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Published August 10, 2023 | Version v0.15.1
Software Open

PartSeg - segmentation and reconstruction tool for 3D microscopy images

Authors/Creators

  • 1. Centre of New Technologies, University of Warsaw, Warsaw, Poland; Institute of Informatics, University of Warsaw, Warsaw, Poland
  • 2. Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
  • 3. Institute of Informatics, University of Warsaw, Warsaw, Poland

Contributors

  • 1. Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland

Description

0.15.1 - 2023-08-09 Bug Fixes
  • Fix possible problem of double registration napari plugin in PartSeg bundle (#974)
  • Bump OS versions for part of testing workflows. (#977)
  • Bump os version for main tests workflow. (#979)
  • Ensure that the module PartSegCore.channel_class is present in bundle (#980)
  • Lower npe2 schema version to work with older napari version (#981)
  • Generate test report per platfom (#978)
  • Importing plugins in bundle keeping proper module names (#983)
  • Fix napari repo workflow (#985)
  • Fix bug in read tiff files with double Q in axes but one related to dummy dimmension (#992)
  • Fix bug that lead to corupted state when saving calculation plan to excel file (#995)
  • Enable python 3.11 test on CI, fix minor errors (#869)
Features
  • Allow to save multiple napari image layers to single tiff file (#1000)
  • Add option to export batch project with data (#996)
Testing
  • [Automatic] Constraints upgrades: imageio, ipython, psygnal, scipy, sentry-sdk (#975)
  • [Automatic] Constraints upgrades: h5py, imagecodecs, imageio, ipykernel, napari, numpy, pandas, pydantic, pyinstaller, scipy, sentry-sdk, tifffile, vispy (#986)
  • [Automatic] Constraints upgrades: imagecodecs, sentry-sdk, tifffile (#997)
  • [Automatic] Constraints upgrades: ipykernel, pydantic (#1002)
  • [Automatic] Constraints upgrades: numpy, pygments, sentry-sdk, superqt (#1007)
Ci
  • [pre-commit.ci] pre-commit autoupdate (#973)
  • [pre-commit.ci] pre-commit autoupdate (#982)
  • [pre-commit.ci] pre-commit autoupdate (#987)
  • [pre-commit.ci] pre-commit autoupdate (#988)
  • [pre-commit.ci] pre-commit autoupdate (#991)
  • [pre-commit.ci] pre-commit autoupdate (#998)
  • [pre-commit.ci] pre-commit autoupdate (#1004)
  • Change markdown linter from pre-commit to mdformat (#1006)
Changes:
  • 3594793889ac03e1b0acb6b470726985c6ce5a8f add release notes
  • d9efd0b0c7f572b5100dc2f9b6c539869439ed32 ci: [pre-commit.ci] pre-commit autoupdate (#1008)
  • 3104c5ceb69486818717b4c7664828754856ebf6 feat: Add option to export batch project with data (#996)
  • 112c4feb5a10fc5d037de52b9dcaaa0b248e14d9 test: [Automatic] Constraints upgrades: numpy, pygments, sentry-sdk, superqt (#1007)
  • 10244c59df6a29f3ad9e328e2c65e74cd342de00 ci: Change markdown linter from pre-commit to mdformat (#1006)
  • 9016e95140949c5566be3810a3080e788862cfc6 ci: [pre-commit.ci] pre-commit autoupdate (#1004)
  • d77717bcb20514c2a69ee8a1aa9b1b24549da401 fix: Enable python 3.11 test on CI, fix minor errors (#869)
  • 4fc34bfed5bc596ca1a7f1c59bcdf78984229157 test: [Automatic] Constraints upgrades: ipykernel, pydantic (#1002)
  • b38933b84ea47fe2b2235087a72081833ebf930d feat: allow to save multiple napari image layers to single tiff file (#1000)

  • 1fb01af346d069f4bb274adef21b3ac941388aa0 ci: [pre-commit.ci] pre-commit autoupdate (#998) <details><summary><b>See More</b></summary>

  • b03118cdcbb109bef5a6905a70fee7bfb1e10db1 test: [Automatic] Constraints upgrades: imagecodecs, sentry-sdk, tifffile (#997)

  • 6945822ba34f4f7d4c8de1f85cb433d0c52b971c fix: Fix bug that lead to corupted state when saving calculation plan to excel file (#995)
  • 152a0267b46d4028cba8f73a954bce486c19a050 fix: Fix bug in read tiff files with double Q in axes but one related to dummy dimmension (#992)
  • 3b08337c2f85c6a0c3268590ff88a209d0a91b09 ci: [pre-commit.ci] pre-commit autoupdate (#991)
  • dd3ca25ee84e39f14dced8bd5c78a65b50f00448 test: [Automatic] Constraints upgrades: h5py, imagecodecs, imageio, ipykernel, napari, numpy, pandas, pydantic, pyinstaller, scipy, sentry-sdk, tifffile, vispy (#986)
  • aacc4284f73ee1b04e8aca6d86be0731fdac3a14 ci: [pre-commit.ci] pre-commit autoupdate (#988)
  • 072f55843e0a0ddf0ff33bb0ca2dc15e46e2bbe8 ci: [pre-commit.ci] pre-commit autoupdate (#987)
  • da4c370447b7cb166567967f75c82c0cf25d313f fix: Fix napari repo workflow (#985) [ #984 ]
  • c7325d44e3ecf0201f60fe9de47f2da07d180b0d fix: importing plugins in bundle keeping proper module names (#983)
  • 43e9bc224612b3c1c4d1a03e738af18924d8a4b2 fix: Generate test report per platfom (#978)
  • 26b4c44eb5d9ebe2b19a45b2f51855cf7db0a918 ci: [pre-commit.ci] pre-commit autoupdate (#982)
  • 0de056e85879e90386cc4a375a83fdb47618eb31 fix: Lower npe2 schema version to work with older napari version (#981)
  • 18aa3ac48b35e3b669dbdc0023900a4442480010 fix: Ensure that the module PartSegCore.channel_class is present in bundle (#980)
  • d8bdb931c4065ca31cdf1d538c1899dbeb2bbabd fix: Bump os version for main tests workflow. (#979) [ #977 ]
  • 889a72828de04662f3c3afdf0d9731f4ad6792e8 fix: Bump OS versions for part of testing workflows. (#977) [ #976 ]
  • d3a26d6a1de816b34811b4b96995d58b618f89ae test: [Automatic] Constraints upgrades: imageio, ipython, psygnal, scipy, sentry-sdk (#975)
  • 91c3c1d72c89454055887f07e641a5df5a9ec2c1 fix: Fix possible problem of double registration napari plugin in PartSeg bundle (#974)
  • 0dff2f0f580f7845efbc97601becf79d56fde694 ci: [pre-commit.ci] pre-commit autoupdate (#973)

This list of changes was auto generated.</details>

Files

4DNucleome/PartSeg-v0.15.1.zip

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Additional details

Related works

Is supplement to
https://github.com/4DNucleome/PartSeg/tree/v0.15.1 (URL)