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Published September 19, 2024 | Version v0.15.4b5
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

0.15.4 - 2024-08-13

๐Ÿš€ Features

  • Add preview of image metadata (#1154)
  • Add option to combine channels using sum and max (#1159)

๐Ÿ› Bug Fixes

  • Fix selection of custom label colors for napari 0.5.0 (#1138)
  • Add pint call to enforce initialization of unit registry (#1146)
  • Workaround for lack of zsd support in czifile (#1142)
  • Fix preparing data for mahotas.haralick to avoid overflow problem (#1150)
  • Fix use_convex type from int to bool for segmentation algorithms (#1152)
  • Prevent propagation of decreasing contrast limits set by user (#1166)
  • Prevent error on searching component if there is no component (#1167)
  • Fix checking if channel requested by MeasurementProfile exists (#1165)
  • Fix trying to access to just deleted measurement profile from edit window. (#1168)
  • Fix bug in code for checking for survey file (#1174)
  • Fix plugin discovery in bundle to register them in napari viewer (#1175)
  • Fix call of logging

๐Ÿ“š Documentation

  • Change homepage URL (#1139)
  • Add link for download macOS arm bundle (#1140)
  • Add changelog for 0.15.4 release
  • Update changelog (#1176)

๐Ÿงช Testing

  • [Automatic] Constraints upgrades: napari, sentry-sdk, sympy (#1128)
  • [Automatic] Constraints upgrades: mahotas, numpy, sentry-sdk, sympy (#1145)
  • [Automatic] Constraints upgrades: numpy, tifffile (#1163)
  • [Automatic] Constraints upgrades: napari, sentry-sdk, tifffile (#1169)
  • [Automatic] Constraints upgrades: magicgui, sentry-sdk (#1172)
  • [Automatic] Constraints upgrades: sympy, tifffile (#1177)

โš™๏ธ Miscellaneous Tasks

  • Speedup tests by use tox-uv (#1141)
  • Get additional dict from PR branch for checking PR title (#1144)
  • Relax numpy constraint (#1143)
  • Allow to skip spellchecking PR title (#1147)
  • [pre-commit.ci] pre-commit autoupdate (#1149)
  • Create only archive with version in name on azures pipeline (#1151)
  • Fix tests for napari from repository (#1148)
  • Use python 3.11 to determine updated packages in PR description (#1160)
  • [pre-commit.ci] pre-commit autoupdate (#1164)
  • [pre-commit.ci] pre-commit autoupdate (#1170)
  • Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
  • [pre-commit.ci] pre-commit autoupdate (#1173)
  • [pre-commit.ci] pre-commit autoupdate (#1178)

Build

  • Remove PyOpenGL-accelerate from dependencies because of numpy incompatibility (#1155)
  • Update install constraints on numpy and qt packages (#1157)
  • Enforce napari 0.5.0 for Qt6 bindings (#1161)
  • Require napari>=0.5.0 only for python 3.9+ (#1162)

Files

4DNucleome/PartSeg-v0.15.4b5.zip

Files (7.8 MB)

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md5:b532cfe8a897615f717c69970766fb33
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Additional details

Related works

Is supplement to
Software: https://github.com/4DNucleome/PartSeg/tree/v0.15.4b5 (URL)