torch-em

What's Changed

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

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.7.3...0.7.4

What's Changed

• Mininstancesampler update by @lufre1 in https://github.com/constantinpape/torch-em/pull/323

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.7.2...0.7.3

What's Changed

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

New Contributors

• @lufre1 made their first contribution in https://github.com/constantinpape/torch-em/pull/322

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.7.1...0.7.2

What's Changed

Support for updated bioimage.io libraries:

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

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.7.0...0.7.1

What's Changed

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

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.6.2...0.7.0

What's Changed

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

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.6.1...0.6.2

What's Changed

• Implement different channel reductions for dice by @constantinpape in https://github.com/constantinpape/torch-em/pull/194

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.6.0...0.6.1

What's Changed

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

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.5.2...0.6.0

To fix conda build.

What's Changed

• Update Teacher Initialization for MT Setup by @anwai98 in https://github.com/constantinpape/torch-em/pull/132
• TissueNet Dataloader by @anwai98 in https://github.com/constantinpape/torch-em/pull/134
• Add deepbacs dataloader by @constantinpape in https://github.com/constantinpape/torch-em/pull/135
• Implement get_dataset for more datasets by @constantinpape in https://github.com/constantinpape/torch-em/pull/137
• Update check_loader to save plots by @anwai98 in https://github.com/constantinpape/torch-em/pull/136
• Dataset updates by @constantinpape in https://github.com/constantinpape/torch-em/pull/138
• Implement NucMM Dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/139
• Implement sponge em dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/142
• Add doc strings to datasets to provide the correct dataset references by @constantinpape in https://github.com/constantinpape/torch-em/pull/143
• Refactor experiments by @constantinpape in https://github.com/constantinpape/torch-em/pull/144
• Update trainer.fit by @constantinpape in https://github.com/constantinpape/torch-em/pull/145

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.5.0...0.5.1

What's Changed

• Implement MeanTeacher Trainer by @constantinpape in https://github.com/constantinpape/torch-em/pull/112
• Add support for torch2 by @constantinpape in https://github.com/constantinpape/torch-em/pull/113
• Update Prob-DA Source UNet Parameters by @anwai98 in https://github.com/constantinpape/torch-em/pull/115
• New datasets and other changes by @constantinpape in https://github.com/constantinpape/torch-em/pull/114
• Load utils by @constantinpape in https://github.com/constantinpape/torch-em/pull/117
• Update Mean-Teacher and FixMatch Self-Training Scheme(s) by @anwai98 in https://github.com/constantinpape/torch-em/pull/116
• Add all necessary tests for mean teacher trainer deserialization by @constantinpape in https://github.com/constantinpape/torch-em/pull/118
• Add 2D Probabilistic UNet by @anwai98 in https://github.com/constantinpape/torch-em/pull/119
• Add Argument - Target Domain by @anwai98 in https://github.com/constantinpape/torch-em/pull/121
• Update Evaluation with Distribution Alignment by @anwai98 in https://github.com/constantinpape/torch-em/pull/122
• Add 2D Probabilistic UNet Training Setup by @anwai98 in https://github.com/constantinpape/torch-em/pull/123
• Add Probabilistic Self-Training (MT) Approaches by @anwai98 in https://github.com/constantinpape/torch-em/pull/125
• Add FixMatch-based Probabilistic Domain Adaptation Setups by @anwai98 in https://github.com/constantinpape/torch-em/pull/126
• Make livecell label extraction more robust against duplicate per obje… by @constantinpape in https://github.com/constantinpape/torch-em/pull/127
• Add CLI for UNet training and prediction by @constantinpape in https://github.com/constantinpape/torch-em/pull/128
• Implement tif support in data loaders by @constantinpape in https://github.com/constantinpape/torch-em/pull/130
• Update Prediction Functions for PUNet Domain Adaptation Setups by @anwai98 in https://github.com/constantinpape/torch-em/pull/129
• Implement classification functionality by @constantinpape in https://github.com/constantinpape/torch-em/pull/120

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.4.1...0.5.0

What's Changed

• fix best_metric < worst_metric by @FynnBe in https://github.com/constantinpape/torch-em/pull/50
• refactor _train_epoch and _validate by @FynnBe in https://github.com/constantinpape/torch-em/pull/51
• refactor DefaultTrainer.from_checkpoint by @FynnBe in https://github.com/constantinpape/torch-em/pull/53
• Deserialize ROI Wrapper WIP by @constantinpape in https://github.com/constantinpape/torch-em/pull/55
• fix error connected to retain_grad() by @JonasHell in https://github.com/constantinpape/torch-em/pull/57
• Add Serializer to DefaultTrainer by @FynnBe in https://github.com/constantinpape/torch-em/pull/54
• fix typo in augmentations by @JonasHell in https://github.com/constantinpape/torch-em/pull/59
• Add sampler that checks if there are a minimum number of instances in the volume by @JonasHell in https://github.com/constantinpape/torch-em/pull/60
• ensure correct behaviour of filters when set manually by @JonasHell in https://github.com/constantinpape/torch-em/pull/61
• Add functionality to mask to-bg-boundaries by @JonasHell in https://github.com/constantinpape/torch-em/pull/62
• Implement advanced rf training for s2d by @constantinpape in https://github.com/constantinpape/torch-em/pull/63
• Update s2d features, extend mito-enhancer training by @constantinpape in https://github.com/constantinpape/torch-em/pull/64
• Enable overwriting the min-shape in modelzoo export by @constantinpape in https://github.com/constantinpape/torch-em/pull/65
• Extend shallow2deep experiments by @constantinpape in https://github.com/constantinpape/torch-em/pull/67
• S2D experiments for training LM enhancers by @constantinpape in https://github.com/constantinpape/torch-em/pull/71
• add noise augmentations for mean teacher approach by @JonasHell in https://github.com/constantinpape/torch-em/pull/68
• fix typo/bug in validation logging by @JonasHell in https://github.com/constantinpape/torch-em/pull/73
• Add axon myelin training by @constantinpape in https://github.com/constantinpape/torch-em/pull/74
• add worst_tiles sampling by @JonasHell in https://github.com/constantinpape/torch-em/pull/77
• Extend s2d functionality by @constantinpape in https://github.com/constantinpape/torch-em/pull/75
• Elastic 3d by @Buglakova in https://github.com/constantinpape/torch-em/pull/79
• adapt default mean teacher augs to work with modelzoo export by @JonasHell in https://github.com/constantinpape/torch-em/pull/82
• adapt _serialize_feature_config() to work with strings by @JonasHell in https://github.com/constantinpape/torch-em/pull/83
• Add tests for augmentations by @constantinpape in https://github.com/constantinpape/torch-em/pull/80
• Add distance transform to label transforms by @constantinpape in https://github.com/constantinpape/torch-em/pull/84
• Add save_root argument to trainer to enable saving files at different… by @constantinpape in https://github.com/constantinpape/torch-em/pull/85
• Use ApplyMask in other masking loss wrappers by @constantinpape in https://github.com/constantinpape/torch-em/pull/86
• Make bioimageio import optional by @constantinpape in https://github.com/constantinpape/torch-em/pull/88
• fix bioimageio import in shallow2deep by @JonasHell in https://github.com/constantinpape/torch-em/pull/89
• Use tifffile to read compressed tif files by @Czaki in https://github.com/constantinpape/torch-em/pull/93
• When loading data for train allow to read data that has channel on first position by @Czaki in https://github.com/constantinpape/torch-em/pull/94
• Implement sampler for the image collection dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/96
• provide reasonable default values for augmentations by @JonasHell in https://github.com/constantinpape/torch-em/pull/97
• Add resnet 3d implementation (based on torchvision) by @constantinpape in https://github.com/constantinpape/torch-em/pull/99
• Update livecell.py by @constantinpape in https://github.com/constantinpape/torch-em/pull/100
• Augmentations by @JonasHell in https://github.com/constantinpape/torch-em/pull/98
• Update spoco losses by @constantinpape in https://github.com/constantinpape/torch-em/pull/87
• implement gradient masking with cropping - new PR by @JonasHell in https://github.com/constantinpape/torch-em/pull/101
• Add Separate Label Path to the LiveCELL Loader by @anwai98 in https://github.com/constantinpape/torch-em/pull/104
• Update Label Type Argument for LiveCELL by @anwai98 in https://github.com/constantinpape/torch-em/pull/105
• Raise value error if dice is called with non-matching shapes by @constantinpape in https://github.com/constantinpape/torch-em/pull/106
• add args to adjust tqdm output by @JonasHell in https://github.com/constantinpape/torch-em/pull/108
• add dense accumulate as additional baseline by @JonasHell in https://github.com/constantinpape/torch-em/pull/107
• Add neurips cell seg dataset; update raw image collection dataset; up… by @constantinpape in https://github.com/constantinpape/torch-em/pull/111
• Update Checksum for UroCell Dataloader by @anwai98 in https://github.com/constantinpape/torch-em/pull/109
• Misc changes WIP by @constantinpape in https://github.com/constantinpape/torch-em/pull/110

New Contributors

• @Buglakova made their first contribution in https://github.com/constantinpape/torch-em/pull/79
• @Czaki made their first contribution in https://github.com/constantinpape/torch-em/pull/93
• @anwai98 made their first contribution in https://github.com/constantinpape/torch-em/pull/104

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.4.0...0.4.1

What's Changed

• Add shape check to U-Net by @constantinpape in https://github.com/constantinpape/torch-em/pull/44
• Implement block skipping in prediction by @constantinpape in https://github.com/constantinpape/torch-em/pull/45
• Update mito-em dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/46
• Add vnc mito loader by @constantinpape in https://github.com/constantinpape/torch-em/pull/47
• Allow logger to generate a (run) id by @FynnBe in https://github.com/constantinpape/torch-em/pull/48
• Add training notebooks by @constantinpape in https://github.com/constantinpape/torch-em/pull/49

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.3.0...0.4.0

What's Changed

• Small fix by @oeway in https://github.com/constantinpape/torch-em/pull/31
• Hpa dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/32
• fix input for ilastik predictor by @JonasHell in https://github.com/constantinpape/torch-em/pull/33
• add boolean to set ilastik threads to 0 by @JonasHell in https://github.com/constantinpape/torch-em/pull/34
• add plt functionality for check_loader by @JonasHell in https://github.com/constantinpape/torch-em/pull/35
• fix n_sample bug in rawDataset and plt bug in check_loader by @JonasHell in https://github.com/constantinpape/torch-em/pull/36
• fix bugs for pseudo-label learning by @JonasHell in https://github.com/constantinpape/torch-em/pull/37
• Update for new build_model signature by @constantinpape in https://github.com/constantinpape/torch-em/pull/38
• Implement shallow2deep for multi-class predictions by @constantinpape in https://github.com/constantinpape/torch-em/pull/39
• Enable partial deserialization of raw and segmentation dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/40
• Enable prediction with channels and add test for it by @constantinpape in https://github.com/constantinpape/torch-em/pull/41
• Support 4d data and labels with channels in segmentation dataset by @constantinpape in https://github.com/constantinpape/torch-em/pull/42

New Contributors

• @oeway made their first contribution in https://github.com/constantinpape/torch-em/pull/31
• @JonasHell made their first contribution in https://github.com/constantinpape/torch-em/pull/33

Full Changelog: https://github.com/constantinpape/torch-em/compare/0.2.0...0.3.0

The core functionality is implemented and first implementations of spoco and shallow2deep added.