Classification and domain adaptation functionality

What's Changed

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

Full Changelog: 0.4.1...0.5.0

0.4.1

What's Changed

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

New Contributors

• @Buglakova made their first contribution in #79
• @Czaki made their first contribution in #93
• @anwai98 made their first contribution in #104

Full Changelog: 0.4.0...0.4.1

Jupyter notebooks

What's Changed

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

Full Changelog: 0.3.0...0.4.0

Import fix for conda-forge

0.3.0post0

Fix import

Support for 4d data and several other fixes

What's Changed

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

New Contributors

• @oeway made their first contribution in #31
• @JonasHell made their first contribution in #33

Full Changelog: 0.2.0...0.3.0

Core functionality

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

For zenodo

0.1.0post1

Fix small issues in export scripts

First release

0.1.0

Fix small issues in export scripts