HistDiff

This is to publish the code entered into GitHub by Derfel Terciano in the Lokey Lab. It is also found at https://github.com/LokeyLab/HistDiff_standalone.

This code is used to compare the distributions of a set of cellular features, quantified for many single cells per microscopy image, across populations (e.g. treated cells versus untreated cells). It is superior to comparing means or medians because it takes into account the shape of the histogram, outputting a number to indicate how much the shape changed. We use this for the first step in handling high content screen data, after the text file comes of applications such as MetaXpress, Harmony, Signals Image Artist, or Cell Profiler.

The version provided here was used in the paper published in Nature Communications, titled "Cell painting in activated cells illuminates phenotypic dark space and uncovers novel drug mechanisms of action." The supporting information for this paper is found at DOI:10.5281/zenodo.19392293. The preprint of the article is found at DOI:10.1101/2025.05.23.655853.