Releases: kreshuklab/panseg
Releases · kreshuklab/panseg
2.0.1
What's Changed
- feat: napari 0.7 by @KRiedmiller in #557
- ci: test on release on all platforms, update actions by @KRiedmiller in #561
- docs: 2.0 release notes by @KRiedmiller in #562
- fix: multichannel export by @KRiedmiller in #565
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #564
Full Changelog: 2.0.0...2.0.1
2.0.0
What's Changed
- feat: stable release of Panseg 2.0
Older changes since last stable version (1.8.0)
- fix: links in docs, docstring warning and theme override by @qin-yu in #269
- fix(docs): teach Qt to find napari icons by @qin-yu in #271
- fix(installation): remove old configs if
KeyError| macOS installation by @qin-yu in #277 - fixes PlantSeg crash on apple silicon #273 by @lorenzocerrone in #275
- check and free VRAM for prediction with oversized patch by @qin-yu in #272
- use RangeSlider to fix #278 | handle
Noneimage by @qin-yu in #279 - ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #284
- Unify and standardise logging in PlantSeg v2 by @qin-yu in #296
- Add important widgets and improve logger further by @qin-yu in #297
- PlantSeg.Core:
ModelZoo,PlantSegImage, andVoxelSizeby @qin-yu in #298 - Tests: Fix all existing tests by @qin-yu in #299
- Use Codecov by @qin-yu in #300
- Automatic patch shape recommendation by @qin-yu in #302
- Test and refactor
.coreandfunctionals.dataprocessingby @qin-yu in #303 - fix(widget-IO): temp fix #282 and auto generate layer name by @qin-yu in #304
- Properly refresh ComboBox choices with functions by @qin-yu in #305
- Compute best patch and halo shapes by default, reduce user effort by @qin-yu in #307
- Make VoxelSize iterable and array-like, remove
.is_validby @qin-yu in #310 - refactor: use
magicgui.types.Separatorby @qin-yu in #311 - Fix TIFF default layer name and hide key widget by @qin-yu in #312
- Fix size finder and widgets for 2D UNet by @qin-yu in #313
- Improve model filters | Use RadioButtons | Custom modality by @qin-yu in #314
- Group widgets for batch
.hide()/.show()by @qin-yu in #317 - Fix and document distance transform watershed for 2D pmaps/images by @qin-yu in #318
- PlantSeg v2 docs base by @qin-yu in #320
- Recover and document over-/under-seg fix by nuclei by @qin-yu in #321
- PlantSeg v2: Finalise docs by @qin-yu in #322
- Add un-/re-do and save-/load-states for proofreading tool by @qin-yu in #323
- Document missing button issue by @qin-yu in #327
- Fix and integrate lifted multicut widget into agglomeration widget by @qin-yu in #328
- Refactor and recover widgets: cropping and label processing by @qin-yu in #330
- PlantSeg v2: Final polishment of GUI by @qin-yu in #326
- refactor(GUI): rename and reorder widgets for intuitive sequential flow by @qin-yu in #331
- PlantSeg v2: full codebase refactor with unified task framework, enhanced prediction/proofreading, and metadata handling by @lorenzocerrone in #285
- Fix version related issues: bump version, comparison and Anaconda upload by @qin-yu in #333
- fix h5 export by @lorenzocerrone in #335
- fix: avoid reading logo file from docs folder by @qin-yu in #336
- New export widget by @lorenzocerrone in #341
- Fix perfomance on mac by @lorenzocerrone in #337
- Fix voxel size unit by @qin-yu in #343
- fix (#344): update windows install instructions by @lorenzocerrone in #347
- Match conda recipe and include
package_datalogo by @qin-yu in #348 - ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #349
- fix: #353 by @lorenzocerrone in #354
- Proofreading improvements by @lorenzocerrone in #355
- Improved Headless + gui by @lorenzocerrone in #356
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #357
- fix: allow more runtime errors in
find_batch_size()by @qin-yu in #359 - fix: allow but warn all runtime errors in 3D
find_a_max_patch_shape()by @qin-yu in #361 - fix: widgets should have optional arg for updating other widgets by @qin-yu in #362
- fix(env): Pydantic v2.10 causes bioimageio.spec issues by @qin-yu in #363
- Fix and promote PlantSeg v1 installation by @qin-yu in #364
- ci(docs): fetch all git history/tags/branches for MkDocs dates by @qin-yu in #366
- Fix smart load | Make extension check case-insensitive by @qin-yu in #368
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #369
- Add image pair operation widget/task/functionals/docs by @qin-yu in #370
- Add inference API and task for all BioImage.IO Model Zoo models by @qin-yu in #338
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #378
- Fix
anaconda_telemetryerror in CI by @qin-yu in #382 - Add tests for and fix nuclei-assisted post-processing by @qin-yu in #381
- Fix Napari relared tests fails by @adambasha0 in #376
- Fix and test advanced prediction with 2D UNet by @qin-yu in #384
- Avoid BioImage.IO Core downloading everything from model zoo entries by @qin-yu in #386
- docs(proofreading): add simple tutorial for proofreading widget by @qin-yu in #387
- Use older ubuntu runner in CI by @qin-yu in #390
- refactor: algorithm and readability of patch size finder by @qin-yu in #388
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #391
- fix(ci): fix Found invalid version predicate in "DOC_RELEASE" by @qin-yu in #394
- CI/tests on pr by @KRiedmiller in #399
- build: pin xarray due to #396 by @qin-yu in #403
- Progress bar by @KRiedmiller in #397
- ci: add workflow for release by @KRiedmiller in #401
- style: uniform quotes, black compatibility by @KRiedmiller in #404
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #405
- ci: build installer by @KRiedmiller in #407
- fix: broken docs due to incompatible python 3.10 by @KRiedmiller in #408
- fix: dependencies by @KRiedmiller in #409
- add refresh button for keys in zarr/h5 files by @KRiedmiller in #402
- Better splash screen by @KRiedmiller in #411
- installer by @KRiedmiller in #412
- fix: unbound variable by @KRiedmiller in #413
- docs: remove outdated section by @KRiedmiller in #414
- fix: update version number shown in the installer by @KRiedmiller in #415
- docs: improve installation instructions by @KRiedmiller in #416
- fix: set prerelease on prereleases by @KRiedmiller in #420
- docs: fix typo by @KRiedmiller in #421
- fix: testing Cellpose data is moved to OSF by @qin-yu in #422
- fix(IO): update
create_zarr()forzarrv3 by @qin-yu in #423 - Show removed instance for foreground filter API/task/widget by @qin-yu in #417
- ci: add commitlint workflow for PR title enforcement by @qin-yu in #424
- build: lift
xarrayandpydanticrestrictions by @qin-yu in...
2.0.0rc18
What's Changed
- feat: export meshes from segmentations by @KRiedmiller in #530
- feat: automatic detection of input layout by @KRiedmiller in #531
- feat: invert axis during import by @KRiedmiller in #533
- fix: guard zmesh import by @KRiedmiller in #556
Full Changelog: 2.0.0rc17...2.0.0rc18
2.0.0rc17
2.0.0rc15
What's Changed
- feat: export meshes from segmentations by @KRiedmiller in #530
- feat: automatic detection of input layout by @KRiedmiller in #531
- feat: invert axis by @KRiedmiller in #533
- fix: update model filter option after training by @KRiedmiller in #537
- fix: correct the choices in the workflow editor for mesh export by @KRiedmiller in #538
- fix: bbox offset by @KRiedmiller in #542
- fix: bigtiff export by @KRiedmiller in #549
- fix: pin versions by @KRiedmiller in #545
- test: io h5 and tiff by @KRiedmiller in #553
- refactor: rename in workflows by @KRiedmiller in #554
Full Changelog: 2.0.0rc10...2.0.0rc15
2.0.0rc14
What's Changed
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in https://github.com/kreshuklab/plant-seg/pull/529
- feat: release 2.0 pop-up by @KRiedmiller in https://github.com/kreshuklab/plant-seg/pull/522
Full Changelog: kreshuklab/plant-seg@2.0.0rc13...2.0.0rc14
2.0.0rc13
What's Changed
- fix: bbox offset (#542) by @KRiedmiller in https://github.com/kreshuklab/plant-seg/pull/546
Full Changelog: kreshuklab/plant-seg@2.0.0rc12...2.0.0rc13
2.0.0rc12
What's Changed
- fix: rescaling during export by @KRiedmiller in https://github.com/kreshuklab/plant-seg/pull/528
Full Changelog: kreshuklab/plant-seg@2.0.0rc11...2.0.0rc12
2.0.0rc11
Full Changelog: kreshuklab/plant-seg@2.0.0rc10...2.0.0rc11
2.0.0rc10
What's Changed
- ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in https://github.com/kreshuklab/plant-seg/pull/524
- fix: model downloads by @KRiedmiller in https://github.com/kreshuklab/plant-seg/pull/526
Full Changelog: kreshuklab/plant-seg@2.0.0rc9...2.0.0rc10