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 https://github.com/kreshuklab/plant-seg/pull/247 & https://github.com/kreshuklab/plant-seg/pull/248
• 📏 Refactor rescaling widget | Rearrange widgets by @lorenzocerrone in https://github.com/kreshuklab/plant-seg/pull/249
  • Improve use of Enum as widget choices and fix types by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/256
• 🤖 Recommend users a halo for U-Nets by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/252

Documentation

• Doc: Data/models, train/add new models, Jupyter Book remnant by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/240
• Doc: API and screenshots by @lorenzocerrone in https://github.com/kreshuklab/plant-seg/pull/249
  • Doc: Fix docs build in CI by @lorenzocerrone in https://github.com/kreshuklab/plant-seg/pull/257
  • Doc: Fix and update rescaling widget screenshot docs by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/259
• Doc: Add revision date and committer plugins by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/260

Tests

• Tests for rescaling widget by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/258

Bug Fix

• Type Fix: np.array is not a type, change to np.ndarray by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/231
• Fix Legacy GUI after v1.7.0 by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/237
• Fix CYX/CZYX pad/halo, fix io.zarr/tests, fix typing, refactor model load by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/233
• Headless: Handle multi-channel prediction output and add docs by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/239
• Test Fix: always-skipped test and misleading name by @qin-yu in https://github.com/kreshuklab/plant-seg/pull/262

Full Changelog: kreshuklab/plant-seg@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

• @qin-yu made their first contribution in #165
• @tibuch made their first contribution in #170
• @jackyko1991 made their first contribution in #180

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

Merge remote-tracking branch 'origin/master'

Improved GUI, code refactoring

1.0.4

update version for release

1.0.3

update version