Releases: kreshuklab/plant-seg
Releases · kreshuklab/plant-seg
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
Introducing compatibility with 2D
1.1.0 Bump version: 1.0.10 → 1.1.0
1.0.5
Improved GUI, code refactoring
1.0.4 update version for release
1.0.3
update version