Cell identification in high-resolution Spatial Transcriptomics
Cellist is a computational method to perform cell segmentation on high-resolution spatial transcriptomics (ST) data, including sequncing-based (e.g. Stereo-seq and Seq-Scope) and imaging-based (e.g. seqFISH+ and STARmap) technologies.
- Build Cellist.
- Release Cellist.
git clone https://github.com/wanglabtongji/Cellist.git
cd Cellist
conda create -n Cellist python=3.10
pip install -r requirements.txt
pip install .For full installation and usage of Cellist, please refer to the documentation.
cellist --help
usage: cellist [-h] [-v] {seg,align,watershed,impute} ...
Cellist (Cell identification in high-resolution Spatial Transcriptomics) is a cell segmentation tool for high-resolution spatial transcriptomics.
positional arguments:
{seg,align,watershed,impute}
seg Run Cellist segmentation on high-resolution spatial transcriptomics.
align Refine alignment between image and spatial transcriptomics.
watershed Run initial watershed segmentation on the staining image.
impute Perform spatially-aware gene imputation within each cluster.
optional arguments:
-h, --help show this help message and exit
-v, --version Print version info.