Releases: kreshuklab/plant-seg
Releases · kreshuklab/plant-seg
2.0.0a5
What's Changed
- ci(pre-commit.ci): autoupdate by @pre-commit-ci in #349
- fix: #353 by @lorenzocerrone in #354
- Proofreading improvements by @lorenzocerrone in #355
- Improved Headless + gui by @lorenzocerrone in #356
Full Changelog: 2.0.0a4...2.0.0a5
2.0.0a4
What's Changed
- fix (#344): update windows install instructions by @lorenzocerrone in #347
- Match conda recipe and include
package_data
logo by @qin-yu in #348
Full Changelog: 2.0.0a3...2.0.0a4
2.0.0a3
What's Changed
- New export widget by @lorenzocerrone in #341
- Fix perfomance on mac by @lorenzocerrone in #337
- Fix voxel size unit by @qin-yu in #343
Full Changelog: 2.0.0a2...2.0.0a3
2.0.0a2
What's Changed
Features
- feat(pred): check and free VRAM for prediction with oversized patch by @qin-yu in #272
- Automatic patch shape recommendation by @qin-yu in #302
- Compute best patch and halo shapes by default, reduce user effort by @qin-yu in #307
- Add un-/re-do and save-/load-states for proofreading tool by @qin-yu in #323
Infrastructure & GUI
and recover after infra refactor
- 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
, andVoxelSize
by @qin-yu in #298 - Tests: Fix all existing tests by @qin-yu in #299
- Test and refactor
.core
andfunctionals.dataprocessing
by @qin-yu in #303 - Properly refresh ComboBox choices with functions by @qin-yu in #305
- Make VoxelSize iterable and array-like, remove
.is_valid
by @qin-yu in #310 - refactor: use
magicgui.types.Separator
by @qin-yu in #311 - 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 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
Bug fixes
- fix(cropping): use RangeSlider to fix #278 | handle
None
image by @qin-yu in #279 - fix(widget-IO): temp fix #282 and auto generate layer name by @qin-yu in #304
- Fix TIFF default layer name and hide key widget by @qin-yu in #312
- Fix and document distance transform watershed for 2D pmaps/images by @qin-yu in #318
- fix h5 export by @lorenzocerrone in #335
- fix: avoid reading logo file from docs folder by @qin-yu in #336
CI/CD
- Use
pre-commit
by @qin-yu in #263 - chore: migrate from
bumpversion
tobump-my-version
by @qin-yu in #266 - chore(pre-commit): add conventional commits by @qin-yu in #267
- 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
- Use Codecov by @qin-yu in #300
- Fix version related issues: bump version, comparison and Anaconda upload by @qin-yu in #333
Docs
- 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
- 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
- Record issue missing button by @qin-yu in #327
New Contributors
- @pre-commit-ci made their first contribution in #265
Full Changelog: 1.8.0...2.0.0-alpha
1.8.0
What's Changed
- 🏠 PlantSeg was moved to https://github.com/kreshuklab/plant-seg/
Features
- 🦒 Execute PlantSeg-compatible models in 🦒 BioImage.IO Model Zoo 🐿️ by @qin-yu in #247 & #248
- 📏 Refactor rescaling widget | Rearrange widgets by @lorenzocerrone in #249
- 🤖 Recommend users a halo for U-Nets by @qin-yu in #252
Documentation
- Doc: Data/models, train/add new models, Jupyter Book remnant by @qin-yu in #240
- Doc: API and screenshots by @lorenzocerrone in #249
- Doc: Fix docs build in CI by @lorenzocerrone in #257
- Doc: Fix and update rescaling widget screenshot docs by @qin-yu in #259
- Doc: Add revision date and committer plugins by @qin-yu in #260
Tests
Bug Fix
- Type Fix:
np.array
is not a type, change tonp.ndarray
by @qin-yu in #231 - Fix Legacy GUI after v1.7.0 by @qin-yu in #237
- Fix
CYX
/CZYX
pad/halo, fixio.zarr
/tests, fix typing, refactor model load by @qin-yu in #233 - Headless: Handle multi-channel prediction output and add docs by @qin-yu in #239
- Test Fix: always-skipped test and misleading name by @qin-yu in #262
Full Changelog: 1.7.0...1.8.0
1.7.0
What's Changed
- 🥳 PlantSeg is on conda-forge as
plant-seg
at anaconda.org/conda-forge/plant-seg - 📖 PlantSeg documentation is published at hci-unihd.github.io/plant-seg/
Bug Fix
- Fix multi-channel output layers in Napari by @qin-yu in #184
- Fix halo implementation and tiling artefact by @qin-yu in #220 & #223
- Fix voxel size precision and font size in Napari GUI by @qin-yu in #227
Features
- New
key
&channel
selection for all interfaces by @qin-yu @lorenzocerrone in #165, #184 & #212 - Add option to set home_path via PLANTSEG_HOME env-variable. by @tibuch in #170
- Add support for training by @wolny in #159
- Add Lifted MultiCut in GUI by @qin-yu in #184
- Add option to only run official models in "Try all Available Models" by @qin-yu in #207
- Add widget: remove objects using a probability map by @qin-yu in #202
- Add validation, adaptation and halo to prediction widgets by @qin-yu in #211
- Add widget managers and rearrange tabs by @lorenzocerrone @qin-yu in #221 & #227
Models
- Ensure compatibility with models trained with pytorch-3dunet by @wolny in #160
- Add a generic nuclear model for GoNuclear paper by @qin-yu in #169 & #193
- Central model records by @qin-yu in #216
Documentation
- Improve docs and create website at https://hci-unihd.github.io/plant-seg/ by @qin-yu in #179, #191, #229 & #230
- Update mamba install by @jackyko1991 in #180
Full Changelog: 1.6.0...1.7.0
New Maintainer
- @qin-yu became a maintainer
New Contributors
Overall improvements and bug fixes
What's Changed
- Move models to zenodo by @wolny in #135
- Improved proofreading by @lorenzocerrone in #132
- Fix incorrect model weights on Zenodo by @wolny in #139
- Minor UI improvements by @lorenzocerrone in #137
- Remove pytorch-3dunet dependency by @wolny in #141
- Improve batch_size selection by @wolny in #147
- Better models names by @lorenzocerrone in #148
- Add nice widgets callbacks by @lorenzocerrone in #149
- Read write zarrs by @Mohinta2892 in #150
- Add zarr support by @lorenzocerrone in #151
New Contributors
- @Mohinta2892 made their first contribution in #150
Full Changelog: 1.5.2...1.6.0
Interactive PlantSeg with napari viewer
Major plantseg update!
What's new:
- A new interactive plantseg mode using napari as a viewer!
- build-in segmentation proofreading
- New experimental headless mode
- New workflows
Usability improvment
- Config file is validate before pipeline start and additional sanity checks have been added.
- Errors are now more human friendly.
- New Meristem 3D/2D models available.
- Several bug fixes.
- clean conda recipe
Usability improvment
- Config file is validate before pipeline start and additional sanity checks have been added.
- Errors are now more human friendly.
- New Meristem 3D/2D models available.
- Several bug fixes