New plugin design, models and automatic segmentation

Version 0.5

This release redesigns the user interface and provides it as napari plugins. It also provides updated models that are now hosted on https://bioimage.io/#/ and several other improvements and new features.

We are working on updating the documentation to reflect this new release ASAP and will also create a 1.0.0 release, focusing on minor improvements and bugfixes, soon to mark the tool as stable.

What's Changed

• Sync dev and master by @constantinpape in #328
• Prototype for annotator plugins by @constantinpape in #304
• Add Lucchi amg results by @anwai98 in #340
• Add SNEMI amg results by @anwai98 in #339
• Add MitoEM results by @anwai98 in #343
• Add Covid-IF results by @anwai98 in #345
• Update Covid-IF Results (for cyto2) by @anwai98 in #346
• Add LiveCELL Vanilla Results by @anwai98 in #348
• Add livecell cellpose results by @anwai98 in #349
• Add scripts for plotting results by @constantinpape in #313
• Refactor livecell evaluation by @anwai98 in #344
• Add EM generalist evaluation by @anwai98 in #320
• Add partial finetuning submission script by @anwai98 in #352
• Add n_objects experiment by @anwai98 in #353
• Implement instance segmentation merging across 3d by @constantinpape in #351
• Add evaluation scripts for experiments by @anwai98 in #354
• Saving the grid search parameters by @anwai98 in #362
• Overwrite existing keybindings to avoid error when re-opening plugin widgets by @GenevieveBuckley in #366
• Add description for plotting scripts by @anwai98 in #365
• Update Mito Nuc Finetuning by @anwai98 in #364
• Add plot scripts for additional experiments by @anwai98 in #360
• Add LM Specialist Evaluation by @anwai98 in #310
• Refactor EM generalist evaluations by @anwai98 in #368
• Minor fix to preprocessing LM datasets by @anwai98 in #374
• Minor fix to saving grid search params by @anwai98 in #373
• Fix test failure due to change in torchvision by @constantinpape in #375
• Refactor plotting scripts by @anwai98 in #372
• Refactor all evaluation scripts by @anwai98 in #376
• Update function signatures by @anwai98 in #377
• Add override to folder paths for evaluation by @anwai98 in #378
• Add description to more plotting scripts by @anwai98 in #367
• Add M1 MacOS runner to github actions jobs by @GenevieveBuckley in #370
• Update LM generalist training (with new decoder setup) by @anwai98 in #379
• Add NeurIPS CellSeg Specialist by @anwai98 in #363
• Refactor CellPose scripts by @anwai98 in #347
• Add plotting scripts for evaluation by @anwai98 in #387
• Minor update to finetuning scripts by @anwai98 in #386
• Minor fix to documentation by @anwai98 in #399
• Update default parameter for foreground smoothing by @anwai98 in #396
• Update evaluation plot scripts by @anwai98 in #401
• Update run_all_finetuning.py - for flexible finetuning models by @anwai98 in #395
• Minor refactor to label transform in LM generalist by @anwai98 in #394
• Add inference for cellpose 3.0 by @anwai98 in #393
• Restore EM boundaries finetuning by @anwai98 in #403
• Update JointSamTrainer's save_checkpoint by @anwai98 in #404
• Shorte widget names and suppress mobile-sam import warnings by @constantinpape in #409
• Batch point seg by @constantinpape in #410
• Minor fix to inference function for instance segmentation by @anwai98 in #411
• Add resource efficient finetuning experiments by @anwai98 in #391
• Add volumetric instance segmentation scripts by @anwai98 in #402
• Compute best grid search parameters by @anwai98 in #413
• Implement new segmentation plugin by @constantinpape in #305
• 331 add options for tiling in the embdding widget by @lufre1 in #419
• Update projection modes by @constantinpape in #418
• Update CLI to enable loading a finetuned model by @constantinpape in #427
• Fix initialization with segmentation result by @constantinpape in #431
• Enable tile based segmentation for more options and add more tests by @constantinpape in #432
• Enable specifying the device in the CLI by @constantinpape in #433
• Parallelize commit operations by @constantinpape in #436
• Add input logits logic to iterative prompting evaluation by @anwai98 in #438
• Add exception message for no objects found by @anwai98 in #443
• Clear annotation in slice or frame only by @constantinpape in #447
• Implement commit restricted to actually segmented slices for 3d annotator by @constantinpape in #448
• Implement commit to file by @constantinpape in #451
• Update model comparison to work with prompt gen syntax by @constantinpape in #453
• Fix issues in loading segmentation result and image series annotator by @constantinpape in #456
• Update image_series_annotator - for flexible inputs by @anwai98 in #454
• Update evaluation scripts for custom experiments by @anwai98 in #442
• Update inference and evaluation top-level scripts (for LIVECell) by @anwai98 in #439
• Amg artifacts by @constantinpape in #458
• Include min_size in multi dim evaluation by @anwai98 in #459
• Unify SAM model loading by @constantinpape in #460
• Update supplementary experiments by @anwai98 in #420
• Update current metric saving in joint trainer by @anwai98 in #461
• Add convenience function for training and add user study scripts by @constantinpape in #457
• Fix issue with segmentation for non-square images and extend tests by @constantinpape in #464
• Improve 3d segmentation by @constantinpape in #462
• 426 enable to hold tiled embeddings in memory by @lufre1 in #429
• Add automatic instance segmentation for 3d with new defaults by @anwai98 in #469
• Update livecell finetuning and evaluation scripts by @anwai98 in #470
• Add scripts for evaluating the user study by @constantinpape in #471
• Update tracking annotator by @constantinpape in #475
• Plotting scripts for the paper by @caroteu in #477
• Add processing scripts for MitoNet benchmarking by @anwai98 in #341
• Update resource efficient finetuning plots by @anwai98 in #449
• Update iterative prompting evaluation script by @anwai98 in #476
• Add ASEM finetuning by @anwai98 in #437
• Add DynamicNuclearNet finetuning by @anwai98 in #474
• Add CREMI specialist by @anwai98 in #421
• Update scripts to run finetuning for new specialists by @anwai98 in #479
• Add more MitoNet benchmark results by @anwai98 in #480
• Implement AIS with tiling by @constantinpape in #481
• Add automatic and interactive segmentation for 3d datasets by @anwai98 in #423
• Update gui design WIP by @constantinpape in #486
• Add plotting scripts for limited data experiments on livecell by @anwai98 in #492
• 490 finish settings for embedding widget by @lufre1 in #493
• Update label transform class name for ASEM (ER) specialist by @anwai98 in #496
• Extend CellPose benchmarking option by @anwai98 in #482
• Minor updates to MitoNet benchmarking by @anwai98 in #497
• Refactor batched interactive segmentation, implementation ideas for a… by @constantinpape in #495
• Minor update to resource efficient finetuning plots by @anwai98 in #499
• Training UI by @constantinpape in #467
• Implement image folder GUI by @constantinpape in #500
• 332 handle non initialized image embeddings better in the plugins by @lufre1 in #498
• Update scripts for qualitative plots by @anwai98 in #465
• Update limited livecell data plots for vit tiny by @anwai98 in #506
• Update embedding signature by @constantinpape in #507
• Update installation instructions in documentation by @anwai98 in #508
• New model updates by @constantinpape in #509
• 505 update installer scripts by @lufre1 in #510
• Minor update to object import in training scheme by @anwai98 in #503
• Add model settings for dynamic updates of widget parameters by @constantinpape in #515
• Update plots for the paper by @anwai98 in #415
• 517 features in embedding widget not working properly by @lufre1 in #519
• Add documentation for LM and EM datasets by @anwai98 in #521
• 520 add info dialog to image series annotator by @lufre1 in #522
• Update user study plots by @constantinpape in #518
• Add time measurements for resource efficient finetuning by @anwai98 in #523
• Add runtimes for benchmarking methods by @anwai98 in #525
• 487 helper texts for menu options in annotator tool by @lufre1 in #524
• 487 helper texts for menu options in annotator tool by @lufre1 in #526
• Update cellpose timings by @anwai98 in #527
• Merge dev in preparation for new release by @constantinpape in #516

New Contributors

• @lufre1 made their first contribution in #419
• @caroteu made their first contribution in #477

Full Changelog: 0.4.1...0.5.0