StereoCell is a tool for generating single-cell gene expression data

• pipeline

It supported on Stitching, Tissue segmentation, Cell segmentation and Cell labelling. Easy installation based on python==3.8 like,

pip install -r requirements.txt

If you need run the segmentation module, download the weights files first, then modify the file -> weights.json. Model zoo,

• manual tool on Windows

It supported on Stitching, Registration, Tissue segmentation and Single cell data visulization. Please download the installation package first, and follow the tutorial step by step. More detail refer this.

We recommend using Manual tool to complete Stitching & Registration module, and Pipeline to complete Segmentation & Cell labelling module

• Sample Data Image(FOV tiles, 3X3) and GeneMatrix

• Manual tool

Refer the tutorial step by step

• About pipeline

python .\cell_bin.py \
--image_path D:\code\mine\github\StereoCell\data\SS2000_regist.tif \
--matrix_path D:\code\mine\github\StereoCell\data\SS2000.gem.gz  \
--out_path D:\code\mine\github\StereoCell\data

python .\stitch.py \
--input D:\\code\\mine\\github\\StereoCell\\data \
--output D:\\code\\mine\\github\\StereoCell\\data\\stitched.tif \
--overlap 0.12

import stitch

input = 'D:\\code\\mine\\github\\StereoCell\\data'
output = 'D:\\code\\mine\\github\\StereoCell\\data\\stitched.tif'
stitch.stitch(input, output, overlap=0.12)

python .\cell.py \
--input D:\StereoCell\data\image_6467_16800_512_512.tif \
-output D:\StereoCell\data\image_cell.tif \

python .\tissue.py \
--input D:\StereoCell\data\image_6467_16800_512_512.tif \
-output D:\StereoCell\data\image_tissue.tif \

python correct.py \
--way fast \
--mask_path D:\StereoCell\data\cell_mask.tif \
--matrix_path D:\StereoCell\data\gene.gem.gz \
--out_path D:\StereoCell\data

import correct

mask_path = 'D:\StereoCell\data\gene.gem.gz'
matrix_path = 'D:\StereoCell\data\cell_mask.tif'
out_path = 'D:\StereoCell\data'
correct.adjust('fast', mask_path, matrix_path, out_path, radius=50, process=10, threshold=20)

Please cite StereoCell in your publications if it helps your research:

@article{StereoCell,
  Author = {BGI Dev Group},
  Year = {2022}
}

https://github.com/matejak/imreg_dft

https://github.com/rezazad68/BCDU-Net

https://github.com/libvips/pyvips