# News and Release Notes

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

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## Version Release Timeline

* 02/2026: [**cryodrgn v4.2.0-b1**](https://github.com/ml-struct-bio/cryodrgn/pull/471) released, the latest pre-release of the upcoming v4.2.0 which will include integration with the cryoDRGN-AI pose search algorithm
* 12/2025: [**cryodrgn v3.5.4**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.4) released, fixing issues using `--vol-ind` with 1-indexing in landscape analysis and using `--first` with `backproject_voxel`
* 11/2025: [**cryodrgn v3.5.3**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.3) 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`&#x20;
* 09/2025: [**cryodrgn v3.5.2**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.2) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.1) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.0) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.4.4) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.4.3) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.4.2) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.4.1) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/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 v3.3.3**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.3.3) released, addressing issues in `backproject`, `write_star`, and `filter`
* 05/2024: [**cryodrgn v3.3.2**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/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 in `parse_pose_star`&#x20;
* 05/2024: [**cryodrgn v3.3.1**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.3.1) 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**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.3.0) released — first non-beta release of [cryoDRGN-ET](https://www.biorxiv.org/content/10.1101/2023.08.18.553799v1), new command `cryodrgn direct_traversal`, improved testing, and cleaned-up Jupyter notebooks
* 03/2024: [**cryodrgn v3.2.0-beta**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.2.0-beta) released with new commands including `cryodrgn_utils clean`, `cryodrgn_utils gen_mask`, and `cryodrgn_utils fsc`
* 12/2023: [**cryodrgn v3.1.0-beta**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/v3.1.0-beta) released with new command `cryodrgn filter` for interactive filtering of particles
* 09/2023: [CryoDRGN-ET](https://www.biorxiv.org/content/10.1101/2023.08.18.553799v1) for subtomogram analysis is now available in beta, as [**cryodrgn v3.0.0-beta**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.0.0-beta)
* 06/2023: documentation clean up, available here on gitbook&#x20;
* 05/2023: [**cryodrgn v2.3.0**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/2.3.0) released with improvements and fixes to ab initio tools.
* 01/2023: [**cryodrgn v2.2.0**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/2.2.0) released with new ab initio reconstruction tools and more.&#x20;
* 07/2022: [**cryodrgn v1.1.0**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/1.1.0) released with updated default architecture
* 05/2022: [**cryodrgn v1.0.0**](https://github.com/ml-struct-bio/cryodrgn/releases/tag/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](https://ez-lab.gitbook.io/cryodrgn-v4.2.0-draft/cryodrgn-et-subtomogram-analysis)
  * creating [new page group](https://app.gitbook.com/o/gYlX75MBAfjzRuXIYbKH/s/z7E99j3jJUSLJDvU43U6/~/changes/37/deprecated-workflows) "Deprecated Workflows" initially populated with `cryodrgn preprocess` material
* June 2023:
  * moving documentation to gitbook (here) — the previous documentation found at [Notion](https://www.notion.so/cryodrgn/cryoDRGN-tutorial-b932c021cb2c415282f182048bac16ff)/sphinx will no longer be updated
  * new page on [making-long-trajectories-with-cryodrgn-graph\_traversal](https://ez-lab.gitbook.io/cryodrgn-v4.2.0-draft/making-long-trajectories-with-cryodrgn-graph_traversal "mention")
