Partseg

🚀 Features

- Allow to set zoom factor from interface in Search Label napari plugin ([538](https://github.com/4DNucleome/PartSeg/pull/538))
- Add controlling of zoom factor of search ROI in main GUI ([540](https://github.com/4DNucleome/PartSeg/pull/540))
- Better serialization mechanism allow for declaration data structure migration locally ([462](https://github.com/4DNucleome/PartSeg/pull/462))
- Make \`\*.obsep" file possible to load in PartSeg Analysis ([564](https://github.com/4DNucleome/PartSeg/pull/564))
- Add option to extract measurement profile or roi extraction profile from batch plan ([568](https://github.com/4DNucleome/PartSeg/pull/568))
- Allow import calculation plan from batch result excel file ([567](https://github.com/4DNucleome/PartSeg/pull/567))
- Improve error reporting when fail to deserialize data ([574](https://github.com/4DNucleome/PartSeg/pull/574))
- Launch PartSeg GUI from napari ([581](https://github.com/4DNucleome/PartSeg/pull/581))

🐛 Bug Fixes

- Fix "Show selected" rendering mode in PartSeg ROI Mask ([565](https://github.com/4DNucleome/PartSeg/pull/565))

🚜 Refactor

- Store PartSegImage.Image channels as separated arrays ([554](https://github.com/4DNucleome/PartSeg/pull/554))
- Remove deprecated modules. ([429](https://github.com/4DNucleome/PartSeg/pull/429))
- Switch serialization backen to `nme` ([569](https://github.com/4DNucleome/PartSeg/pull/569))

📚 Documentation

- Update changelog and add new badges to readme ([580](https://github.com/4DNucleome/PartSeg/pull/580))

🧪 Testing

- Add test of creating AboutDialog ([539](https://github.com/4DNucleome/PartSeg/pull/539))
- Setup test for python 3.10. Disable class_generator test for this python ([570](https://github.com/4DNucleome/PartSeg/pull/570))

Bugfix

- Add access by operator \[\] to pydantic.BaseModel base structures for keep backward compatybility ([579](https://github.com/4DNucleome/PartSeg/pull/579))

Build

- *(deps)* Bump sentry-sdk from 1.5.2 to 1.5.3 in /requirements ([512](https://github.com/4DNucleome/PartSeg/pull/512))
- *(deps)* Bump ipython from 8.0.0 to 8.0.1 in /requirements ([513](https://github.com/4DNucleome/PartSeg/pull/513))
- *(deps)* Bump pandas from 1.3.5 to 1.4.0 in /requirements ([514](https://github.com/4DNucleome/PartSeg/pull/514))
- *(deps)* Bump oiffile from 2021.6.6 to 2022.2.2 in /requirements ([521](https://github.com/4DNucleome/PartSeg/pull/521))
- *(deps)* Bump numpy from 1.22.1 to 1.22.2 in /requirements ([524](https://github.com/4DNucleome/PartSeg/pull/524))
- *(deps)* Bump tifffile from 2021.11.2 to 2022.2.2 in /requirements ([523](https://github.com/4DNucleome/PartSeg/pull/523))
- *(deps)* Bump qtpy from 2.0.0 to 2.0.1 in /requirements ([522](https://github.com/4DNucleome/PartSeg/pull/522))
- *(deps)* Bump sentry-sdk from 1.5.3 to 1.5.4 in /requirements ([515](https://github.com/4DNucleome/PartSeg/pull/515))
- *(deps)* Bump pyinstaller from 4.8 to 4.10 in /requirements ([545](https://github.com/4DNucleome/PartSeg/pull/545))
- *(deps)* Bump pillow from 9.0.0 to 9.0.1 in /requirements ([549](https://github.com/4DNucleome/PartSeg/pull/549))
- *(deps)* Bump sphinx from 4.4.0 to 4.5.0 in /requirements ([561](https://github.com/4DNucleome/PartSeg/pull/561))
- *(deps)* Bump tifffile from 2022.2.9 to 2022.3.25 in /requirements ([562](https://github.com/4DNucleome/PartSeg/pull/562))
- *(deps)* Bump sympy from 1.10 to 1.10.1 in /requirements ([556](https://github.com/4DNucleome/PartSeg/pull/556))
- *(deps)* Bump sentry-sdk from 1.5.7 to 1.5.8 in /requirements ([557](https://github.com/4DNucleome/PartSeg/pull/557))

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)

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)

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)

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)

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)