This repository contains supporting scripts and codes used in the analysis for the paper: "High-content morphological profiling by Cell Painting in 3D spheroids".
Cell Painting is a popular assay for morphological profiling of 2D monolayer cell cultures.
In the paper, we propose a scalable method to apply Cell Painting in 3D.
The workflow is largely based on existing analysis strategies,
with some adaptations to enable single-cell morphological profiling of 3D spheroids.
This repository contains a collection of notebooks for processing CellProfiler features of 3D spheroids and creating figures that accompany the manuscript.
More on this will follow. We aim to make the images, cell pose models, and feature files available in a suitable repository.