A generalist algorithm for cell and nucleus segmentation that can be optimized for your own data and perform image restoration

Documentation

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Source code

Slurm script

Running the GUI

Invoking cellpose with no options will bring up the gui.
 

$ module load cellpose
$ cellpose

Image

In a batch script:

#SBATCH --job-name=cellpose
#SBATCH --time=1:00:00
#SBATCH --partition=gpu
#SBATCH --gres=gpu:v100:1
#SBATCH --ntasks=4
#SBATCH --mem=16GB
module load cellpose
cellpose --train --dir /path/to/images/ --pretrained_model None --chan 3 --chan2 0 --use_gpu --verbose