This repository is for analyzing the Axiom OASIS imaging data. Scripts for downloading the data from the Cell Painting Gallery are included in the 0_data_download folder. The main analysis is in the 1_snakemake folder, and exploratory notebooks for visualizing results and comparing across pipeline variations are in the 2_downstream_analysis folder.
The scripts in 0_prepare_data compile profiles, metadata, and image locations across plates and batches, and ensure that formatting is consistent across different cell representations. These compiled files are the inputs to the snakemake pipeline. To make things easier, we've deposited a copy of the compiled inputs on Zenodo. The script 4A_download_compiled_inputs.py can be run instead of scripts 1A - 2E.
If you are only interested in viewing example images from OASIS, check out the 2_downstream_analysis/other_notebooks/Plot_images.ipynb notebook. It contains instructions for downloading the necessary metadata for downloading images from AWS and functions for combining them into nice plots.