0.1.0

What's Changed

• Bump micro version by @ioangatop in #486
• update docs config links to point to v0.0.2 by @roman807 in #487
• Update paper citation by @ioangatop in #489
• Update the vision dataset return types to tv_tensors by @ioangatop in #478
• Refactor embeddings writer by @ioangatop in #461
• fixed phikon configs by @roman807 in #493
• Refactor core embeddings based datasets by @ioangatop in #495
• Add doc tests and minor fixes by @ioangatop in #492
• support setting download as env-variable by @roman807 in #514
• Rename DOWNLOAD env var to DOWNLOAD_DATA by @ioangatop in #534
• Allow head model as dict and parse it as object in configure_model by @ioangatop in #541
• Add support for WSI-level classification by @roman807 in #542
• Support semantic segmentation downstream evaluation tasks by @ioangatop in #517
• make sure multiwsidatasets are validated (updated) by @roman807 in #545
• Add MoNuSac segmentation dataset by @ioangatop in #549
• Add CoNSeP dataset with patching by @nkaenzig in #547
• Fix normalisation in ResizeAndClamp transform by @ioangatop in #555
• Update dependency jsonargparse to v4.30.0 by @renovate in #540
• Update dependency jsonargparse to v4.31.0 by @renovate in #560
• Update actions/checkout digest to 692973e by @renovate in #536
• Add support for offline total segmentator training by @ioangatop in #504
• Change overwrite default value to True in EmbeddingWriter by @nkaenzig in #558
• Allow local checkpoint to be loaded in TimmEncoder by @ioangatop in #566
• Update main README by @ioangatop in #563
• Add BCSS dataset by @nkaenzig in #559
• Update segmentation metrics by @ioangatop in #571
• Add support for phikon as encoder for segmentation tasks by @ioangatop in #570
• Add ignore_index functionality in segmentation metrics by @ioangatop in #574
• Add LiTS radiology ct segmentation dataset and task by @ioangatop in #567
• Fix LiTS dataset validation by @ioangatop in #577
• Fix the embeddings saving dataset by @ioangatop in #579
• Remove cpu accelerator from LiTS config by @ioangatop in #581
• Add Dice segmentation loss by @ioangatop in #587
• 589 fix dice loss function for ignore index argument by @ioangatop in #590
• Fix LiTS transforms by @ioangatop in #594
• update leaderboard and documentation with WSI segmentation datasets by @roman807 in #596
• Use core.models.wrappers API to load encoder models by @nkaenzig in #598
• Add model registry for accessing backbones by name by @nkaenzig in #591
• Update .lock file to solve exceptiongroup dependency issue in CI by @nkaenzig in #605
• Add support for running timm models with default configs by @nkaenzig in #607
• Add H-optimus-0 model to registry by @nkaenzig in #599
• Add Prov-GigaPath model to registry by @nkaenzig in #600
• Add hibou models to registry by @nkaenzig in #609
• Copy metadata entries to CPU in embeddings writer by @nkaenzig in #611
• Allow to call timm models with timm/model_name on BackboneModelRegistry by @ioangatop in #613
• Make dataset root fully configurable through env variable by @nkaenzig in #617
• Bugfix for monusac worker issue by @nkaenzig in #619
• Set multiprocessing start method to spawn for EmbeddingsDataset by @nkaenzig in #621
• Update segmentation visualisation default arguments to show one column per group by @ioangatop in #623
• Add WandbLogger by @nkaenzig in #628
• Set available auto download to False for camelyon16 by @nkaenzig in #626
• Bump major version 1.0.0 by @ioangatop in #615
• Corrected number of classes in CoNSeP configs by @nkaenzig in #632
• Refactoring of forward method in model wrapper classes by @nkaenzig in #633
• Remove dynamic_img_size from timm/{timm_model} registry function by @nkaenzig in #638
• Update leaderboard style to heatmap by @roman807 in #631
• Udpate timm & torchmetrics dependency by @ioangatop in #640
• bump to 0.1.0 by @ioangatop in #643

Full Changelog: 0.0.2...0.1.0