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