.readthedocs.yaml
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
tox.ini
.github/workflows/deploy.yml
docs/Makefile
docs/api.rst
docs/conf.py
docs/empanada-napari.rst
docs/index.rst
docs/make.bat
docs/release.rst
docs/requirements.txt
docs/tutorial.rst
docs/_static/compare_2d_full.png
docs/_static/console.png
docs/_static/delete_labels.png
docs/_static/demo.gif
docs/_static/dir2d_pick.png
docs/_static/downsampling_better.png
docs/_static/empanada.png
docs/_static/empanada_logo.png
docs/_static/export2d.png
docs/_static/favicon.ico
docs/_static/finetune_model.png
docs/_static/ft_annotate.png
docs/_static/ft_example.png
docs/_static/get_info.png
docs/_static/inference_2d.png
docs/_static/inference_3d.png
docs/_static/jump_label.png
docs/_static/logo.png
docs/_static/merge_labels.png
docs/_static/merge_split.png
docs/_static/mini_compare.png
docs/_static/model_info.png
docs/_static/model_output.png
docs/_static/open_folder.png
docs/_static/ortho_params.png
docs/_static/paint_er.png
docs/_static/paint_erase.png
docs/_static/paint_mito.png
docs/_static/paint_nuclei.png
docs/_static/panoptic_result.png
docs/_static/panoptic_train.png
docs/_static/pick_patches.png
docs/_static/picked_patches.png
docs/_static/planes.png
docs/_static/plugin-install-dialog.png
docs/_static/plugin-menu.png
docs/_static/plugin_2d.png
docs/_static/register_new_model.png
docs/_static/save3d.png
docs/_static/select_batch_mode.png
docs/_static/split_labels.png
docs/_static/store_training_dataset.png
docs/_static/train_model.png
docs/_static/transpose.png
docs/_static/view3d.png
docs/api/array_utils.rst
docs/api/config_loaders.rst
docs/api/consensus.rst
docs/api/losses.rst
docs/api/metrics.rst
docs/api/zarr_utils.rst
docs/plugin/best-practice.rst
docs/plugin/install.rst
docs/plugin/modules.rst
docs/plugin/tutorials.rst
docs/tutorial/config.rst
docs/tutorial/datasets.rst
docs/tutorial/evaluation.rst
docs/tutorial/export.rst
docs/tutorial/logging.rst
docs/tutorial/models.rst
docs/tutorial/training.rst
empanada/__init__.py
empanada/_version.py
empanada/array_utils.py
empanada/config_loaders.py
empanada/consensus.py
empanada/losses.py
empanada/metrics.py
empanada/zarr_utils.py
empanada/data/__init__.py
empanada/data/_base.py
empanada/data/bc_dataset.py
empanada/data/panoptic_dataset.py
empanada/data/single_class_instance_dataset.py
empanada/data/volume_dataset.py
empanada/data/utils/__init__.py
empanada/data/utils/sampler.py
empanada/data/utils/target_creation.py
empanada/data/utils/transforms.py
empanada/evaluation/__init__.py
empanada/evaluation/evaluator.py
empanada/evaluation/instance_metrics.py
empanada/evaluation/panoptic_metrics.py
empanada/evaluation/semantic_metrics.py
empanada/inference/__init__.py
empanada/inference/engines.py
empanada/inference/filters.py
empanada/inference/matcher.py
empanada/inference/patterns.py
empanada/inference/postprocess.py
empanada/inference/rle.py
empanada/inference/tile.py
empanada/inference/tracker.py
empanada/inference/watershed.py
empanada/models/__init__.py
empanada/models/blocks.py
empanada/models/heads.py
empanada/models/panoptic_bifpn.py
empanada/models/panoptic_deeplab.py
empanada/models/point_rend.py
empanada/models/decoders/__init__.py
empanada/models/decoders/aspp.py
empanada/models/decoders/bifpn.py
empanada/models/decoders/panoptic_deeplab.py
empanada/models/encoders/__init__.py
empanada/models/encoders/regnet.py
empanada/models/encoders/resnet.py
empanada/models/quantization/__init__.py
empanada/models/quantization/panoptic_bifpn.py
empanada/models/quantization/panoptic_deeplab.py
empanada/models/quantization/point_rend.py
empanada/models/quantization/decoders/__init__.py
empanada/models/quantization/decoders/panoptic_deeplab.py
empanada/models/quantization/encoders/__init__.py
empanada/models/quantization/encoders/regnet.py
empanada/models/quantization/encoders/resnet.py
empanada_dl.egg-info/PKG-INFO
empanada_dl.egg-info/SOURCES.txt
empanada_dl.egg-info/dependency_links.txt
empanada_dl.egg-info/requires.txt
empanada_dl.egg-info/top_level.txt
projects/mitonet/configs/finetune.yaml
projects/mitonet/configs/mmm_median_inference.yaml
projects/mitonet/configs/mmm_median_inference_celegans.yaml
projects/mitonet/configs/mmm_median_inference_fly_brain.yaml
projects/mitonet/configs/mmm_median_inference_glycolytic_muscle.yaml
projects/mitonet/configs/mmm_median_inference_hela.yaml
projects/mitonet/configs/mmm_median_inference_lucchi.yaml
projects/mitonet/configs/mmm_panoptic_bifpn_pointrend.yaml
projects/mitonet/configs/mmm_panoptic_deeplab_bc.yaml
projects/mitonet/configs/mmm_panoptic_deeplab_pointrend.yaml
projects/mitonet/configs/mmm_ws_inference_fly_brain.yaml
projects/mitonet/configs/train_ablation/ablation_finetune.yaml
projects/mitonet/configs/train_ablation/ablation_instance_decoder.yaml
projects/mitonet/configs/train_ablation/ablation_point_rend.yaml
projects/mitonet/scripts/evaluate3d.py
projects/mitonet/scripts/evaluate3d_bc.py
projects/mitonet/scripts/legacy_data/crop2d_with_masks.py
projects/mitonet/scripts/legacy_data/deduplicate3d_with_masks.py
projects/mitonet/scripts/legacy_data/filter_nn.py
projects/mitonet/scripts/legacy_data/organize_from_deduplicated.py
projects/mitonet/scripts/zooniverse/create_flipbooks.py
projects/mitonet/scripts/zooniverse/group_tem_segs.py
projects/mitonet/scripts/zooniverse/merge_seg_dirs.py
projects/mitonet/scripts/zooniverse/merge_zoo_segs.py
projects/mitonet/scripts/zooniverse/split_proof_stack.py
scripts/export_model.py
scripts/finetune.py
scripts/inference3d_multigpu.py
scripts/pdl_inference3d.py
scripts/train.py
scripts/train_bc.py
tests/test_array_utils.py
tests/test_consensus.py
tests/test_data_post.py
tests/test_matcher.py
tests/test_metrics.py
tests/test_tiling.py
tests/test_tracking.py
tests/test_data/instance/dataset1/images/ins_seg.tiff
tests/test_data/instance/dataset1/masks/ins_seg.tiff
tests/test_data/panoptic/dataset1/images/pan_seg.tiff
tests/test_data/panoptic/dataset1/masks/pan_seg.tiff