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GFF NF1 organoid image profiling

In this repository, we perform image analysis and image-based profiling on NF1 organoids derived from patients treated with a modified Cell Painting assay.

In our assay, we have the following channels:

  • 405 = nucleus (Hoechst)
  • 488 = endoplasmic reticulum (ER)
  • 555 = actin, Golgi, and plasma membrane (AGP)
  • 640 = mitochondria (Mito)
  • TRANS = Brightfield

Preliminary data

We have collected a preliminary plate of data with includes NF1 organoids derived from patients, which contain multiple different cell types (e.g., Schwann cells, fibroblasts, etc.). This plate contains 16 treatments (either 1 uM or 10uM dose) and DMSO 1%. The layout is as shown below:

NF0014 preliminary plate

Environments

We utilize three environments for our repository.

  1. CellProfiler environment: This environment installs CellProfiler, which we use for the illumination correction and feature extraction modules.
  2. R environment: This environment is specific to R, which we use for generating figures.
  3. Preprocessing environment: This environment installs preprocessing softwares (pycytominer, CytoTable, coSMicQC) to format the morphological readouts as single-cell profiles.

These environments can be installed either via conda or mamba. Below is an example of how to install via the terminal.

# Make sure to be in this repo as the current directory
mamba env create -f ...