The data used in this project is a modified Cell Painting assay on cardiac fibroblasts.

In this modified Cell Painting, there are five channels:

• d0 (Nuclei)
• d1 (Endoplasmic Reticulum)
• d2 (Golgi/Plasma Membrane)
• d3 (Mitochondria)
• d4 (F-actin)

We applied this modified Cell Painting assay using the following plate design for the first two plates:

• localhost220512140003_KK22-05-198

• localhost220513100001_KK22-05-198_FactinAdjusted

For the third plate, we are using the following plate design:

• localhost230405150001

In this plate, there are only two different patients, one with a healthy heart and one that had a failing heart.

For the fourth plate, we used the following plate design:

• localhost231120090001

For this fourth plate, we are looking at different patients with the same heart failure type and patients with healthy hearts. We want to assess if there are morphological differences between cells that come from different patients but suffer the same type of heart failure, which is dilated cardiomyopathy.

See our platemaps for more details.

The goals of this project are:

1. To identify morphology features from cardiac fibroblasts that distinguish cardiac patients.
2. To discover a cell morphology biomarker associated with drug treatment to reverse fibrosis scarring caused by cardiac arrest.

For all modules, we use one main environment for the repository, which includes all packages needed including installing CellProfiler v4.2.4 among other packages.

To create the environment, run the below code block:

# Run this command in terminal to create the conda environment
conda env create -f cfret_main_env.yml

Make sure that the conda environment is activated before running notebooks or scripts:

conda activate cfret_data