgn filterfor interactive filtering of particles09/2023: CryoDRGN-ET for subtomogram analysis is now available in beta, as cryodrgn version 3.0.0-beta
06/2023: documentation clean up, available here on gitbook
05/2023: cryodrgn version 2.3.0 released with improvements and fixes to ab initio tools.
01/2023: cryodrgn version 2.2.0 released with new ab initio reconstruction tools and more.
07/2022: cryodrgn version 1.1.0 released with updated default architecture
05/2022: cryodrgn version 1.0.0 released with new landscape analysis, cryodrgn_utils, and more
Software Change Log
Comprehensive notes on all releases including minor and patch versions can be found at the Github repository: https://github.com/zhonge/cryodrgn/releases
Documentation Change Log
May 2024:
updating and expanding tutorial on using cryoDRGN v3 for subtomogram analysis
creating new page group "Deprecated Workflows" initially populated with
cryodrgn preprocessmaterial
June 2023:
moving documentation to gitbook (here) — the previous documentation found at Notion/sphinx will no longer be updated
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