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.