News and Release Notes

a timeline of updates to cryoDRGN

Use commands such as `pip install 'cryodrgn==3.5.4'` (replacing with your preferred version number) to install a specific past version of cryoDRGN!

Version Release Timeline

• 03/2026: cryodrgn v4.2.0 released, integrating the cryoDRGN-AI pose search algorithm with the command cryodrgn abinit

• 12/2025: cryodrgn v3.5.4 released, fixing issues using --vol-ind with 1-indexing in landscape analysis and using --first with backproject_voxel

• 11/2025: cryodrgn v3.5.3 released, with fixes to landscape analysis to account for the previous switch to 1-indexing as well as faster generation of landscape volumes using --multigpu

• 09/2025: cryodrgn 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 v3.5.1 released, with new --force-ntilts to only include particles with x available tilts in backproject_voxel, plotting classes in z-latent-space using scatterplots, and fixing bug with ragged tilt-series inputs to interactive filtering

• 08/2025: cryodrgn v3.5.0 released, with 1-indexing for output volumes and epochs, train_dec for reconstruction with an auto-decoder, automatic analyze executed on the last epoch of training, and a unified parse_star command

• 04/2025: cryodrgn v3.4.4 released, with new support for Python 3.12, as well as introducing --shuffle-seed to fix randomness of batch iteration during training

• 12/2024: cryodrgn v3.4.3 released, adding a utility make_movies for animations of volumes created by cryoDRGN models, as well improving the interactive filtering interface

• 11/2024: cryodrgn v3.4.2 released, adding auto mixed-precision training to ab-initio reconstruction for faster training, alongside speedups to parse_pose_star and analyze_landscape_full

• 10/2024: cryodrgn v3.4.1 released, adding support for float16-formatted input .mrcs image stacks and addressing issues with downsample, filter, and volume evaluation

• 09/2024: cryodrgn v3.4.0 released, introducing plotting by class labels, support for RELION 3.1, and calculation of phase-randomized Fourier Shell correlations

• 06/2024: cryodrgn v3.3.3 released, addressing issues in backproject, write_star, and filter

• 05/2024: cryodrgn v3.3.2 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 in parse_pose_star

• 05/2024: cryodrgn v3.3.1 released with new ability to create files per micrograph in filter_star using --micrograph-files as well as replacing train_nn/vae AMP error messages with warnings

• 04/2024: cryodrgn v3.3.0 released — first non-beta release of cryoDRGN-ET, new command cryodrgn direct_traversal, improved testing, and cleaned-up Jupyter notebooks

• 03/2024: cryodrgn v3.2.0-beta released with new commands including cryodrgn_utils clean, cryodrgn_utils gen_mask, and cryodrgn_utils fsc

• 12/2023: cryodrgn v3.1.0-beta released with new command cryodrgn filter for interactive filtering of particles

• 09/2023: CryoDRGN-ET for subtomogram analysis is now available in beta, as cryodrgn v3.0.0-beta

• 06/2023: documentation clean up, available here on gitbook

• 05/2023: cryodrgn v2.3.0 released with improvements and fixes to ab initio tools.

• 01/2023: cryodrgn v2.2.0 released with new ab initio reconstruction tools and more.

• 07/2022: cryodrgn v1.1.0 released with updated default architecture

• 05/2022: cryodrgn v1.0.0 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 preprocess material

• June 2023:

  • moving documentation to gitbook (here) — the previous documentation found at Notion/sphinx will no longer be updated

  • new page on Making long trajectories with cryoDRGN graph_traversal