LICENSE
README.md
pyproject.toml
setup.py
test/test_classification.py
test/test_cli.py
test/test_segmentation.py
test/data/__init__.py
test/data/test_dataset_wrapper.py
test/data/test_image_collection_dataset.py
test/data/test_raw_dataset.py
test/data/test_sampler.py
test/data/test_segmentation_dataset.py
test/data/test_tensor_dataset.py
test/loss/__init__.py
test/loss/test_cldice.py
test/loss/test_contrastive.py
test/loss/test_contrastive_impl.py
test/loss/test_dice.py
test/loss/test_loss_wrapper.py
test/loss/test_spoco.py
test/metric/__init__.py
test/metric/test_cldice.py
test/metric/test_metric.py
test/model/__init__.py
test/model/test_punet.py
test/model/test_resnet3d.py
test/model/test_unet.py
test/model/test_unetr.py
test/self_training/__init__.py
test/self_training/test_fix_match.py
test/self_training/test_mean_teacher.py
test/trainer/__init__.py
test/trainer/test_default_trainer.py
test/trainer/test_spoco_trainer.py
test/transform/__init__.py
test/transform/test_augmentations.py
test/transform/test_generic.py
test/transform/test_invertible_augmentations.py
test/transform/test_label_transforms.py
test/transform/test_raw.py
test/util/__init__.py
test/util/test_imageio.py
test/util/test_modelzoo.py
test/util/test_prediction.py
test/util/test_segmentation.py
test/util/test_util.py
torch_em/__init__.py
torch_em/__version__.py
torch_em/cli.py
torch_em/multi_gpu_training.py
torch_em/segmentation.py
torch_em.egg-info/PKG-INFO
torch_em.egg-info/SOURCES.txt
torch_em.egg-info/dependency_links.txt
torch_em.egg-info/entry_points.txt
torch_em.egg-info/requires.txt
torch_em.egg-info/top_level.txt
torch_em/classification/__init__.py
torch_em/classification/classification.py
torch_em/classification/classification_dataset.py
torch_em/classification/classification_logger.py
torch_em/classification/classification_trainer.py
torch_em/data/__init__.py
torch_em/data/concat_dataset.py
torch_em/data/dataset_wrapper.py
torch_em/data/image_collection_dataset.py
torch_em/data/pseudo_label_dataset.py
torch_em/data/raw_dataset.py
torch_em/data/raw_image_collection_dataset.py
torch_em/data/sampler.py
torch_em/data/segmentation_dataset.py
torch_em/data/tensor_dataset.py
torch_em/data/datasets/__init__.py
torch_em/data/datasets/util.py
torch_em/data/datasets/electron_microscopy/__init__.py
torch_em/data/datasets/electron_microscopy/aimseg.py
torch_em/data/datasets/electron_microscopy/asem.py
torch_em/data/datasets/electron_microscopy/astih.py
torch_em/data/datasets/electron_microscopy/axondeepseg.py
torch_em/data/datasets/electron_microscopy/axonem.py
torch_em/data/datasets/electron_microscopy/betaseg.py
torch_em/data/datasets/electron_microscopy/cellmap.py
torch_em/data/datasets/electron_microscopy/cem.py
torch_em/data/datasets/electron_microscopy/cremi.py
torch_em/data/datasets/electron_microscopy/deepict.py
torch_em/data/datasets/electron_microscopy/densecell.py
torch_em/data/datasets/electron_microscopy/emneuron.py
torch_em/data/datasets/electron_microscopy/emps.py
torch_em/data/datasets/electron_microscopy/fafb.py
torch_em/data/datasets/electron_microscopy/fafb_nuclei.py
torch_em/data/datasets/electron_microscopy/fib25.py
torch_em/data/datasets/electron_microscopy/hemibrain.py
torch_em/data/datasets/electron_microscopy/human_cortex_h01.py
torch_em/data/datasets/electron_microscopy/human_organoids.py
torch_em/data/datasets/electron_microscopy/hydra_vulgaris.py
torch_em/data/datasets/electron_microscopy/isbi2012.py
torch_em/data/datasets/electron_microscopy/kasthuri.py
torch_em/data/datasets/electron_microscopy/lucchi.py
torch_em/data/datasets/electron_microscopy/malecns.py
torch_em/data/datasets/electron_microscopy/manc.py
torch_em/data/datasets/electron_microscopy/microns.py
torch_em/data/datasets/electron_microscopy/microns_nuclei.py
torch_em/data/datasets/electron_microscopy/mitoem.py
torch_em/data/datasets/electron_microscopy/mitoemv2.py
torch_em/data/datasets/electron_microscopy/mousecc.py
torch_em/data/datasets/electron_microscopy/nisb.py
torch_em/data/datasets/electron_microscopy/nuc_mm.py
torch_em/data/datasets/electron_microscopy/platynereis.py
torch_em/data/datasets/electron_microscopy/probtem.py
torch_em/data/datasets/electron_microscopy/snemi.py
torch_em/data/datasets/electron_microscopy/sponge_em.py
torch_em/data/datasets/electron_microscopy/synapseweb_hippocampus.py
torch_em/data/datasets/electron_microscopy/uro_cell.py
torch_em/data/datasets/electron_microscopy/vnc.py
torch_em/data/datasets/electron_microscopy/waenet.py
torch_em/data/datasets/electron_microscopy/wildenberg.py
torch_em/data/datasets/electron_microscopy/zebrafinch.py
torch_em/data/datasets/histopathology/__init__.py
torch_em/data/datasets/histopathology/bcss.py
torch_em/data/datasets/histopathology/conic.py
torch_em/data/datasets/histopathology/consep.py
torch_em/data/datasets/histopathology/cpm.py
torch_em/data/datasets/histopathology/cryonuseg.py
torch_em/data/datasets/histopathology/cytodark0.py
torch_em/data/datasets/histopathology/glas.py
torch_em/data/datasets/histopathology/glysac.py
torch_em/data/datasets/histopathology/hest.py
torch_em/data/datasets/histopathology/janowczyk.py
torch_em/data/datasets/histopathology/lizard.py
torch_em/data/datasets/histopathology/lynsec.py
torch_em/data/datasets/histopathology/monusac.py
torch_em/data/datasets/histopathology/monuseg.py
torch_em/data/datasets/histopathology/nuclick.py
torch_em/data/datasets/histopathology/nuinsseg.py
torch_em/data/datasets/histopathology/orion_crc.py
torch_em/data/datasets/histopathology/pannuke.py
torch_em/data/datasets/histopathology/panoptils.py
torch_em/data/datasets/histopathology/pcns.py
torch_em/data/datasets/histopathology/puma.py
torch_em/data/datasets/histopathology/segpath.py
torch_em/data/datasets/histopathology/srsanet.py
torch_em/data/datasets/histopathology/tnbc.py
torch_em/data/datasets/light_microscopy/__init__.py
torch_em/data/datasets/light_microscopy/aisegcell.py
torch_em/data/datasets/light_microscopy/arvidsson.py
torch_em/data/datasets/light_microscopy/bac_mother.py
torch_em/data/datasets/light_microscopy/balf.py
torch_em/data/datasets/light_microscopy/bbbc030.py
torch_em/data/datasets/light_microscopy/bbbc034.py
torch_em/data/datasets/light_microscopy/bccd.py
torch_em/data/datasets/light_microscopy/bitdepth_nucseg.py
torch_em/data/datasets/light_microscopy/blastospim.py
torch_em/data/datasets/light_microscopy/bmgd.py
torch_em/data/datasets/light_microscopy/brain_organoids.py
torch_em/data/datasets/light_microscopy/brifiseg.py
torch_em/data/datasets/light_microscopy/cartocell.py
torch_em/data/datasets/light_microscopy/celegans_atlas.py
torch_em/data/datasets/light_microscopy/cellbindb.py
torch_em/data/datasets/light_microscopy/cellpose.py
torch_em/data/datasets/light_microscopy/cellseg_3d.py
torch_em/data/datasets/light_microscopy/cisd.py
torch_em/data/datasets/light_microscopy/covid_if.py
torch_em/data/datasets/light_microscopy/cshaper.py
torch_em/data/datasets/light_microscopy/ctc.py
torch_em/data/datasets/light_microscopy/cvz_fluo.py
torch_em/data/datasets/light_microscopy/deepbacs.py
torch_em/data/datasets/light_microscopy/deepseas.py
torch_em/data/datasets/light_microscopy/dic_hepg2.py
torch_em/data/datasets/light_microscopy/dsb.py
torch_em/data/datasets/light_microscopy/dynamicnuclearnet.py
torch_em/data/datasets/light_microscopy/e11bio.py
torch_em/data/datasets/light_microscopy/embedseg_data.py
torch_em/data/datasets/light_microscopy/enseg.py
torch_em/data/datasets/light_microscopy/evican.py
torch_em/data/datasets/light_microscopy/glioma_c6.py
torch_em/data/datasets/light_microscopy/gonuclear.py
torch_em/data/datasets/light_microscopy/hpa.py
torch_em/data/datasets/light_microscopy/idr0095.py
torch_em/data/datasets/light_microscopy/ifnuclei.py
torch_em/data/datasets/light_microscopy/liconn.py
torch_em/data/datasets/light_microscopy/livecell.py
torch_em/data/datasets/light_microscopy/lpc_nucseg.py
torch_em/data/datasets/light_microscopy/lsm_mouse_embryo.py
torch_em/data/datasets/light_microscopy/medussa.py
torch_em/data/datasets/light_microscopy/microbeseg.py
torch_em/data/datasets/light_microscopy/mndino.py
torch_em/data/datasets/light_microscopy/morphonet.py
torch_em/data/datasets/light_microscopy/morphoseg.py
torch_em/data/datasets/light_microscopy/mouse_embryo.py
torch_em/data/datasets/light_microscopy/mucic.py
torch_em/data/datasets/light_microscopy/neurips_cell_seg.py
torch_em/data/datasets/light_microscopy/neurosphere.py
torch_em/data/datasets/light_microscopy/nis3d.py
torch_em/data/datasets/light_microscopy/nisnet3d.py
torch_em/data/datasets/light_microscopy/nuc_morph.py
torch_em/data/datasets/light_microscopy/omnipose.py
torch_em/data/datasets/light_microscopy/oocyteseg.py
torch_em/data/datasets/light_microscopy/orgaextractor.py
torch_em/data/datasets/light_microscopy/organoid.py
torch_em/data/datasets/light_microscopy/organoidnet.py
torch_em/data/datasets/light_microscopy/orgasegment.py
torch_em/data/datasets/light_microscopy/orgline.py
torch_em/data/datasets/light_microscopy/parhyale_regen.py
torch_em/data/datasets/light_microscopy/phmamm.py
torch_em/data/datasets/light_microscopy/plantseg.py
torch_em/data/datasets/light_microscopy/pnas_arabidopsis.py
torch_em/data/datasets/light_microscopy/scaffold_a549.py
torch_em/data/datasets/light_microscopy/segpc.py
torch_em/data/datasets/light_microscopy/slimia.py
torch_em/data/datasets/light_microscopy/spheroids_hepg2.py
torch_em/data/datasets/light_microscopy/synthmt.py
torch_em/data/datasets/light_microscopy/tissuenet.py
torch_em/data/datasets/light_microscopy/toiam.py
torch_em/data/datasets/light_microscopy/u20s.py
torch_em/data/datasets/light_microscopy/usiigaci.py
torch_em/data/datasets/light_microscopy/vgg_hela.py
torch_em/data/datasets/light_microscopy/vibrio_cholerae.py
torch_em/data/datasets/light_microscopy/vicar.py
torch_em/data/datasets/light_microscopy/wing_disc.py
torch_em/data/datasets/light_microscopy/xpress.py
torch_em/data/datasets/light_microscopy/yeastcellseg.py
torch_em/data/datasets/light_microscopy/yeastms.py
torch_em/data/datasets/light_microscopy/yeastsam.py
torch_em/data/datasets/light_microscopy/yeaz.py
torch_em/data/datasets/medical/__init__.py
torch_em/data/datasets/medical/abus.py
torch_em/data/datasets/medical/acdc.py
torch_em/data/datasets/medical/acouslic_ai.py
torch_em/data/datasets/medical/amd_sd.py
torch_em/data/datasets/medical/amos.py
torch_em/data/datasets/medical/autopet.py
torch_em/data/datasets/medical/btcv.py
torch_em/data/datasets/medical/busi.py
torch_em/data/datasets/medical/camus.py
torch_em/data/datasets/medical/cbis_ddsm.py
torch_em/data/datasets/medical/chaos.py
torch_em/data/datasets/medical/cholecseg8k.py
torch_em/data/datasets/medical/covid19_seg.py
torch_em/data/datasets/medical/covid_qu_ex.py
torch_em/data/datasets/medical/ct_cadaiver.py
torch_em/data/datasets/medical/curvas.py
torch_em/data/datasets/medical/dca1.py
torch_em/data/datasets/medical/drive.py
torch_em/data/datasets/medical/dsad.py
torch_em/data/datasets/medical/duke_liver.py
torch_em/data/datasets/medical/feta24.py
torch_em/data/datasets/medical/fundus_avseg.py
torch_em/data/datasets/medical/han_seg.py
torch_em/data/datasets/medical/hil_toothseg.py
torch_em/data/datasets/medical/idrid.py
torch_em/data/datasets/medical/ircadb.py
torch_em/data/datasets/medical/isic.py
torch_em/data/datasets/medical/isles.py
torch_em/data/datasets/medical/jnuifm.py
torch_em/data/datasets/medical/jsrt.py
torch_em/data/datasets/medical/kits.py
torch_em/data/datasets/medical/kvasir.py
torch_em/data/datasets/medical/leg_3d_us.py
torch_em/data/datasets/medical/lgg_mri.py
torch_em/data/datasets/medical/m2caiseg.py
torch_em/data/datasets/medical/mbh_seg.py
torch_em/data/datasets/medical/mice_tumseg.py
torch_em/data/datasets/medical/micro_usp.py
torch_em/data/datasets/medical/montgomery.py
torch_em/data/datasets/medical/motum.py
torch_em/data/datasets/medical/msd.py
torch_em/data/datasets/medical/oasis.py
torch_em/data/datasets/medical/oimhs.py
torch_em/data/datasets/medical/osic_pulmofib.py
torch_em/data/datasets/medical/palm.py
torch_em/data/datasets/medical/panorama.py
torch_em/data/datasets/medical/papila.py
torch_em/data/datasets/medical/pengwin.py
torch_em/data/datasets/medical/piccolo.py
torch_em/data/datasets/medical/plethora.py
torch_em/data/datasets/medical/psfhs.py
torch_em/data/datasets/medical/ravir.py
torch_em/data/datasets/medical/sa_med2d.py
torch_em/data/datasets/medical/sega.py
torch_em/data/datasets/medical/segthy.py
torch_em/data/datasets/medical/siim_acr.py
torch_em/data/datasets/medical/spider.py
torch_em/data/datasets/medical/toothfairy.py
torch_em/data/datasets/medical/uwaterloo_skin.py
torch_em/data/datasets/medical/verse.py
torch_em/loss/__init__.py
torch_em/loss/affinity_side_loss.py
torch_em/loss/cldice.py
torch_em/loss/combined_loss.py
torch_em/loss/contrastive.py
torch_em/loss/contrastive_impl.py
torch_em/loss/dice.py
torch_em/loss/distance_based.py
torch_em/loss/spoco_loss.py
torch_em/loss/wrapper.py
torch_em/metric/__init__.py
torch_em/metric/cldice.py
torch_em/metric/instance_segmentation_metric.py
torch_em/model/__init__.py
torch_em/model/probabilistic_unet.py
torch_em/model/resnet3d.py
torch_em/model/unet.py
torch_em/model/unetr.py
torch_em/model/vim.py
torch_em/model/vit.py
torch_em/self_training/__init__.py
torch_em/self_training/augmentations.py
torch_em/self_training/fix_match.py
torch_em/self_training/logger.py
torch_em/self_training/loss.py
torch_em/self_training/mean_teacher.py
torch_em/self_training/probabilistic_unet_trainer.py
torch_em/self_training/pseudo_labeling.py
torch_em/self_training/uni_match_v2.py
torch_em/shallow2deep/__init__.py
torch_em/shallow2deep/prepare_shallow2deep.py
torch_em/shallow2deep/pseudolabel_training.py
torch_em/shallow2deep/shallow2deep_dataset.py
torch_em/shallow2deep/shallow2deep_eval.py
torch_em/shallow2deep/shallow2deep_model.py
torch_em/shallow2deep/transform.py
torch_em/trainer/__init__.py
torch_em/trainer/default_trainer.py
torch_em/trainer/flashoptim_trainer.py
torch_em/trainer/logger_base.py
torch_em/trainer/spoco_trainer.py
torch_em/trainer/tensorboard_logger.py
torch_em/trainer/wandb_logger.py
torch_em/transform/__init__.py
torch_em/transform/augmentation.py
torch_em/transform/defect.py
torch_em/transform/generic.py
torch_em/transform/invertible_augmentations.py
torch_em/transform/label.py
torch_em/transform/nnunet_raw.py
torch_em/transform/raw.py
torch_em/util/__init__.py
torch_em/util/debug.py
torch_em/util/grid_search.py
torch_em/util/image.py
torch_em/util/modelzoo.py
torch_em/util/prediction.py
torch_em/util/reporting.py
torch_em/util/segmentation.py
torch_em/util/submit_slurm.py
torch_em/util/test.py
torch_em/util/training.py
torch_em/util/util.py
torch_em/util/validation.py