├── .gitattributes ├── .gitignore ├── AUTHORS.md ├── LICENSE ├── README.md ├── codecov.yml ├── deepprofiler ├── __init__.py ├── __main__.py ├── dataset │ ├── __init__.py │ ├── compression.py │ ├── illumination_correction.py │ ├── illumination_statistics.py │ ├── image_dataset.py │ ├── indexing.py │ ├── metadata.py │ ├── pixels.py │ ├── sampling.py │ ├── target.py │ └── utils.py ├── imaging │ ├── __init__.py │ ├── augmentations.py │ ├── boxes.py │ └── cropping.py └── learning │ ├── __init__.py │ ├── metric.py │ ├── model.py │ ├── profiling.py │ ├── tf2train.py │ ├── training.py │ └── validation.py ├── example_data.tar.gz ├── figures ├── cell_painting_cnn.png ├── cell_painting_cnn_perf.png ├── deepprofilerqr.svg ├── logo │ ├── banner.afdesign │ ├── banner.png │ ├── logo.afdesign │ └── logo.png ├── tree-structure.png └── workflow.png ├── plugins ├── __init__.py ├── crop_generators │ ├── __init__.py │ ├── crop_generator.py │ ├── full_image_crop_generator.py │ ├── online_labels_crop_generator.py │ ├── repeat_channel_crop_generator.py │ └── sampled_crop_generator.py ├── metrics │ ├── __init__.py │ ├── average_class_precision.py │ └── top_k.py └── models │ ├── __init__.py │ ├── autoencoder.py │ ├── cnn.py │ ├── densenet.py │ ├── efficientnet.py │ ├── inception_resnet_v2.py │ └── resnet.py ├── scripts ├── __init__.py ├── create_metadata_index.py └── locations.py ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── conftest.py ├── deepprofiler ├── __init__.py ├── dataset │ ├── __init__.py │ ├── test_compression.py │ ├── test_illumination_correction.py │ ├── test_illumination_statistics.py │ ├── test_image_dataset.py │ ├── test_indexing.py │ ├── test_metadata.py │ ├── test_pixels.py │ ├── test_target.py │ └── test_utils.py ├── imaging │ ├── __init__.py │ ├── test_augmentations.py │ ├── test_boxes.py │ └── test_cropping.py └── learning │ ├── __init__.py │ ├── test_metric.py │ ├── test_model.py │ ├── test_profiling.py │ ├── test_training.py │ └── test_validation.py ├── files └── config │ └── test.json └── plugins ├── __init__.py ├── crop_generators ├── __init__.py └── test_crop_generator.py ├── metrics └── test_top_k.py └── models ├── __init__.py ├── test_autoencoder.py ├── test_cnn.py ├── test_densenet.py ├── test_efficientnet.py ├── test_inception_resnet_v2.py └── test_resnet.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytomining/DeepProfiler/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytomining/DeepProfiler/HEAD/.gitignore -------------------------------------------------------------------------------- /AUTHORS.md: -------------------------------------------------------------------------------- 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