0.16.4

0.16.4 - 2025-10-21

🚀 Features

• Set units for viewer spawned from the view menu (#1308)
• Add saving color maps in OME tiffs (#1312)
• Add saving and reading of time scale in ImageJ and OME TIFF files (#1323)

🐛 Bug Fixes

• Fit ROI shape to image to solve problem of saving data in batch process (#1288)
• If save dialog is used to select directory save it in history not parent (#1289)
• Fix --pre test by stopping using the deprecated sentry_sdk method (#1304)
• Fix saving in batch if the data is mask segmentation project (#1309)
• Clean elements outside mask for multiple otsu method (#1319)

📚 Documentation

• Update changelog for 0.16.4

🧪 Testing

• [Automatic] Constraints upgrades: pandas (#1285)
• [Automatic] Constraints upgrades: ipykernel, numpy, scipy, sentry-sdk (#1287)
• [Automatic] Constraints upgrades: imagecodecs, ipykernel, napari, sentry-sdk (#1290)
• [Automatic] Constraints upgrades: napari, psygnal, sentry-sdk, superqt (#1295)
• [Automatic] Constraints upgrades: pandas, requests (#1297)
• [Automatic] Constraints upgrades: ipython, numpy, pydantic, qtconsole, scipy, sentry-sdk, tifffile, xlsxwriter (#1301)
• [Automatic] Constraints upgrades: partsegcore-compiled-backend, psygnal, sentry-sdk (#1305)
• [Automatic] Constraints upgrades: ipython, napari, pandas, pydantic, tifffile (#1311)
• [Automatic] Constraints upgrades: pydantic, sentry-sdk (#1316)
• [Automatic] Constraints upgrades: h5py, ipykernel, numpy, psygnal, pydantic, sentry-sdk, tifffile (#1322)

⚙️ Miscellaneous Tasks

• [pre-commit.ci] pre-commit autoupdate (#1286)
• [pre-commit.ci] pre-commit autoupdate (#1291)
• [pre-commit.ci] pre-commit autoupdate (#1296)
• [pre-commit.ci] pre-commit autoupdate (#1298)
• Add more wait on coderabbit review (#1300)
• Use prek for initial check of code format (#1299)
• [pre-commit.ci] pre-commit autoupdate (#1302)
• Use most recent macOS images on GitHub Actions (#1310)
• [pre-commit.ci] pre-commit autoupdate (#1306)
• [pre-commit.ci] pre-commit autoupdate (#1313)
• Add cooldown of dependabot PR (#1317)
• Update licensing metadata to follow modern standards (#1314)
• Make test log more readable by using 120 columns and colors (#1320)
• [pre-commit.ci] pre-commit autoupdate (#1318)
• Add changelog for 0.16.4 (#1321)
• Use ruff formatter in place of black (#1324)

🛡️ Security

• (deps) Bump actions/download-artifact from 4 to 5 in the github-actions group (#1292)
• (deps) Bump pyvista/setup-headless-display-action from 3 to 4 (#1294)
• (deps) Bump actions/checkout from 4 to 5 in the github-actions group (#1293)
• (deps) Bump actions/setup-python from 5 to 6 in the github-actions group (#1303)
• (deps) Bump github/codeql-action from 3 to 4 (#1315)

0.16.4rc0

0.16.4 - 2025-10-15

🚀 Features

• Set units for viewer spawned from the view menu (#1308)
• Add saving color maps in OME tiffs (#1312)

🐛 Bug Fixes

• Fit ROI shape to image to solve problem of saving data in batch process (#1288)
• If save dialog is used to select directory save it in history not parent (#1289)
• Fix --pre test by stopping using the deprecated sentry_sdk method (#1304)
• Fix saving in batch if the data is mask segmentation project (#1309)
• Clean elements outside mask for multiple otsu method (#1319)

🧪 Testing

• [Automatic] Constraints upgrades: pandas (#1285)
• [Automatic] Constraints upgrades: ipykernel, numpy, scipy, sentry-sdk (#1287)
• [Automatic] Constraints upgrades: imagecodecs, ipykernel, napari, sentry-sdk (#1290)
• [Automatic] Constraints upgrades: napari, psygnal, sentry-sdk, superqt (#1295)
• [Automatic] Constraints upgrades: pandas, requests (#1297)
• [Automatic] Constraints upgrades: ipython, numpy, pydantic, qtconsole, scipy, sentry-sdk, tifffile, xlsxwriter (#1301)
• [Automatic] Constraints upgrades: partsegcore-compiled-backend, psygnal, sentry-sdk (#1305)
• [Automatic] Constraints upgrades: ipython, napari, pandas, pydantic, tifffile (#1311)
• [Automatic] Constraints upgrades: pydantic, sentry-sdk (#1316)

⚙️ Miscellaneous Tasks

• [pre-commit.ci] pre-commit autoupdate (#1286)
• [pre-commit.ci] pre-commit autoupdate (#1291)
• [pre-commit.ci] pre-commit autoupdate (#1296)
• [pre-commit.ci] pre-commit autoupdate (#1298)
• Add more wait on coderabbit review (#1300)
• Use prek for initial check of code format (#1299)
• [pre-commit.ci] pre-commit autoupdate (#1302)
• Use most recent macOS images on GitHub Actions (#1310)
• [pre-commit.ci] pre-commit autoupdate (#1306)
• [pre-commit.ci] pre-commit autoupdate (#1313)
• Add cooldown of dependabot PR (#1317)
• Update licensing metadata to follow modern standards (#1314)
• Make test log more readable by using 120 columns and colors (#1320)
• [pre-commit.ci] pre-commit autoupdate (#1318)

🛡️ Security

• (deps) Bump actions/download-artifact from 4 to 5 in the github-actions group (#1292)
• (deps) Bump pyvista/setup-headless-display-action from 3 to 4 (#1294)
• (deps) Bump actions/checkout from 4 to 5 in the github-actions group (#1293)
• (deps) Bump actions/setup-python from 5 to 6 in the github-actions group (#1303)

0.16.3

0.16.3 - 2025-07-10

🐛 Bug Fixes

• Do not use default parameters in default leaf (#1283)

🧪 Testing

• [Automatic] Constraints upgrades: napari, numpy, pydantic, sentry-sdk, tifffile, vispy (#1273)
• [Automatic] Constraints upgrades: h5py, ipython, magicgui, numpy, pandas, pydantic, requests, sentry-sdk, superqt, tifffile, xlrd (#1276)
• [Automatic] Constraints upgrades: numpy, pygments, scipy, simpleitk, superqt, xlsxwriter (#1278)
• [Automatic] Constraints upgrades: ipython, napari, partsegcore-compiled-backend, psygnal, sentry-sdk (#1281)

⚙️ Miscellaneous Tasks

• Block sentry==3.0.0a1 for pre-tests (#1272)
• Add fallback version for setuptools_scm (#1271)
• [pre-commit.ci] pre-commit autoupdate (#1270)
• Use ubuntu 22.04 when building pyinstaller bundle (#1275)
• [pre-commit.ci] pre-commit autoupdate (#1274)
• [pre-commit.ci] pre-commit autoupdate (#1277)
• Block sentry alpha 3.0.0a1 and 3.0.0a2 (#1279)
• Block pytest-qt==4.5.0 (for pyside2 compatibility) (#1282)
• [pre-commit.ci] pre-commit autoupdate (#1280)
• Migrate Windows images from 2019 to 2022 in Azure Pipelines and GitHub Actions (#1284)

0.16.2

0.16.2 - 2025-05-12

🧪 Testing

• [Automatic] Constraints upgrades: numpy, partsegcore-compiled-backend, tifffile (#1253)
• [Automatic] Constraints upgrades: imagecodecs, ipython, pydantic, sentry-sdk, superqt, tifffile (#1255)
• [Automatic] Constraints upgrades: ipython, napari, numpy, packaging, pydantic, sentry-sdk, simpleitk, sympy, xlsxwriter (#1266)
• [Automatic] Constraints upgrades: oiffile, psygnal, scipy, sentry-sdk, tifffile (#1267)

⚙️ Miscellaneous Tasks

• [pre-commit.ci] pre-commit autoupdate (#1251)
• Prepare for napari 0.6.0 deprecations (#1256)
• [pre-commit.ci] pre-commit autoupdate (#1254)
• [pre-commit.ci] pre-commit autoupdate (#1259)
• Update workflow to use Ubuntu 22.04 instead of 20.04 (#1261)
• [pre-commit.ci] pre-commit autoupdate (#1260)
• Try to fix Upgrade dependencies workflow part 2 (#1265)
• [pre-commit.ci] pre-commit autoupdate (#1268)

🛡️ Security

• (deps) Bump peter-evans/create-pull-request from 6 to 7 (#1262)
• (deps) Bump codecov/codecov-action from 4 to 5 (#1263)

0.16.1

0.16.1 - 2025-03-10

🐛 Bug Fixes

• Fix rendering of alternative representation if there are more components in the alternative representation than in ROI (#1240)
• Enable czifile workaround for 2019.7.2.1 (#1246)

🧪 Testing

• [Automatic] Constraints upgrades: ipython, magicgui, numpy, partsegcore-compiled-backend, pydantic (#1231)
• [Automatic] Constraints upgrades: imagecodecs (#1233)
• [Automatic] Constraints upgrades: oiffile, pygments, scipy, superqt (#1234)
• [Automatic] Constraints upgrades: imageio, napari, numpy, partsegcore-compiled-backend, pydantic, pygments, scipy, sentry-sdk, simpleitk, tifffile, xlsxwriter (#1236)
• [Automatic] Constraints upgrades: ipython, xlsxwriter (#1239)
• [Automatic] Constraints upgrades: numpy, partsegcore-compiled-backend, psygnal, qtpy, scipy, sentry-sdk (#1241)
• [Automatic] Constraints upgrades: czifile, h5py, ipython, qtawesome, sentry-sdk, tifffile, traceback-with-variables (#1247)

⚙️ Miscellaneous Tasks

• [pre-commit.ci] pre-commit autoupdate (#1232)
• [pre-commit.ci] pre-commit autoupdate (#1235)
• [pre-commit.ci] pre-commit autoupdate (#1237)
• Drop python 3.9 tests for napari repository (#1244)
• Block ipykernel 7.0.0a1 (#1248)
• [pre-commit.ci] pre-commit autoupdate (#1242)
• Switch to get_qapp from get_app to handle napari deprecation (#1249)

0.16.0

0.16.0 - 2024-12-21

🚀 Features

• Allow set units that will be used for load/save data using PartSeg as napari plugin (#1228)
• Show filename when importing with PartSeg in napari (#1226)

🐛 Bug Fixes

• Fix error when image changed during segmentation (#1218)
• Fix pre release tests (#1219)
• Drop imagej LUTs of size 24*x (#1227)

🧪 Testing

• [Automatic] Constraints upgrades: h5py, imageio, ipython, napari, numpy, sentry-sdk (#1201)
• [Automatic] Constraints upgrades: sentry-sdk (#1214)
• [Automatic] Constraints upgrades: ipython, traceback-with-variables (#1221)
• [Automatic] Constraints upgrades: numpy, packaging, pydantic, qtconsole, qtpy, sentry-sdk, traceback-with-variables (#1223)
• [Automatic] Constraints upgrades: imageio, ipython, pydantic (#1225)
• [Automatic] Constraints upgrades: napari, numpy, pydantic, sentry-sdk, six, superqt, tifffile (#1229)

⚙️ Miscellaneous Tasks

• Stop using mambaforge in tests (#1203)
• [pre-commit.ci] pre-commit autoupdate (#1202)
• [pre-commit.ci] pre-commit autoupdate (#1204)
• Remove defining default version of language in pre-commit configuration (#1208)
• [pre-commit.ci] pre-commit autoupdate (#1209)
• Drop python 3.8 (#1206)
• Use PublishPipelineArtifact in place of PublishBuildArtifacts to reduce CI fragility (#1213)
• Update CI configuration to use more modern OS and python versions (#1207)
• Fix upgrade-dependencies.yamldocs constraints (#1215)
• [pre-commit.ci] pre-commit autoupdate (#1216)
• Add changelog 0.16.0a1
• [pre-commit.ci] pre-commit autoupdate (#1222)
• [pre-commit.ci] pre-commit autoupdate (#1230)

0.16.0a1

0.16.0 - 2024-10-22

This release drop support for python 3.8 and napari below 0.4.19.

🐛 Bug Fixes

• Fix error when image changed during segmentation (#1218)
• Fix pre release tests (#1219)

🧪 Testing

• [Automatic] Constraints upgrades: h5py, imageio, ipython, napari, numpy, sentry-sdk (#1201)
• [Automatic] Constraints upgrades: sentry-sdk (#1214)

⚙️ Miscellaneous Tasks

• Stop using mambaforge in tests (#1203)
• [pre-commit.ci] pre-commit autoupdate (#1202)
• [pre-commit.ci] pre-commit autoupdate (#1204)
• Remove defining default version of language in pre-commit configuration (#1208)
• [pre-commit.ci] pre-commit autoupdate (#1209)
• Drop python 3.8 (#1206)
• Use PublishPipelineArtifact in place of PublishBuildArtifacts to reduce CI fragility (#1213)
• Update CI configuration to use more modern OS and python versions (#1207)
• Fix upgrade-dependencies.yamldocs constraints (#1215)
• [pre-commit.ci] pre-commit autoupdate (#1216)

0.15.4

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)

0.15.4b7

0.15.4 - 2024-08-13

🚀 Features

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

🐛 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

📚 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)

⚙️ 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)

0.15.4b6

0.15.4 - 2024-08-13

🚀 Features

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

🐛 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

📚 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)

⚙️ 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)