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DeepProfilerExperiments

This is a supplementary repository for DeepProfiler software and the related analysis pre-print.

Please see our DeepProfiler handbook for documentation.

In the folders ta-orf, bbbc022 and cdrp of this repository you can find Jupyter notebooks for downstream analysis and configuration files (folder config) to reproduce training experiments and run feature extraction afterwards, plus configuration files to run feature extraction with Cell Painting CNN or EfficientNet pre-trained on ImageNet dataset. Ground truth annotations are in data folders used in the publication.

profiling folder contains libraries and utils functions for downstream analysis notebooks.

bbbc021 contains Jupyter notebooks for downstream analysis of the BBBC021 dataset. This is legacy code.