Description:

PartSeg 0.15.3

PartSeg

















PartSeg is a GUI and a library for segmentation algorithms. PartSeg also provide napari plugins for IO and labels measurement.
This application is designed to help biologist with segmentation based on threshold and connected components.

Tutorials

Tutorial: Chromosome 1 (as gui) link
Data for chromosome 1 tutorial link
Tutorial: Different neuron types (as library) link

Installation


From binaries:

Windows (build on Windows 10)
Linux (build on Ubuntu 20.04)
macOS (build on macOS 13)
There are reported problems with permissions systems on macOS. If you have a problem with starting the application, please try to run it from the terminal.



With pip:

From pypi: pip install PartSeg[all]
From repository: pip install git+https://github.com/4DNucleome/PartSeg.git



With conda:

conda install -c conda-forge partseg
mamba install -c conda-forge partseg - As mamba is faster than conda



With napari:
If you do not know how to setup python environment on your system you may use napari to run PartSeg.
It is a GUI for scientific image analysis. PartSeg is also a plugin for napari so could be installed from plugin dialog.
To install napari bundle please download it napari bundle
and follow installation instructions.


Installation troubleshooting information could be found in wiki: wiki.
If this information does not solve problem you can open issue.
Qt 6 support
PartSeg development branch support (and stable since 0.15.0) has experimental Qt6 support. Test are passing but not whole GUI code is covered by tests. Inf you Find any problem please report it.
Running
If you downloaded binaries, run the PartSeg (or PartSeg.exe for Windows) file inside the PartSeg folder
If you installed from repository or from pip, you can run it with PartSeg command or python -m PartSeg.
First option does not work on Windows.
PartSeg export few commandline options:

--no_report - disable error reporting
--no_dialog - disable error reporting and error dialog. Use only when running from terminal.
roi - skip launcher and start ROI analysis gui
mask- skip launcher and start ROI mask gui

napari plugin
PartSeg provides napari plugins for io to allow reading projects format in napari viewer.
Save Format
Saved projects are tar files compressed with gzip or bz2.
Metadata is saved in data.json file (in json format).
Images/masks are saved as *.npy (numpy array format).
Interface
Launcher. Choose the program that you will launch:

Main window of Segmentation Analysis:

Main window of Segmentation Analysis with view on measurement result:

Window for creating a set of measurements:

Main window of Mask Segmentation:

Laboratory
Laboratory of Functional and Structural Genomics
http://4dnucleome.cent.uw.edu.pl/
Cite as
Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction
from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021).
https://doi.org/10.1186/s12859-021-03984-1
Changelog
All notable changes to this project will be documented in this file.
0.15.3 - 2024-07-08
🚀 Features

Pydantic 2 compatibility (#1084)

🐛 Bug Fixes

Fix rendering icons in colormap preview (#1040)
Fix test for validation length of message for sentry-sdk 2.0 release (#1098)
When fix reader check lowercase extension for validate compatibility (#1097)
Fix napari 0.5.0 compatibility (#1116)

🚜 Refactor

Fix Qt flags (#1041)
Fix qt flags in roi mask code (#1042)
Fix qt flags in roi analysis (#1043)
Migrate from setup.cfg to pyproject.toml (#1070)

📚 Documentation

Allow to use newer release of build docs dependencies (#1057)

🧪 Testing

[Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, ipython, numpy, oiffile, pandas, psygnal, pyinstaller, qtconsole, qtpy, sentry-sdk, simpleitk, superqt, tifffile, xlsxwriter (#1020)
[Automatic] Constraints upgrades: h5py, imageio, ipython, numpy, packaging, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, superqt, tifffile, xlsxwriter (#1027)
[Automatic] Constraints upgrades: imageio, magicgui, xlsxwriter (#1030)
[Automatic] Constraints upgrades: ipykernel, pandas, qtpy (#1032)
[Automatic] Constraints upgrades: imageio, ipykernel, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk (#1035)
[Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, magicgui, pandas, pyinstaller, qtawesome, sentry-sdk, tifffile (#1048)
[Automatic] Constraints upgrades: ipykernel, numpy, pandas, partsegcore-compiled-backend, pydantic, scipy, sentry-sdk (#1058)
Improve test of PartSegImage (#1072)
Improve test suite for PartSegCore (#1077)
[Automatic] Constraints upgrades: imageio, ipykernel, local-migrator, napari, numpy, pandas, partsegcore-compiled-backend, pyinstaller, sentry-sdk, tifffile, vispy, xlsxwriter (#1063)
[Automatic] Constraints upgrades: magicgui, packaging, psygnal, pyinstaller, sentry-sdk, superqt (#1086)
[Automatic] Constraints upgrades: psygnal, pydantic, sentry-sdk, vispy (#1090)
[Automatic] Constraints upgrades: h5py, ipykernel, mahotas, pandas, psygnal, pydantic, pyinstaller, qtawesome, scipy, sentry-sdk, superqt (#1092)
[Automatic] Constraints upgrades: imageio, tifffile (#1100)
[Automatic] Constraints upgrades: pydantic, sentry-sdk, superqt, tifffile (#1102)
[Automatic] Constraints upgrades: psygnal, pygments, qtconsole, sentry-sdk, superqt, tifffile (#1105)
[Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy (#1107)
[Automatic] Constraints upgrades: pydantic (#1112)

⚙️ Miscellaneous Tasks

[pre-commit.ci] pre-commit autoupdate (#1019)
Remove plugin page preview as it is no longer maintained (#1021)
[pre-commit.ci] pre-commit autoupdate (#1022)
[pre-commit.ci] pre-commit autoupdate (#1026)
[pre-commit.ci] pre-commit autoupdate (#1031)
[pre-commit.ci] pre-commit autoupdate (#1034)
Use new semgrep configuration (#1039)
Upload raw coverage information (#1044)
[pre-commit.ci] pre-commit autoupdate (#1036)
Run coverage upload in separate steep (#1053)
Generate local report in Tests workflow and use proper script for fetch report (#1054)
Move coverage back to main workflow (#1055)
[pre-commit.ci] pre-commit autoupdate (#1056)
[pre-commit.ci] pre-commit autoupdate (#1059)
Update actions/upload-artifact and actions/download-artifact from 3 to 4 (#1062)
[pre-commit.ci] pre-commit autoupdate (#1064)
Group actions update (#1065)
[pre-commit.ci] pre-commit autoupdate (#1068)
Remove requirement of 2 builds upload to codecov.io (#1073)
Re add tests to coverage report (#1074)
Switch from setup.cfg to pyproject.toml in workflows (#1076)
Fix compiling pyinstaller pre-deps (#1075)
Add codespell to pre-commit and fix pointed bugs (#1078)
Add new ruff rules and apply them (#1079)
[pre-commit.ci] pre-commit autoupdate (#1080)
[pre-commit.ci] pre-commit autoupdate (#1081)
Fix upgrade depenecies workflow (#1083)
Block using mpmath==1.4.0a0 and sentry-sdk 2.0.0a1/a2 in pre-test (#1085)
[pre-commit.ci] pre-commit autoupdate (#1089)
Fix jupyter failing test by using constraints (#1093)
[pre-commit.ci] pre-commit autoupdate (#1091)
[pre-commit.ci] pre-commit autoupdate (#1096)
Add python 3.12 testing (#1087)
Exclude pyside2 on python 3.11 and 3.12 from testing (#1099)
[pre-commit.ci] pre-commit autoupdate (#1101)
[pre-commit.ci] pre-commit autoupdate (#1103)
Bump macos runners to macos-13 (both azure and GHA) (#1113)
[pre-commit.ci] pre-commit autoupdate (#1108)
Remove pyqt5 from constraints (#1118)
Add workflow for releases from GHA (#1117)
Add actionlint to CI to early prevent bug in github workflows (#1119)
Fix release workflow, by update permissions
Check if release notes are properly created (#1122)
Proper use enum in checking new version (#1123)
Refactor and simplify menu bar creation, add workaround for macOS numpy problem (#1124)
Simplify release workflow (#1126)
Fix make_release.yml to proper detect release, attempt 3 (#1127)

🛡️ Security

(deps) Bump actions/checkout from 3 to 4 (#1029)
(deps) Bump conda-incubator/setup-miniconda from 2 to 3 (#1038)
(deps) Bump aganders3/headless-gui from 1 to 2 (#1047)
(deps) Bump actions/checkout from 3 to 4 (#1045)
(deps) Bump hynek/build-and-inspect-python-package from 1 to 2 (#1050)
(deps) Bump actions/setup-python from 4 to 5 (#1046)
(deps) Bump github/codeql-action from 2 to 3 (#1051)
(deps) Bump peter-evans/create-pull-request from 5 to 6 (#1067)
(deps) Bump codecov/codecov-action from 3 to 4 (#1066)

Build

Fix not bundling Font Awesome 6 Free-Solid-900.otf file to executable (#1114)
Update readme and release to point to GitHub releases (#1115)
Do not create archive twice when create bundle (#1120)
Enable macOS-arm bundle builds (#1121)

0.15.2 - 2023-08-28
🐛 Bug Fixes

Fix range threshold selection of algorithms (#1009)
When run batch check if file extension is supported by loader (#1016)
Do not allow to select and render corrupted batch plans (#1015)

🧪 Testing

[Automatic] Constraints upgrades: imagecodecs, ipykernel, magicgui, psygnal, scipy, superqt, tifffile (#1011)
[Automatic] Constraints upgrades: imageio, pyinstaller, tifffile (#1018)

⚙️ Miscellaneous Tasks

Use faster version of black (#1010)
[pre-commit.ci] pre-commit autoupdate (#1013)

0.15.1 - 2023-08-08
🚀 Features

Allow to save multiple napari image layers to single tiff file (#1000)
Add option to export batch project with data (#996)

🐛 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 platform (#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 dimension (#992)
Fix bug that lead to corrupted state when saving calculation plan to excel file (#995)
Enable python 3.11 test on CI, fix minor errors (#869)

🧪 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)

⚙️ Miscellaneous Tasks

[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)
[pre-commit.ci] pre-commit autoupdate (#1008)

0.15.0 - 2023-05-30
🚀 Features

Add PARTSEG_SENTRY_URL env variable support and basic documentation about error reporting (#802)
Allow to see underlying exception when show warning caused by exception (#829)
Add voxel size measurement and allow to overwrite voxel size in batch (#853)
Add alpha support for Qt6 (#866)
Add option to create projection alongside z-axis (#919)
Add napari image custom representation for better error report via sentry (#861)
Add import and export operation for labels and colormaps (#936)
Implement napari widgets for colormap and labels control (#935)
Add forget all button to multiple files widget (#942)
Do not abort processing whole mask segmentation project during exception on single component (#943)
Add distance based watersheed to flow methods (#915)
Add napari widgets for all group of algorithms (#958)
Add napari widget to copy labels along z-axis (#968)

🐛 Bug Fixes

Print all exceptions instead of the latest one in exception dialog (#799)
Fix ROIExtractionResult __str__and __repr__ to use ROIExtractionResult not SegmentationResult (#810)
Fix code to address changes in napari repository (#817)
Fix problem with resize of multiline widgets (#832)
Fix tox configuration to run all required tests (#840)
Fix MSO step_limit description in GUI (#843)
Fix redefined-while-unusedimport code for python 3.9.7 (#844)
Fix warnings reported by Deepsource (#846)
Ensure that "ROI" layer is in proper place for proper visualization (#856)
Fix tests of napari widgets (#862)
Fix build of bundle for a new psygnal release (#863)
Fix minimal requirements pipeline (#877)
Update pyinstaller configuration (#926)
Use text icon, not pixmap icon in colormap and labels list (#938)
Resolve warnings when testing custom save dialog. (#941)
Add padding zeros for component num when load Mask seg file to ROI GUI (#944)
Proper calculate bounds for watershed napari widget (#969)
Fix bug in the wrong order of axis saved in napari contribution (#972)

🚜 Refactor

Simplify and refactor github workflows. (#864)
Better load Mask project in Roi Analysis (#921)
Use more descriptive names in pylint: disable (#922)
Remove pkg_resources usage as it is deprecated (#967)
Convert napari plugin to npe2 (#966)

📚 Documentation

Update README and project metadata (#805)
Create release notes for PartSeg 0.15.0 (#971)

🎨 Styling

Change default theme to dark, remove blinking windows on startup. (#809)

🧪 Testing

[Automatic] Dependency upgrades: packaging, pyinstaller, pyopengl-accelerate, tifffile, xlsxwriter (#932)
[Automatic] Constraints upgrades: fonticon-fontawesome6, imageio, numpy, partsegcore-compiled-backend, pygments, sentry-sdk (#937)
[Automatic] Constraints upgrades: imageio, ipython, pandas, requests, sentry-sdk (#948)
[Automatic] Constraints upgrades: ipython, nme, qtconsole, requests, sentry-sdk (#955)
[Automatic] Constraints upgrades: ipykernel, local-migrator, pyinstaller, sentry-sdk, sympy (#957)
[Automatic] Constraints upgrades: sentry-sdk, xlsxwriter (#959)
[Automatic] Constraints upgrades: requests (#961)
[Automatic] Constraints upgrades: imageio, pandas, pydantic, pyopengl-accelerate, sentry-sdk, xlsxwriter (#970)

⚙️ Miscellaneous Tasks

Improve ruff configuration, remove isort (#815)
Use fail_on_no_env feature from tox-gh-actions (#842)
Add python 3.11 to list of supported versions (#867)
Disable python 3.11 test because of timeout (#870)
Bump ruff to 0.0.218, remove flake8 from pre-commit (#880)
Replace GabrielBB/xvfb-action@v1 by aganders3/headless-gui, part 2 (#887)
Better minimal requirements test (#888)
Improve regexp for proper generate list of packages in update report (#894)
Add check for PR title (#933)
Update codecov configuration to wait on two reports before post information (#934)
[pre-commit.ci] pre-commit autoupdate (#945)
Migrate from nme to local_migrator (#951)
[pre-commit.ci] pre-commit autoupdate (#956)
[pre-commit.ci] pre-commit autoupdate (#964)

🛡️ Security

(deps) Bump peter-evans/create-pull-request from 4 to 5 (#928)

Bugfix

Fix bug with generation of form for model with hidden field (#920)

Dep

[Automatic] Dependency upgrades (#824)
[Automatic] Dependency upgrades (#828)
[Automatic] Dependency upgrades: ipykernel, packaging (#838)
[Automatic] Dependency upgrades: imageio, ipykernel, napari, numpy, sentry (#850)
[Automatic] Dependency upgrades: imagecodecs, ipykernel, numpy, psygnal (#859)
[Automatic] Dependency upgrades: pydantic, pygments, xlsxwriter (#874)
[Automatic] Dependency upgrades: imageio, packaging, scipy, xlsxwriter (#878)
[Automatic] Dependency upgrades: ipykernel, requests, sentry, xlsxwriter (#884)
[Automatic] Dependency upgrades: h5py, imagecodecs, imageio, ipykernel, pandas, sentry, tifffile (#889)
[Automatic] Dependency upgrades: ipython, pyqt5 (#893)
[Automatic] Dependency upgrades: imageio, ipykernel, ipython, numpy, openpyxl, psygnal, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, tifffile, xlsxwriter (#897)
[Automatic] Dependency upgrades: imageio, psygnal (#905)
[Automatic] Dependency upgrades: ipython, magicgui, scipy, sentry-sdk, tifffile (#906)
[Automatic] Dependency upgrades: imagecodecs, imageio, ipykernel, openpyxl, pydantic, pyinstaller, qtawesome, qtconsole, sentry-sdk, tifffile, xlsxwriter (#908)
[Automatic] Dependency upgrades: imageio, ipykernel, ipython, pandas, psygnal, pydantic, pygments, pyinstaller, qtpy, sentry-sdk, tifffile (#917)

0.14.6 - 2022-11-13
🐛 Bug Fixes

Fix bug when loading already created project causing hide of ROI layer (#787)

0.14.5 - 2022-11-09
🚀 Features

Add option for ensure type in EventedDict and use it to validate profiles structures (#776)
Add option to create issue from error report dialog (#782)
Add option for multiline field in algorithm parameters (#766)

🐛 Bug Fixes

Fix scalebar color (#774)
Fix bug when saving segmentation parameters in mask analysis (#781)
Fix multiple error related to loading new file in interactive mode (#784)

🚜 Refactor

Optimize CLI actions (#772)
Clean warnings about threshold methods (#783)

Build

(deps) Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775)

0.14.4 - 2022-10-24
🚀 Features

Load alternatives labeling when open PartSeg projects in napari (#731)
Add option to toggle scale bar (#733)
Allow customize settings directory using the PARTSEG_SETTINGS_DIR environment variable (#751)
Separate recent algorithms from general application settings (#752)
Add multiple otsu as threshold method with selection range of components (#710)
Add function to load components from Mask Segmentation with background in ROI Analysis (#768)

🐛 Bug Fixes

Fix typos
Fix get_theme calls to prepare for napari 0.4.17 (#729)
Fix saving pipeline from GUI (#756)
Fix profile export/import dialogs (#761)
Enable compare button if ROI is available (#765)
Fix bug in cut with roi to do not make black artifacts (#767)

🧪 Testing

Add new build and inspect wheel action (#747)

⚙️ Miscellaneous Tasks

Prepare pyinstaller configuration for napari 0.4.17 (#748)
Add ruff linter (#754)

Bugfix

Fix sentry tests (#742)
Fix reporting error in load settings from drive (#725)

Build

(deps) Bump actions/checkout from 2 to 3 (#716)
(deps) Bump actions/download-artifact from 1 to 3 (#709)

0.14.3 - 2022-08-18
🐛 Bug Fixes

Delay setting image if an algorithm is still running (#627)
Wrong error report when no component is found in restartable segmentation algorithm. (#633)
Fix process of build documentation (#653)

🚜 Refactor

Clean potential vulnerabilities (#630)

🧪 Testing

Add more tests for common GUI elements (#622)
Report coverage per package. (#639)
Update conda environment to not use PyQt5 in test (#646)
Add tests files to calculate coverage (#655)

Build

(deps) Bump qtpy from 2.0.1 to 2.1.0 in /requirements (#613)
(deps) Bump pyinstaller from 5.0.1 to 5.1 in /requirements (#629)
(deps) Bump tifffile from 2022.4.28 to 2022.5.4 in /requirements (#619)
(deps) Bump codecov/codecov-action from 1 to 3 (#637)
(deps) Bump requests from 2.27.1 to 2.28.0 in /requirements (#647)
(deps) Bump actions/setup-python from 3 to 4 (#648)
(deps) Bump pyqt5 from 5.15.6 to 5.15.7 in /requirements (#652)
(deps) Bump sentry-sdk from 1.5.12 to 1.6.0 in /requirements (#659)
(deps) Bump numpy from 1.22.4 to 1.23.0 in /requirements (#660)
(deps) Bump lxml from 4.9.0 to 4.9.1 in /requirements (#665)
(deps) Bump mahotas from 1.4.12 to 1.4.13 in /requirements (#662)
(deps) Bump pyinstaller from 5.1 to 5.2 in /requirements (#667)

0.14.2 - 2022-05-05
🐛 Bug Fixes

Fix bug in save label colors between sessions (#610)
Register PartSeg plugins before start napari widgets. (#611)
Mouse interaction with components work again after highlight. (#620)

🚜 Refactor

Limit test run (#603)
Filter and solve warnings in tests (#607)
Use QAbstractSpinBox.AdaptiveDecimalStepType in SpinBox instead of hardcoded bounds (#616)
Clean and test PartSeg.common_gui.universal_gui_part (#617)

📚 Documentation

Update changelog (#621)

🧪 Testing

Speedup test by setup cache for pip (#604)
Setup cache for azure pipelines workflows (#606)

Build

(deps) Bump sentry-sdk from 1.5.10 to 1.5.11 in /requirements (#615)

0.14.1 - 2022-04-27
🚀 Features

Use pygments for coloring code in exception window (#591)
Add option to calculate Measurement per Mask component (#590)

🐛 Bug Fixes

Update build wheels and sdist to have proper version tag (#583)
Fix removing the first measurement entry in the napari Measurement widget (#584)
Fix compatybility bug for conda Pyside2 version (#595)
Error when synchronization is loaded and new iloaded image has different dimensionality than currently loaded. (#598)

🚜 Refactor

Refactor the create batch plan widgets and add test for it (#587)
Drop napari below 0.4.12 (#592)
Update the order of ROI Mask algorithms to be the same as in older PartSeg versions (#600)

Build

(deps) Bump partsegcore-compiled-backend from 0.13.11 to 0.14.0 in /requirements (#582)
(deps) Bump simpleitk from 2.1.1 to 2.1.1.2 in /requirements (#589)
(deps) Bump pyinstaller from 4.10 to 5.0 in /requirements (#586)

0.14.0 - 2022-04-14
🚀 Features

Allow to set zoom factor from interface in Search Label napari plugin (#538)
Add controlling of zoom factor of search ROI in main GUI (#540)
Better serialization mechanism allow for declaration data structure migration locally (#462)
Make `*.obsep" file possible to load in PartSeg Analysis (#564)
Add option to extract measurement profile or roi extraction profile from batch plan (#568)
Allow import calculation plan from batch result excel file (#567)
Improve error reporting when fail to deserialize data (#574)
Launch PartSeg GUI from napari (#581)

🐛 Bug Fixes

Fix "Show selected" rendering mode in PartSeg ROI Mask (#565)

🚜 Refactor

Store PartSegImage.Image channels as separated arrays (#554)
Remove deprecated modules. (#429)
Switch serialization backen to nme (#569)

📚 Documentation

Update changelog and add new badges to readme (#580)

🧪 Testing

Add test of creating AboutDialog (#539)
Setup test for python 3.10. Disable class_generator test for this python (#570)

Bugfix

Add access by operator [] to pydantic.BaseModel base structures for keep backward compatybility (#579)

Build

(deps) Bump sentry-sdk from 1.5.2 to 1.5.3 in /requirements (#512)
(deps) Bump ipython from 8.0.0 to 8.0.1 in /requirements (#513)
(deps) Bump pandas from 1.3.5 to 1.4.0 in /requirements (#514)
(deps) Bump oiffile from 2021.6.6 to 2022.2.2 in /requirements (#521)
(deps) Bump numpy from 1.22.1 to 1.22.2 in /requirements (#524)
(deps) Bump tifffile from 2021.11.2 to 2022.2.2 in /requirements (#523)
(deps) Bump qtpy from 2.0.0 to 2.0.1 in /requirements (#522)
(deps) Bump sentry-sdk from 1.5.3 to 1.5.4 in /requirements (#515)
(deps) Bump pyinstaller from 4.8 to 4.10 in /requirements (#545)
(deps) Bump pillow from 9.0.0 to 9.0.1 in /requirements (#549)
(deps) Bump sphinx from 4.4.0 to 4.5.0 in /requirements (#561)
(deps) Bump tifffile from 2022.2.9 to 2022.3.25 in /requirements (#562)
(deps) Bump sympy from 1.10 to 1.10.1 in /requirements (#556)
(deps) Bump sentry-sdk from 1.5.7 to 1.5.8 in /requirements (#557)

0.13.15
Bug Fixes

Using translation instead of translation_grid for shifting layers. (#474)
Bugs in napari plugins (#478)
Missing mask when using roi extraction from napari (#479)
Fix segmentation fault on macos machines (#487)
Fixes for napari 0.4.13 (#506)

Documentation

Create 0.13.15 release (#511)
Add categories and preview page workflow for the napari hub (#489)

Features

Assign properties to mask layer in napari measurement widget (#480)

Build

Bump qtpy from 1.11.3 to 2.0.0 in /requirements (#498)
Bump pydantic from 1.8.2 to 1.9.0 in /requirements (#496)
Bump sentry-sdk from 1.5.1 to 1.5.2 in /requirements (#497)
Bump sphinx from 4.3.1 to 4.3.2 in /requirements (#500)
Bump pyinstaller from 4.7 to 4.8 in /requirements (#502)
Bump pillow from 8.4.0 to 9.0.0 in /requirements (#501)
Bump requests from 2.26.0 to 2.27.1 in /requirements (#495)
Bump numpy from 1.21.4 to 1.22.0 in /requirements (#499)
Bump numpy from 1.22.0 to 1.22.1 in /requirements (#509)
Bump sphinx from 4.3.2 to 4.4.0 in /requirements (#510)

0.13.14
Bug Fixes

ROI alternative representation (#471)
Change additive to translucent in rendering ROI and Mask (#472)

Features

Add morphological watershed segmentation (#469)
Add Bilateral image filter (#470)

0.13.13
Bug Fixes

Fix bugs in the generation process of the changelog for release. (#428)
Restoring ROI on home button click in compare viewer (#443)
Fix Measurement name prefix in bundled PartSeg. (#458)
Napari widgets registration in pyinstaller bundle (#465)
Hide points button if no points are loaded, hide Mask checkbox if no mask is set (#463)
Replace Label data instead of adding/removing layers - fix blending layers (#464)

Features

Add threshold information in layer annotation in the Multiple Otsu ROI extraction method (#430)
Add option to select rendering method for ROI (#431)
Add callback mechanism to ProfileDict, live update of ROI render parameters (#432)
Move the info bar on the bottom of the viewer (#442)
Add options to load recent files in multiple files widget (#444)
Add ROI annotations as properties to napari labels layer created by ROI Extraction widgets (#445)
Add signals to ProfileDict, remove redundant synchronization mechanisms (#449)
Allow ignoring updates for 21 days (#453)
Save all components if no components selected in mask segmentation (#456)
Add modal dialog for search ROI components (#459)
Add full measurement support as napari widget (#460)
Add search labels as napari widget (#467)

Refactor

Export common code for load/save dialog to one place (#437)
Change most of call QFileDialog to more generic code (#440)

Testing

Add test for PartSeg.common_backend module (#433)

0.13.12
Bug Fixes

Importing the previous version of settings (#406)
Cutting without masking data (#407)
Save in subdirectory in batch plan (#414)
Loading plugins for batch processing (#423)

Features

Add randomization option for correlation calculation (#421)
Add Imagej TIFF writer for image. (#405)
Mask create widget for napari (#395)
In napari roi extraction method show information from roi extraction method (#408)
Add *[0-9].tif button in batch processing window (#412)
Better label representation in 3d view (#418)

Refactor

Use Font Awesome instead of custom symbols (#424)

0.13.11
Bug Fixes

Adding mask in Prepare Plan for batch (#383)
Set proper completion mode in SearchComboBox (#384)
Showing warnings on the error with ROI load (#385)

Features

Add CellFromNucleusFlow "Cell from nucleus flow" cell segmentation method (#367)
When cutting components in PartSeg ROI mask allow not masking outer data (#379)
Theme selection in GUI (#381)
Allow return points from ROI extraction algorithm (#382)
Add measurement to get ROI annotation by name. (#386)
PartSeg ROI extraction algorithms as napari plugins (#387)
Add Pearson, Mander's, Intensity, Spearman colocalization measurements (#392)
Separate standalone napari settings from PartSeg embedded napari settings (#397)

Performance

Use faster calc bound function (#375)

Refactor

Remove CustomApplication (#389)

0.13.10

change tiff save backend to ome-tiff
add DistanceROIROI and ROINeighbourhoodROI measurements

0.13.9

annotation show bugfix

0.13.8

napari deprecation fixes
speedup simple measurement
bundle plugins initial support

0.13.7

add measurements widget for napari
fix bug in pipeline usage

0.13.6

Hotfix release
Prepare for a new napari version

0.13.5

Small fixes for error reporting
Fix mask segmentation

0.13.4

Bugfix for outdated profile/pipeline preview

0.13.3

Fix saving roi_info in multiple files and history

0.13.2

Fix showing label in select label tab

0.13.1

Add Haralick measurements
Add obsep file support

0.13.0

Add possibility of custom input widgets for algorithms
Switch to napari Colormaps instead of custom one
Add points visualization
Synchronization widget for builtin (View menu) napari viewer
Drop Python 3.6

0.12.7

Fixes for napari 0.4.6

0.12.6

Fix prev_mask_get
Fix cache mechanism on mask change
Update PyInstaller build

0.12.5

Fix bug in pipeline execute

0.12.4

Fix ROI Mask windows related build (signal not properly connected)

0.12.3

Fix ROI Mask

0.12.2

Fix windows bundle

0.12.1

History of last opened files
Add ROI annotation and ROI alternatives
Minor bugfix

0.12.0

Toggle multiple files widget in View menu
Toggle Left panel in ROI Analysis in View Menu
Rename Mask Segmentation to ROI Mask
Add documentation for interface
Add Batch processing tutorial
Add information about errors to batch processing output file
Load image from the batch prepare window
Add search option in part of list and combo boxes
Add drag and drop mechanism to load list of files to batch window.

0.11.5

add side view to viewer
fix horizontal view for Measurements result table

0.11.4

bump to napari 0.3.8 in bundle
fix bug with not presented segmentation loaded from project
add frame (1 pix) to image cat from base one based on segmentation
pin to Qt version to 5.14

0.11.3

prepare for napari 0.3.7
split napari io plugin on multiple part
better reporting for numpy array via sentry
fix setting color for mask marking

0.11.2

Speedup image set in viewer using async calls
Fix bug in long name of sheet with parameters

0.11.1

Add screenshot option in View menu
Add Voxels measurements

0.11.0

Make sprawl algorithm name shorter
Unify capitalisation of measurement names
Add simple measurements to mask segmentation
Use napari as viewer
Add possibility to preview additional output of algorithms (In View menu)
Update names of available Algorithm and Measurement to be more descriptive.

0.10.8

fix synchronisation between viewers in Segmentation Analysis
fix batch crash on error during batch run, add information about file on which calculation fails
add changelog preview in Help > About

0.10.7

in measurements, on empty list of components mean will return 0

0.10.6

fix border rim preview
fix problem with size of image preview
zoom with scroll and moving if rectangle zoom is not marked

0.10.5

make PartSeg PEP517 compatible.
fix multiple files widget on Windows (path normalisation)

0.10.4

fix slow zoom

0.10.3

deterministic order of elements in batch processing.

0.10.2

bugfixes

0.10.1

bugfixes

0.10.0

Add creating custom label coloring.
Change execs interpreter to python 3.7.
Add masking operation in Segmentation Mask.
Change license to BSD.
Allow select root type in batch processing.
Add median filter in preview.

0.9.7

fix bug in compare mask

0.9.6

fix bug in loading project with mask
upgrade PyInstaller version (bug GHSA-7fcj-pq9j-wh2r)

0.9.5

fix bug in loading project in "Segmentation analysis"

0.9.4

read mask segmentation projects
choose source type in batch
add initial support to OIF and CZI file format
extract utils to PartSegCore module
add automated tests of example notebook
reversed mask
load segmentation parameters in mask segmentation
allow use sprawl in segmentation tool
add radial split of mask for measurement
add all measurement results in batch, per component sheet

0.9.3

start automated build documentation
change color map backend and allow for user to create custom color map.
segmentation compare
update test engines
support of PySide2

0.9.2.3

refactor code to make easier create plugin for mask segmentation
create class base updater for update outdated algorithm description
fix save functions
fix different bugs

0.9.2.2

extract static data to separated package
update marker of fix range and add mark of gauss in channel control

0.9.2.1

add VoteSmooth and add choosing of smooth algorithm

0.9.2


add pypi base check for update


remove resetting image state when change state in same image


in stack segmentation add options to picking components from segmentation's


in mask segmentation add:

preview of segmentation parameters per component,
save segmentation parameters in save file
new implementation of batch mode.



0.9.1


Add multiple files widget


Add Calculating distances between segmented object and mask


Batch processing plan fixes:

Fix adding pipelines to plan
Redesign mask widget



modify measurement backend to allow calculate multi channel measurements.


0.9
Begin of changelog

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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