yuqiyuqitan/CellSeg_lgTis

CellSeg: a robust, pre‑trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images

CellSeg

Fork for Docker

docker pull andrewrech/cellseg:latest

docker run -it --rm \
  -v /toplevel/data/folder:/home/jovyan/work \
  -e GRANT_SUDO=yes \
  andrewrech/cellseg:latest

Edit run.py to point to your data folders, then run:

source ~/CellSeg/start.bash

...
Segmented crop in 5.329453229904175 seconds.
Segmented crop in 3.884769916534424 seconds.
Segmented crop in 4.497356414794922 seconds.
Segmented crop in 4.965950965881348 seconds.
...