CFReT Project

Data

The data used in this project is a modified Cell Painting assay on cardiac fibroblasts from 3 patients that suffered from cardiac arrest.

In this modified Cell Painting, there are five channels:

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

Plate maps

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

Plate 1 = localhost220512140003_KK22-05-198

Plate 2 = localhost220513100001_KK22-05-198_FactinAdjusted

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

Plate 3 = localhost230405150001

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

See our platemaps for more details.

Goals

The goals of this project are:

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

Repository Structure

Module	Purpose	Description
0.download_data	Download CFReT pilot data	Download pilot images for the CFReT project
1.preprocessing_data	Perform Illumination Correction (IC)	Use `BaSiCPy` to perform IC on images per channel
2.cellprofiler_processing	Apply feature extraction pipeline	Extract hundreds of morphology features per imaging channel
3.process_cfret_features	Get morphology features analysis ready	Apply `pycytominer` to perform single cell normalization and feature selection
4.analyze_data	Analyze the single cell profiles to achieve goals listed above	Several independent analyses to describe data and test hypotheses

Create main CFReT conda environment

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: