Cellist 1.1.0

Cellist (Cell identification in high-resolution Spatial Transcriptomics) is a cell segmentation tool for high-resolution spatial transcriptomics.

Cellist

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.

Change Log

v0.0.1a

• Build Cellist.

v1.0.0

• Release Cellist.

v1.1.0

• Update Cellist model.
• Support Cellist for image-based segmentation.

Install 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 .

Documentation

For full installation and usage of Cellist, please refer to the documentation.

Usage

cellist --help
usage: cellist [-h] [-v] {seg,align,watershed,cellpose,impute} ...

Cellist (Cell identification in high-resolution Spatial Transcriptomics) is a cell segmentation tool for high-
resolution spatial transcriptomics.

positional arguments:
  {seg,align,watershed,cellpose,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.
    cellpose            Run initial cellpose 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.