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