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
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:
We utilize three environments for our repository.
- CellProfiler environment: This environment installs CellProfiler, which we use for the illumination correction and feature extraction modules.
- R environment: This environment is specific to R, which we use for generating figures.
- 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 ...