0.7.6

This release adds a several new datasets and fixes issues with other dataset implementations.

What's Changed

• Minor fix to OIMHS dataset by @anwai98 in #424
• Remove other irrelevant labels for LEG 3D US dataset by @anwai98 in #425
• Ignore inputs with empty labels for SIIM ACR dataset by @anwai98 in #426
• Add argument to get expected image-label pairs for CBIS DDSM data by @anwai98 in #427
• Minor fix to preprocessing MoNuSaC by @anwai98 in #429
• Minor fix to PUMA dataset by @anwai98 in #430
• Minor fix to filtering mismatching image-label pairs by @anwai98 in #431
• Add NuClick dataset by @anwai98 in #428
• Make splits for lizard dataset by @anwai98 in #434
• Add CellBinDB dataset by @anwai98 in #435
• Add full set of DSB dataset by @anwai98 in #436
• Minor fix to check for zipfile in CPM dataset by @anwai98 in #437
• Update documentation by @anwai98 in #438
• Minor fix to removing alpha channel in TNBC data by @anwai98 in #439
• Add BriFiSeg dataset by @anwai98 in #440
• Add YeaZ dataset by @anwai98 in #441
• Add DeepSeas dataset by @anwai98 in #442
• Ad explicit splits for histopathology datasets by @anwai98 in #444
• Add support for resizing inputs to patch shape by @anwai98 in #445
• Add CVZ Fluo dataset by @anwai98 in #446
• Remove minor debugging artifact in CPM dataset by @anwai98 in #449
• Misc improvements by @constantinpape in #450
• Add data splits for motum dataset by @anwai98 in #454
• Add data splits to papila dataset by @anwai98 in #453
• Add data splits for PSFHS dataset by @anwai98 in #455
• Add AMD-SD dataset by @anwai98 in #451
• Add Mice TumSeg data by @anwai98 in #452
• Add resize inputs for JSRT data by @anwai98 in #457
• Cosmetic changes by @constantinpape in #458
• Add CoNSeP dataset by @anwai98 in #417
• Minor refactor to LM datasets by @anwai98 in #459
• Minor update to three-channel logic in tissuenet by @anwai98 in #460
• Fix typo in LIVECell dataset by @anwai98 in #461
• Add type annotations to major functionalities by @anwai98 in #297
• Add docstring to other functionalities by @anwai98 in #464
• Add download functionality support for synapse hosted datasets by @anwai98 in #465
• Complete doc strings by @constantinpape in #463
• Update environment files and github workflows by @constantinpape in #467
• Minor update to inform about creating custom data splits by @anwai98 in #468
• Minor update to OSIC PulmoFib preprocessing scripts by @anwai98 in #470
• Add KiTS dataset by @anwai98 in #469
• Add custom splits for CryoNuSeg dataset by @anwai98 in #472
• Add GlaS dataset by @anwai98 in #474
• Minor fix to NuClick dataset arguments by @titusgriebel in #475
• Minor update medical imaging datasets for consistency by @anwai98 in #476
• Fix return type for BUSI data paths by @anwai98 in #477
• Minor fix to argument positions in MitoEM dataset by @anwai98 in #478
• Minor update to expose padding mode and make resize flexible by @anwai98 in #479
• Bump version to 0.7.6 by @constantinpape in #481

New Contributors

• @titusgriebel made their first contribution in #475

Full Changelog: 0.7.5...0.7.6

0.7.5

What's Changed

• Update summary writer import by @constantinpape in #390
• Minor update to process outputs for gdrive download by @anwai98 in #391
• Fix plantseg get paths by @anwai98 in #393
• Add VICAR dataset by @anwai98 in #394
• Add Arvidsson dataset by @anwai98 in #395
• Add LyNSeC data by @anwai98 in #396
• Add SRSA-Net dataset by @anwai98 in #397
• Add BitSeg NucSeg dataset by @anwai98 in #398
• Add IFNuclei dataset by @anwai98 in #399
• Add TNBC dataset by @anwai98 in #400
• Add PALM dataset by @anwai98 in #402
• Add PSFHS dataset by @anwai98 in #403
• Add CadAIver dataset by @anwai98 in #405
• Add MOTUM dataset by @anwai98 in #404
• Add TOIAM dataset by @anwai98 in #408
• Refactor medical imaging datasets for experiments by @anwai98 in #406
• Add BlastoSPIM dataset by @anwai98 in #410
• Add notebook for tiling window-based prediction by @anwai98 in #409
• Minor fix to enabling both quote types by @anwai98 in #342
• Update vision mamba backbone to latest updates by @anwai98 in #401
• Add support to avoid overwriting trained models by @anwai98 in #411
• Add SegPC dataset by @anwai98 in #412
• Add PUMA dataset by @anwai98 in #413
• Add NuInsSeg dataset by @anwai98 in #414
• Add Janowczyk dataset by @anwai98 in #415
• Add CPM dataset by @anwai98 in #416
• exchanged napari progress with tqdm by @lufre1 in #418
• Minor update to cryonuseg dataset by @anwai98 in #419
• Add brain organoids dataset by @anwai98 in #420
• Update legacy editable install for torch_em by @anwai98 in #346
• Bump to 0.7.5 by @constantinpape in #423

Full Changelog: 0.7.4...0.7.5

0.7.4

What's Changed

• Add HeLA VGG dataset for cell counting in phase-contrast microscopy by @constantinpape in #325
• Add GoNuclear datasets by @constantinpape in #327
• Minor typo in deserialize warnings raised by SegmentationDataset by @anwai98 in #328
• Minor fix to spider dataset by @anwai98 in #317
• Add padding to SegmentationDataset by @anwai98 in #330
• Add ResizeLongestSideInputs transform by @anwai98 in #329
• Update mixed precision training code by @constantinpape in #331
• Add resize transform support for 3d by @anwai98 in #332
• changed order of segmentationdataset's get_sample function logic: sam… by @lufre1 in #334
• Minor fix to resize transform for inputs by @anwai98 in #336
• Implement deepict dataset by @constantinpape in #337
• Update GoNuclear dataset for returning different target types by @anwai98 in #338
• Remove artifacts in volumes and minor fix to cell labels for GoNuclear by @anwai98 in #340
• Minor update to MitoEM rat sample labels download link by @anwai98 in #339
• Fix plantseg volumes - remove slices with artifacts by @anwai98 in #344
• Extend functionality to obtain original inputs from resized inputs by @anwai98 in #348
• Add DIC HepG2 dataset by @anwai98 in #349
• Update design for storing input channels in HPA dataset by @anwai98 in #351
• Minor update to load_model: Support loading directly from checkpoint by @anwai98 in #352
• Move top-level imports for specific packages to function-level by @anwai98 in #353
• Add OmniPose dataset by @anwai98 in #326
• Add rois back to dataset kwargs in Platynereis (Cilia) by @anwai98 in #354
• Add CellPose dataset by @anwai98 in #272
• Set non_blocking to True for tensor device allocation by @anwai98 in #357
• Minor updates to DeepBacs dataset by @anwai98 in #359
• Minor update to TissueNet dataset by @anwai98 in #360
• Minor update to DynamicNuclearNet dataset by @anwai98 in #361
• Minor update to PanNuke dataset by @anwai98 in #362
• Update lizard dataset - change download to kaggle api by @anwai98 in #363
• Minor updates to OrgaSegment dataset by @anwai98 in #364
• Minor updates to EM datasets by @anwai98 in #365
• Update ASEM dataset by @anwai98 in #366
• Add function in datasets to get input paths by @anwai98 in #367
• Add function to return input paths in histopathology datasets by @anwai98 in #369
• Add EMNeuron dataset by @anwai98 in #370
• Add SegThy dataset by @anwai98 in #375
• Add LEG 3D US dataset by @anwai98 in #374
• Add PANORAMA dataset by @anwai98 in #373
• Add CryoNuSeg dataset by @anwai98 in #372
• Add LGG MRI dataset by @anwai98 in #376
• Add OASIS dataset by @anwai98 in #377
• Add ToothSeg dataset by @anwai98 in #324
• Add MBH Seg dataset by @anwai98 in #289
• Add Acouslic-AI dataset by @anwai98 in #288
• Add PENGWIN dataset by @anwai98 in #287
• Add Curvas dataset by @anwai98 in #286
• Move platynereis file templates to global dict by @anwai98 in #380
• Add ToothFairy2 dataset by @anwai98 in #285
• 378 add ensuring patch shape for raw dataset by @lufre1 in #379
• Add VerSe dataset by @anwai98 in #277
• Add Covid-QU-EX dataset by @anwai98 in #271
• Add Kvasir-SEG dataset by @anwai98 in #267
• Add RAVIR dataset by @anwai98 in #259
• Add Usiigaci dataset by @anwai98 in #383
• Add JSRT dataset by @anwai98 in #248
• Add CHAOS dataset by @anwai98 in #278
• Add ISLES dataset by @anwai98 in #254
• added sampler logic to mean_teacher by @lufre1 in #385
• Add CartoCell dataset by @anwai98 in #386
• Update documentation for dataset and dataloaders by @anwai98 in #387
• Update version.py by @constantinpape in #388

Full Changelog: 0.7.3...0.7.4

0.7.3

What's Changed

• Mininstancesampler update by @lufre1 in #323

Full Changelog: 0.7.2...0.7.3

0.7.2

What's Changed

• Update location to datasets submodule by @anwai98 in #245
• Update ViM-UNet documentation by @anwai98 in #246
• Change instance norm settings in U-Net to avoid boundary artifacts by @constantinpape in #247
• Add SIIM ACR Pneumothorax dataset by @anwai98 in #256
• Add CAMUS dataset by @anwai98 in #257
• Add DRIVE dataset by @anwai98 in #260
• Add Papila dataset by @anwai98 in #262
• Update torch_em datasets by @constantinpape in #252
• Add BUSI dataset by @anwai98 in #268
• Update dataset doc path by @anwai98 in #265
• Add stuff for doc by @constantinpape in #269
• Add Plethora dataset by @anwai98 in #263
• Update default optimizer to AdamW by @anwai98 in #284
• Add SA-Med2D-20M dataset by @anwai98 in #282
• Add Medical Segmentation Decathlon dataset by @anwai98 in #224
• Add OSIC Pulmonary Fibrosis dataset by @anwai98 in #281
• Minor update SA-Med2d 20M dataset by @anwai98 in #290
• Add Montgomery dataset by @anwai98 in #249
• Add IDRiD dataset by @anwai98 in #266
• Add UWaterloo Skin dataset by @anwai98 in #261
• Minor updates to CAMUS dataset by @anwai98 in #292
• Add OrgaSegment dataset by @anwai98 in #231
• Add FeTa dataset by @anwai98 in #293
• Add OIMHS dataset by @anwai98 in #291
• Add JNU-IFM dataset by @anwai98 in #270
• Add MicroUSP dataset by @anwai98 in #279
• Add Seg-A dataset by @anwai98 in #276
• Multi gpu training by @constantinpape in #283
• Create splits for OIMHS data by @anwai98 in #300
• Restore old norm layer defaults by @constantinpape in #303
• Update resize functionality for SIIM ACR by @anwai98 in #308
• Minor update to preprocessing logic for Papila by @anwai98 in #307
• Add resizing to OSIC PulmoFib dataset by @anwai98 in #306
• Add CholecSeg8k dataset by @anwai98 in #305
• Add Duke Liver dataset by @anwai98 in #304
• Add PICCOLO dataset by @anwai98 in #302
• Add CBIS DDSM dataset by @anwai98 in #301
• Add m2caiseg dataset by @anwai98 in #280
• Add DCA1 dataset by @anwai98 in #309
• Add ISIC dataset by @anwai98 in #250
• Minor fix to UNETR mini-batch norm by @anwai98 in #310
• Add AMOS dataset by @anwai98 in #255
• Add Toothfairy dataset by @anwai98 in #313
• Minor fix to adapt label conversion scripts for papila by @anwai98 in #312
• Minor updates to drive dataset by @anwai98 in #314
• Minor update to SegA data structure by @anwai98 in #316
• Add SPIDER dataset by @anwai98 in #315
• Add HaN Seg dataset by @anwai98 in #275
• Add ACDC dataset by @anwai98 in #251
• Add Covid19 Lung and Infection Segmentation Dataset by @anwai98 in #253
• Add organoidnet dataset by @constantinpape in #318
• Cellseg 3d by @constantinpape in #319
• added label transform class encorporating min_size of labels by @lufre1 in #322
• Bump version by @constantinpape in #321

New Contributors

• @lufre1 made their first contribution in #322

Full Changelog: 0.7.1...0.7.2

0.7.1

What's Changed

Support for updated bioimage.io libraries:

• Update links to the vimunet benchmarking by @anwai98 in #239
• Minor touch-up updates to torch-em docs by @anwai98 in #241
• Add random colors generator for instance plotting by @anwai98 in #244
• Add documentation on datasets and dataloaders by @anwai98 in #234
• Bump bioimageio dependency by @constantinpape in #243

Full Changelog: 0.7.0...0.7.1

0.7.0

What's Changed

• Fix missing attribute for dicelosswithlogits by @anwai98 in #220
• Minor fix to ctc exception message by @anwai98 in #221
• Minor update to sort encoder outputs by @anwai98 in #219
• Add DynamicNuclearNet data - from DeepCell by @anwai98 in #228
• Add top-level ViM-UNet description file by @anwai98 in #235
• Add ViM-UNet by @anwai98 in #236
• Set DynamicNuclearNet download default to False by @anwai98 in #230
• Add ASEM dataset by @anwai98 in #226
• Enable passing external pbar to trainer by @constantinpape in #232
• Bump version by @constantinpape in #238

Full Changelog: 0.6.2...0.7.0

0.6.2

What's Changed

• Implement grid-search for distance based segmentation by @constantinpape in #193
• Update the sampling mechanism in the image collection dataset by @constantinpape in #195
• Fix AxonDeepSeg by @anwai98 in #196
• Bump Version by @anwai98 in #197
• Update NucMM dataset by @anwai98 in #199
• Fix mitoem rat volume download by @anwai98 in #202
• Minor update to UNETR by @anwai98 in #203
• Minor fix to covid-if data description by @anwai98 in #206
• Update grid-search by @constantinpape in #209
• Update ISBI dataset download by @anwai98 in #210
• Minor fix to NeurIPS CellSeg dataset by @anwai98 in #212
• Update UNETR upsampling by @anwai98 in #211
• Add BTCV dataloader by @anwai98 in #171
• Add CTC dataset by @constantinpape in #214
• Add AutoPET dataset by @anwai98 in #213
• Refactor CTC dataset by @anwai98 in #215
• Update UNETR - making the training modular by @anwai98 in #217
• Add test set for CTC dataset by @anwai98 in #216
• Add current_metric while saving checkpoints by @anwai98 in #223

Full Changelog: 0.6.1...0.6.2

0.6.1

What's Changed

• Implement different channel reductions for dice by @constantinpape in #194

Full Changelog: 0.6.0...0.6.1

Transformer based segmentation functionality

What's Changed

• Implement UNETR by @constantinpape in #146
• Fixes and Updates for UNETR by @anwai98 in #148
• Minor Fix to UNETR Decoder by @anwai98 in #149
• Add imagecodecs to the dependencies to fix CI by @constantinpape in #150
• Add PanNuke Dataloader by @anwai98 in #153
• Refactor UNETR Training by @anwai98 in #151
• Add Monai's UNETR by @anwai98 in #155
• Add BCSS Dataset by @anwai98 in #156
• Add PanNuke Check Script by @anwai98 in #159
• Updates to MoNuSeg by @anwai98 in #157
• Add Watershed Segmentation Functionality by @anwai98 in #160
• Add MoNuSAC Dataset by @anwai98 in #158
• Raise download prompt - NeurIPS CellSeg by @anwai98 in #161
• Raise warning for Lizard data download by @anwai98 in #163
• Add type annotations - PanNuke by @anwai98 in #165
• Add splits for BCSS dataset by @anwai98 in #164
• UNETR Training with Affinities by @anwai98 in #166
• Save train time in checkpoint by @constantinpape in #169
• Add Raw Transform - nnUNet by @anwai98 in #170
• Bring main up-to-date by @constantinpape in #173
• Add ViT-MAE and Refactor ViT(s) by @anwai98 in #172
• Distance label trafos by @constantinpape in #177
• Fix UNETR Model for LIVECell by @anwai98 in #174
• Add LIVECell Distance Map Experiments by @anwai98 in #175
• Add distance based loss by @constantinpape in #178
• Fix issues in ViT initialization and update UNETR state loading by @constantinpape in #180
• Misc updates to transforms, loss and UNETR by @constantinpape in #181
• Fix UNETR Training - Update Rescaling Inputs by @anwai98 in #179
• Sync dev by @constantinpape in #184
• WIP - Instance Segmentation Experiments by @anwai98 in #187
• Dev by @constantinpape in #188
• Update DeepBacs Loader by @anwai98 in #189
• Implement mitolab benchmark datasets by @constantinpape in #190
• Update UNETR to enable resize to longest side by @constantinpape in #192

Full Changelog: 0.5.2...0.6.0