PartSeg - segmentation and reconstruction tool for 3D microscopy images

0.15.4 - 2024-09-27

🚀 Features

• Add preview of image metadata (#1154)
• Add option to combine channels using sum and max (#1159)
• Add metadata viewer as napari widget (#1195)
• Read channel colors from *.czi metadata (#1198)
• Use image color when add layer to napari (#1200)

🐛 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 problem with setting range of auto-generated widget (#1187)
• Fix reading channel names from single channel czi files (#1194)

🚜 Refactor

• Make warnings error in tests (#1192)
• Merge all channel-specific attributes of the Image class (#1191)

📚 Documentation

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

🧪 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)
• [Automatic] Constraints upgrades: imageio, napari, numpy (#1180)
• Constraints upgrades: sentry-sdk and fix tests (#1182)
• napari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile (#1183)
• [Automatic] Constraints upgrades: numpy, pydantic (#1188)
• [Automatic] Constraints upgrades: imagecodecs, pandas, pydantic, sentry-sdk, sympy, tifffile (#1190)

⚙️ 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)
• Fix call of logger to properly pass arguments to messages (#1179)
• Fix coverage files upload by enable hidden files upload (#1186)
• [pre-commit.ci] pre-commit autoupdate (#1184)
• Use PyQt6 in pre-tests (#1196)
• Add missed code from #1191 (#1197)
• [pre-commit.ci] pre-commit autoupdate (#1189)
• Auto add "skip check PR title" label in update dependencies PR (#1199)

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)