0.download_data

Download images from each plate from the NF1 Schwann cell project

In this module, we download the images and platemap metadata for each plate from Figshare, which is a open-source repository that holds data/figures/etc. to preserve and share. The plates for this project are located at NF1 Schwann Cell Genotype Cell Painting Assay on Figshare.

Run the download_plates notebook

Note: Confirm that the shell name in the cp_analysis.sh file is correct for your machine (e.g. Linux = bash, MacOS = zsh).

To download the images for each plate and separate the metadata from the images, run the download_plates.ipynb notebook as a python script using the code block below:

# Run this script in terminal
cd 0.download_data
source download_plates.sh

To download 5 plates from figshare, it took about 58 minutes. There is the option to parallelize this in the future depending on needs.