.gitignore
LICENSE
MANIFEST.in
README.md
mmLab_backend_demo.ipynb
pyproject.toml
requirements.txt
setup.py
tox.ini
.github/workflows/python-publish.yml
.vscode/settings.json
demo/KNN_code/KNN.py
demo/KNN_code/KNN_DINOv3_EMCellFound.py
demo/KNN_code/KNN_DINOv3_Meta_hugg.py
demo/KNN_code/KNN_DINOv3_Meta_local.py
demo/KNN_code/KNN_Dino.py
demo/KNN_code/KNN_ImageNet.py
demo/KNN_code/KNN_ImageNet_hugg.py
demo/KNN_code/KNN_all4one.py
demo/KNN_code/KNN_mocov3.py
demo/KNN_code/knn_local_vit_common.py
notebooks/EMCFsys_UserGuide_Chinese.md
notebooks/EMCFsys_UserGuide_English.md
notebooks/TutorialForVersion0.0.10.md
notebooks/buildForMMlab.md
notebooks/image/EMCFsys_UserGuide/1786027624248.png
notebooks/image/EMCFsys_UserGuide_English/1786113597122.png
notebooks/image/TutorialForVersion0.0.10/1785991050954.png
notebooks/image/UserGuide/01_plugin_menu.png
notebooks/image/UserGuide/02_image_resize.png
notebooks/image/UserGuide/03_model_manager.png
notebooks/image/UserGuide/04_semantic_training.png
notebooks/image/UserGuide/05_semantic_inference.png
notebooks/image/UserGuide/06_classification_training.png
notebooks/image/UserGuide/07_classification_training_extra.png
notebooks/image/UserGuide/08_instance_seg_training.png
notebooks/image/UserGuide/09_instance_seg_inference.png
notebooks/image/UserGuide/10_dataset_validator.png
notebooks/image/UserGuide/11_SuperResolution_singleInference.png
notebooks/image/UserGuide/12_SuperResolution_BatchInference.png.png
notebooks/image/UserGuide/13_LabelmeToSemanticMasks_dataset.png
notebooks/image/UserGuide/14_LabelmeToInstance_dataset.png
notebooks/image/UserGuide/15_PhenotypeAnalysis.png
source/Napari_emcfsys_GUI.png
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
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source/image-2.png
source/image-20.png
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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/model_cache.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/Mask2Former.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/dinov3.py
src/emcfsys/EMCellFound/models/model_factory.py
src/emcfsys/EMCellFound/ops/__init__.py
src/emcfsys/EMCellFound/ops/ms_deform_attn.py
src/emcfsys/EMCellFound/ops/point_sampling.py
src/emcfsys/EMCellFound/ops/csrc/common_cuda_helper.hpp
src/emcfsys/EMCellFound/ops/csrc/ms_deform_attn_bind.cpp
src/emcfsys/EMCellFound/ops/csrc/ms_deform_attn_cuda.cu
src/emcfsys/EMCellFound/ops/csrc/ms_deform_attn_cuda_kernel.cuh
src/emcfsys/EMCellFound/ops/csrc/pytorch_cuda_helper.hpp
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_dinov3.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_mask2former_ops.py
tests/test_model_cache.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