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Recent Releases of tomotwin-cryoet

tomotwin-cryoet - v0.9.1

What's Changed

  • Update changes link by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/98
  • Update installation.rst by @YousefMetwally in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/99
  • Single forward run for embedding of anchor, negative and positive volumes. by @YousefMetwally in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/103
  • Update installation.rst by @YousefMetwally in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/104
  • Update torchtrainer.py by @YousefMetwally in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/105
  • Update cuml and pandas by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/111
  • change default neighbors to 64 by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/112

New Contributors

  • @YousefMetwally made their first contribution in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/99

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.9.0...v0.9.1

- Python
Published by thorstenwagner over 1 year ago

tomotwin-cryoet - v0.9.0

With TomoTwin v0.9.0 we introduce a new target manager for napari. The documentation of the clustering workflow has been updated accordingly. Also, locate is now parallelized using dask and is now much faster :-)

What's Changed

  • Update rapids to 23.10 by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/48
  • Update pytorch-metric-learning by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/87
  • Locate is now using dask by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/90
  • Remove tomotwin from env file by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/91
  • Switch to SPDX-License-Identifiers by @kephale in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/96
  • Fast locate, new rapids and updated tutorial by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/89

New Contributors

  • @kephale made their first contribution in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/96

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.8.0...v0.9.0

- Python
Published by thorstenwagner almost 2 years ago

tomotwin-cryoet - v0.8.0

What's Changed

This release mainly improves the user experience when working with the clustering workflow. The changes you will notice are:

  • BREAKING CHANGE: When calculating a umap, no label mask is created anymore.Instead, this map is now computed in the background within napari and is transparent to the user. This also means that you don't have to select a label layer anymore when loading a umap (PR #82 MPI-Dortmund/napari-tomotwin#22). However, this is a breaking change, so you need to recalculate your umaps to take advantage of it.
  • Napari no longer freezes when loading umaps and shows a progress bar while loading (MPI-Dortmund/napari-tomotwin#20)
  • When selecting clusters in the umap, there is a time delay between the selection and the actual highlighting. Now this process is 2x-3x faster (PR BiAPoL/napari-clusters-plotter#283 BiAPoL/napari-clusters-plotter#282)
  • When saving cluster targets, the appropriate embedding file is automatically selected if possible (PR MPI-Dortmund/napari-tomotwin#26). This means that the user does not have to remember which embedding belongs to which umap.
  • Saving cluster targets (medoids) is now 5x faster (https://github.com/MPI-Dortmund/napari-tomotwin/pull/23).

Minor changes

  • Add median filter strategy by @GavinR1 in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/76 and https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/79
  • Stop making tomotwin_tools crash on non gpu machines. by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/78
  • Add short training tutorial by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/81

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/0.7.0...v0.8.0

- Python
Published by thorstenwagner about 2 years ago

tomotwin-cryoet - v0.8.0b1

What's Changed

Breaking changes:

  • Write embeddings metadata + positions into umap attributes @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/82
  • Remove calculation of label mask by thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/82

The above change have the effect, that already calculated umaps to not work anymore. However, you can easily recreate them with tomotwin_tools.py umap. With argument -m you can even provide the old fitted model. In that way you will get the same umap as before.

Minor changes

  • Add median filter strategy by @GavinR1 in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/76 and https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/79
  • Stop making tomotwin_tools crash on non gpu machines. by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/78
  • Add short training tutorial by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/81

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/0.7.0...v0.8.0b1

- Python
Published by thorstenwagner about 2 years ago

tomotwin-cryoet - v0.7.0

What's Changed

With this release we add new tools for advanced strategies that describe how to speed up the calculation of embeddings, potentially improve their umaps, and refine references/targets!

Improve reference/targets with umaps (Strategy 1)

Add new umap and filter options by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/64

Faster embeddings with median filtering (Strategy 2)

Add fast median mask estimation by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/66

Other

  • increase timeout of the dataloader to 180 seconds. by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/57
  • --save_after_improvement saves models after each epoch by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/60
  • Check & correct for duplicate embedded subvolumes by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/61
  • Fix padding when creating heatmaps during locate with --write_heatmaps by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/65

Documentation

  • Add strategies pages to the documentation and link them by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/67 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/68 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/69 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/70 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/71

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.6.1...0.7.0

- Python
Published by thorstenwagner over 2 years ago

tomotwin-cryoet - v0.6.1

What's Changed

  • Use random port for distributed processing by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/54
  • Use stable pytorch 2.1 by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/52
  • Fix read the docs building by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/55
  • Fix 'too many open files' problem by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/56

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.6.0.3...v0.6.1

- Python
Published by thorstenwagner over 2 years ago

tomotwin-cryoet - v0.6.0.1

What's Changed

  • tomotwim_embed.py is now 1.6x faster and linearly scales across multiple GPUs by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/40
    • Exploiting new the compile option of the latest pytorch 2.1 nightly build.
    • Internally DistributedDataParallel is used instead of DataParallel
    • Unpin pytorch version by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/46

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.5.1...v0.6.0.1

- Python
Published by thorstenwagner over 2 years ago

tomotwin-cryoet - v0.5.0

What's Changed

TomoTwin

  • Add option to specify a mask during embedding by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/27
  • Accept key error when evaluation is running and use more flexibel label idenetification by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/32
  • Fix bug when extracting label from filename by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/33

Napari tools

  • napari-tomotwin has been updated to version 0.2 to add medoid cluster target calculation by @thorstenwagner . Learn more at https://github.com/MPI-Dortmund/napari-tomotwin/releases/tag/v0.2.0
  • napari-boxmanager has been updated to version 0.4 by @thorstenwagner. Learn more at https://github.com/MPI-Dortmund/napari-boxmanager/releases/tag/v0.4.0

Documentation

  • Added citation file (citation.cff) to nature methods by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/22
  • Added some developer information @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/26
  • Added documentation for masking by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/28
  • Updated changelist for version 0.5 by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/34
  • Various updates by @GavinR1 and @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/23 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/30 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/31 https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/29

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.4.3...v0.5.0

- Python
Published by thorstenwagner over 2 years ago

tomotwin-cryoet - v0.4.3

What's Changed

  • Add the citation.cff by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/18
  • Automatic release by GitHub actions on pypi by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/19
  • Updated dependencies and new installation instructions by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/21

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.4.2.2...v0.4.3

- Python
Published by thorstenwagner almost 3 years ago

tomotwin-cryoet - TomoTwin v0.4.2

This is the official clustering workflow release :-) We updated the tutorial and added all the necessary tools. Reinstall to get all the necessary tools!

What's Changed

  • Make pytest and coverage running by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/8
  • Refactor locate and add unit tests by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/9
  • Added more unit tests, documentation and did some refactoring by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/10
  • Clustering workflow release by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/11
  • add changes for 0.4.0 by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/12
  • update installation instructions by @thorstenwagner in https://github.com/MPI-Dortmund/tomotwin-cryoet/pull/13

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.3.0...v0.4.2

- Python
Published by thorstenwagner almost 3 years ago

tomotwin-cryoet - v0.3.0

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.2.2...v0.3.0

- Python
Published by thorstenwagner about 3 years ago

tomotwin-cryoet - v0.2.2

Full Changelog: https://github.com/MPI-Dortmund/tomotwin-cryoet/compare/v0.2.1.6...v0.2.2

- Python
Published by thorstenwagner about 3 years ago