.gitattributes
.gitignore
AGENTS.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE.md
README.md
ROADMAP.md
example_data.tar.gz
pyproject.toml
uv.lock
.github/CODEOWNERS
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.github/dependabot.yml
.github/actions/setup-env/action.yaml
.github/workflows/integration-test.yml
.github/workflows/publish.yml
deepprofiler/__init__.py
deepprofiler/__main__.py
deepprofiler/profiling.py
deepprofiler.egg-info/PKG-INFO
deepprofiler.egg-info/SOURCES.txt
deepprofiler.egg-info/dependency_links.txt
deepprofiler.egg-info/entry_points.txt
deepprofiler.egg-info/requires.txt
deepprofiler.egg-info/top_level.txt
deepprofiler/dataset/__init__.py
deepprofiler/dataset/compression.py
deepprofiler/dataset/illumination_correction.py
deepprofiler/dataset/illumination_statistics.py
deepprofiler/dataset/image_dataset.py
deepprofiler/dataset/indexing.py
deepprofiler/dataset/metadata.py
deepprofiler/dataset/pixels.py
deepprofiler/dataset/target.py
deepprofiler/dataset/utils.py
deepprofiler/imaging/__init__.py
deepprofiler/imaging/boxes.py
deepprofiler/imaging/cropping.py
figures/cell_painting_cnn.png
figures/cell_painting_cnn_perf.png
figures/deepprofilerqr.svg
figures/tree-structure.png
figures/workflow.png
figures/logo/banner.afdesign
figures/logo/banner.png
figures/logo/logo.afdesign
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scripts/__init__.py
scripts/create_metadata_index.py
scripts/locations.py
tests/__init__.py
tests/conftest.py
tests/data/cpg0000/README.md
tests/data/cpg0000/BR00116991/A01-1/Nuclei.csv
tests/data/cpg0000/BR00116991/A01-1/r01c01f01p01-ch1sk1fk1fl1.tiff
tests/data/cpg0000/BR00116991/A01-1/r01c01f01p01-ch2sk1fk1fl1.tiff
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tests/deepprofiler/__init__.py
tests/deepprofiler/dataset/__init__.py
tests/deepprofiler/dataset/test_compression.py
tests/deepprofiler/dataset/test_illumination_correction.py
tests/deepprofiler/dataset/test_illumination_statistics.py
tests/deepprofiler/dataset/test_image_dataset.py
tests/deepprofiler/dataset/test_indexing.py
tests/deepprofiler/dataset/test_metadata.py
tests/deepprofiler/dataset/test_pixels.py
tests/deepprofiler/dataset/test_target.py
tests/deepprofiler/dataset/test_utils.py
tests/deepprofiler/imaging/__init__.py
tests/deepprofiler/imaging/test_boxes.py
tests/deepprofiler/imaging/test_cropping.py
tests/deepprofiler/profiling/__init__.py
tests/deepprofiler/profiling/test_cell_painting_cnn_v1.py
tests/deepprofiler/profiling/test_profiling.py
tests/files/config/test.json