scSpatial

Tool for accessing curated pre-processed segmented spatial cytometry datasets. These data measure the spatial coordinates of single cells and will likely have corresponding protein/rna abundances, morphology measurements and cell masks. Relevent technologies include IMC, CODEX, seqFISH and CycIF.

Uploading Data

New data is gradually being added. Our goal is to make this library the standard for accessing high-quality, spatially oriented single-cell data. If you have a dataset that you want to add, it must be publicly available (i.e. on Mendeley). Then, fork the github repository and create a new branch:

git clone https://github.com/<github_username>/scSpatial
cd scSpatial

Use the add_new_dataset.sh script to add the files necessary for creating a new dataset:

authorname="<author's name>"
biosystem="<one-word e.g. BreastCancer or Melanoma or Diabetes>"
version="1.0"
git checkout -b ${authorname}-${biosystem}
bash add_new_dataset.sh $authorname $biosystem $version

The script will warn if the user is attempting to overwrtie an existing set of files and ask for confirmation.