.gitignore
LICENSE
MANIFEST.in
README.md
demo_notebook.ipynb
pyproject.toml
requirements.txt
tox.ini
.github/workflows/python-publish.yml
.vscode/settings.json
demo/KNN.py
demo/KNN_DINOv3.py
demo/KNN_Dino.py
demo/KNN_ImageNet.py
demo/KNN_ImageNet_hugg.py
demo/KNN_all4one.py
demo/KNN_mocov3.py
demo/knn_local_vit_common.py
demo/knn_tsne_utils.py
notebooks/DevelopmentGuide.md
notebooks/TutorialForVersion0.0.10.md
notebooks/UserGuide.md
source/convert_label.png
source/convert_label_example.png
source/image-1.png
source/image-10.png
source/image-11.png
source/image-12.png
source/image-13.png
source/image-14.png
source/image-15.png
source/image-16.png
source/image-17.png
source/image-18.png
source/image-19.png
source/image-2.png
source/image-20.png
source/image-21.png
source/image-22.png
source/image-3.png
source/image-4.png
source/image-5.png
source/image-6.png
source/image-7.png
source/image-8.png
source/image-9.png
source/image.png
source/inference_gui.png
src/emcfsys/__init__.py
src/emcfsys/_reader.py
src/emcfsys/_sample_data.py
src/emcfsys/_version.py
src/emcfsys/_widget.py
src/emcfsys/_writer.py
src/emcfsys/napari.yaml
src/emcfsys.egg-info/PKG-INFO
src/emcfsys.egg-info/SOURCES.txt
src/emcfsys.egg-info/dependency_links.txt
src/emcfsys.egg-info/entry_points.txt
src/emcfsys.egg-info/requires.txt
src/emcfsys.egg-info/scm_file_list.json
src/emcfsys.egg-info/scm_version.json
src/emcfsys.egg-info/top_level.txt
src/emcfsys/EMCellFiner/hat/models/hat_arch.py
src/emcfsys/EMCellFiner/hat/models/hat_model.py
src/emcfsys/EMCellFiner/hat/models/img_utils.py
src/emcfsys/EMCellFiner/hat/models/inference_hat.py
src/emcfsys/EMCellFound/inference.py
src/emcfsys/EMCellFound/train.py
src/emcfsys/EMCellFound/datasets/__init__.py
src/emcfsys/EMCellFound/datasets/classification_folder.py
src/emcfsys/EMCellFound/datasets/coco_instance.py
src/emcfsys/EMCellFound/datasets/segmentation2D.py
src/emcfsys/EMCellFound/metrics/metrics.py
src/emcfsys/EMCellFound/models/BackboneWrapper.py
src/emcfsys/EMCellFound/models/DeepLabv3Plus.py
src/emcfsys/EMCellFound/models/EMCellFoundViT.py
src/emcfsys/EMCellFound/models/PSPNet.py
src/emcfsys/EMCellFound/models/RTMInstanceSeg.py
src/emcfsys/EMCellFound/models/UNet.py
src/emcfsys/EMCellFound/models/UperNet.py
src/emcfsys/EMCellFound/models/backbone_registry.py
src/emcfsys/EMCellFound/models/classifier.py
src/emcfsys/EMCellFound/models/model_factory.py
src/emcfsys/EMCellFound/transforms/augmentations.py
src/emcfsys/EMCellFound/transforms/transforms.py
src/emcfsys/EMCellFound/utils/checkpoint.py
src/emcfsys/PhenotypeAnalysis/__init__.py
src/emcfsys/PhenotypeAnalysis/functions.py
src/emcfsys/utils/__init__.py
src/emcfsys/utils/classification_tasks.py
src/emcfsys/utils/coco_instance_inspector.py
src/emcfsys/utils/dataset_validator.py
src/emcfsys/utils/emcellfiner_tasks.py
src/emcfsys/utils/fps.py
src/emcfsys/utils/image_resize_ops.py
src/emcfsys/utils/inference_tasks.py
src/emcfsys/utils/instance_segmentation_tasks.py
src/emcfsys/utils/io_utils.py
src/emcfsys/utils/labelme_coco_tasks.py
src/emcfsys/utils/labelme_semantic_tasks.py
src/emcfsys/utils/model_registry.py
src/emcfsys/utils/training_artifacts.py
src/emcfsys/utils/training_tasks.py
src/emcfsys/utils/viewer_ops.py
tests/__init__.py
tests/conftest.py
tests/test_classification_tasks.py
tests/test_dataset_validator.py
tests/test_emcellfiner_tasks.py
tests/test_image_resize_ops.py
tests/test_img.tif
tests/test_inference_tasks.py
tests/test_instance_segmentation.py
tests/test_io_utils.py
tests/test_labelme_semantic_tasks.py
tests/test_model_registry.py
tests/test_reader.py
tests/test_sample_data.py
tests/test_training_tasks.py
tests/test_widget.py
tests/test_writer.py