0.3.0

This release introduces two new features:

• Segmentation from shapes other than bounding boxes (ellipses and polygons)
• Automatic instance segmentation for 3d

In addition we have refactored and improved the training code, which speeds up model finetuning.

See below for a more detailed changelog.

What's Changed

• More doc updates by @constantinpape in #162
• Using predictor device when setting image embedding by @JoOkuma in #163
• micro-sam napari plugin by @GenevieveBuckley in #165
• Fix YAML formatting errors so Github actions will run by @GenevieveBuckley in #166
• Implement 3d auto segmentation by @constantinpape in #169
• fixed annotator_3d missing embedding path by @tc2fh in #170
• Supporting Apple Silicon devices by @GenevieveBuckley in #178
• Add MPS Pytorch support for batched_mask_to_box function by @GenevieveBuckley in #180
• Add support for MPS device by @constantinpape in #176
• Clear torch memory cache in tests by @GenevieveBuckley in #179
• Implement runtime benchmarks by @constantinpape in #182
• Add initial support for vit tiny model from mobileSAM by @constantinpape in #174
• Clean up by @constantinpape in #184
• Trying to improve performance for MPS by @constantinpape in #183
• Add docstring about how to run benchmarks by @GenevieveBuckley in #187
• Implement RLE computation with numba by @constantinpape in #190
• Refactoring Iterative Training Scheme by @anwai98 in #192
• Implement prototype for segmentation of complex shapes by @constantinpape in #196
• Fix CLI for embedding precomputation by @constantinpape in #209
• Refactor Prompt Generators by @anwai98 in #210
• Fix tuple annotations by @constantinpape in #213
• Fix prompt gens by @constantinpape in #211
• Change keybinding for volume segmentation (remove clash with napari layer visibility keybinding) by @GenevieveBuckley in #207
• Next release by @constantinpape in #172
• Implement integration test for training by @constantinpape in #198
• Minor Fix - Livecell Patch Shape by @anwai98 in #216
• Add imagecodecs dependency by @constantinpape in #217
• Update Casting of Instance Estimations by @anwai98 in #218
• Update Documentation by @anwai98 in #220
• Fix Imports in Livecell Inference by @anwai98 in #219
• Fix Box Prompting in Inference by @anwai98 in #221
• Merge fixes into master by @constantinpape in #224
• Histopatho model by @constantinpape in #193
• Add prediction with box prompts to training integration tests by @constantinpape in #225
• Bump version for release 0.3.0 by @constantinpape in #226

New Contributors

• @tc2fh made their first contribution in #170

Full Changelog: 0.2.2...0.3.0