0.4.0

What's Changed

• More comprehensive .gitignore file at repository root by @GenevieveBuckley in #222
• CI testing - automatic code coverage reports by @GenevieveBuckley in #214
• Simple GUI test for CI by @GenevieveBuckley in #223
• Improve test train by @constantinpape in #233
• Update CI on master by @constantinpape in #232
• Make numba optional by @constantinpape in #238
• Add documentation for how to run micro-sam via BAND by @constantinpape in #229
• Add LM Generalist Finetuning by @anwai98 in #228
• Fixes for test_training.py failures by @GenevieveBuckley in #245
• Add EM Generalist Finetuning (2) by @anwai98 in #247
• Developer documentation by @GenevieveBuckley in #243
• Documenation build script - add check for missing docs files by @GenevieveBuckley in #250
• Merge master into dev by @constantinpape in #252
• Add support for batched inference with prompts by @constantinpape in #253
• Implement singleton state and use it in the 2d annotator by @constantinpape in #240
• Add Histopathology Generalist Training by @anwai98 in #248
• Fix Bounding Box Sorting by @anwai98 in #257
• Refactor Iterative Prompting Evaluation by @anwai98 in #254
• Add 3d segmentation functionality by @constantinpape in #255
• Fix EM Generalist Raw Transform by @anwai98 in #259
• Update Evaluation - Iterative Prompting by @anwai98 in #260
• Embedding widget for napari plugin by @GenevieveBuckley in #235
• Use a consistent cache directory by @GenevieveBuckley in #268
• Fixup README 404s by @claydugo in #270
• Fix typo in function name _segment_slice_widget by @GenevieveBuckley in #273
• Update Description - LiveCELL Inference by @anwai98 in #271
• Use qtpy by @constantinpape in #275
• Experiments with Mask Inputs Probability by @anwai98 in #265
• Merge dev into master by @constantinpape in #278
• Keep master and dev in sync by @constantinpape in #279
• napari widget to set cache directory (for model weights and sample data downloads) by @GenevieveBuckley in #277
• Run github actiosns CI tests on Windows, Mac and Linux by @GenevieveBuckley in #267
• Improve device handling by @constantinpape in #251
• Increase test coverage by @constantinpape in #280
• Fixup typo by @claydugo in #281
• Fix Plugin Link by @anwai98 in #282
• Download models with pooch by @GenevieveBuckley in #276
• Add xxh128 version of hashes for model by @hmaarrfk in #284
• Update Rescaling Inputs by @anwai98 in #286
• Add Joint Training by @anwai98 in #288
• Fix load_checkpoint by @anwai98 in #290
• Update LiveCELL Specialist Fine-tuning by @anwai98 in #291
• Update livecell evaluation scripts by @constantinpape in #296
• New instance segmentation by @constantinpape in #297
• Update finetune_hela.py by @Mobinapournemat in #294
• Fix Resizing Input Prompts by @anwai98 in #299
• Minor fix to Instance Segmentation by @anwai98 in #302
• Simplify training implementations by @constantinpape in #301
• Make grid search functionality more flexible by @constantinpape in #300
• Update livecell finetuning by @anwai98 in #303
• Update LM Generalists by @anwai98 in #292
• Update LM Generalist Dist. Trafo. by @anwai98 in #306
• Update README.md - Minor doc fix by @anwai98 in #307
• Add EM Mito-Nuc Generalist by @anwai98 in #295
• Implement grid search for livecell training and update instance seg grid search by @constantinpape in #308
• Minor update to EM finetuning by @anwai98 in #309
• Minor typo in em mito nuc by @anwai98 in #311
• Add EM Boundaries Generalist by @anwai98 in #312
• Minor updates to finetuning desc. by @anwai98 in #314
• Update LiveCELL inference scripts by @anwai98 in #315
• Fix instance segmentation checkpoint loading by @anwai98 in #318
• Add livecell specialist results by @anwai98 in #317
• Add livecell (lm) generalist results by @anwai98 in #319
• Minor fix to livecell eval. scripts by @anwai98 in #316
• Minor fix to experiment path convention by @anwai98 in #323
• Refactor files in scripts by @anwai98 in #321
• Update mitonet results by @anwai98 in #325
• Update to new finetuned models by @constantinpape in #326
• Changes for new release by @constantinpape in #327

New Contributors

• @claydugo made their first contribution in #270
• @hmaarrfk made their first contribution in #284
• @Mobinapournemat made their first contribution in #294

Full Changelog: 0.3.0...0.4.0

0.3.0post1

Fix tests for conda forge.

0.3.0pos2

Release for 0.3.0 binaries.

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

0.2.2

What's Changed

• Refactor state precomputation by @constantinpape in #155
• Documentation updates by @constantinpape in #152
• Fixing typo 'f.atrs' to 'f.attrs' by @JoOkuma in #156
• Serialize amg state to the cpu so that it can be loaded without a GPU by @constantinpape in #157
• Make embedding file checks more robust by @constantinpape in #158
• Precompute embeddings in 2d example; set default box extension to 0.0… by @constantinpape in #159

New Contributors

• @JoOkuma made their first contribution in #156

Full Changelog: 0.2.1...0.2.2

0.2.1post1

Release for building binaries.

0.2.1

What's Changed

• Remove opencv dependency by @constantinpape in #147
• Fix amg state precomputation for image series annotator by @constantinpape in #148
• Support RGB data in micro_sam.evaluation.model_comparison by @constantinpape in #149
• Finetune example by @constantinpape in #150

Full Changelog: 0.2.0...0.2.1

Post release for binaries

Merge pull request #146 from computational-cell-analytics/post-release

Bump version and update texts for installer

0.2.0

What's Changed

• Add sam_annotator to packages by @constantinpape in #107
• Update documentation for the annotation tools by @constantinpape in #108
• Add installer script by @paulhfu in #91
• Add the preliminary finetuned EM models by @constantinpape in #111
• Fix download name for new models by @constantinpape in #112
• Don't segment current slice if it contains a division in tracking ann… by @constantinpape in #114
• Fix resetting the tracking state when clearing tracking annotations by @constantinpape in #117
• Eval Pipeline for FT by @anwai98 in #119
• Implement use_best_multimask for segment_from_points by @constantinpape in #120
• Refactor inference and evaluation code by @constantinpape in #121
• More evaluation updates by @constantinpape in #122
• 99_custom_models_gui_support by @paulhfu in #115
• 109_fix_macos_installer by @paulhfu in #124
• Add AMG by @anwai98 in #125
• Refactor AMG by @constantinpape in #127
• Fix Multimasking by @anwai98 in #131
• 130_fix_file_dialogs by @paulhfu in #133
• Minor updates to the trainer and doc strings by @constantinpape in #134
• Iterative Prompting for Inference by @anwai98 in #135
• Fix iterative prompting by @constantinpape in #138
• Add button to save the lineage in the tracking annotator by @constantinpape in #139
• Training and Evaluation Functionality by @constantinpape in #123
• Use normal instance segmentation functionality in 2d annotator and pr… by @constantinpape in #140
• AMG Updates by @constantinpape in #142
• Add links for new finetuned models by @constantinpape in #143
• Implement generalist model evaluation experiments by @constantinpape in #144
• Bump version by @constantinpape in #145

Full Changelog: 0.1.2...0.2.0

0.1.2.post2

Test release for building the binaries