This is a version of cytopacq developed by the CBIA in Brno, Czech Republic, that has been containerized to be run with docker or apptainer.
It contains all the defaults modules and can be run in the following way:
docker run -it --rm -v LOCAL_FOLDER:/data ghcr.io/tp81/cytopacq:master
You can also clone this repository and build&run it locally
git clone https://github.com/tp81/cytopacq.git
cd cytopacq
docker build -t cytopacq .
docker run cytopacq -v LOCAL_FOLDER:/data
Mapping the LOCAL_FOLDER is optional but recommended. It avoids cluttering the container and with the --rm option, all traces created by cytopacq will be erased upon exit.
You can also run it using apptainer if you are in an HPC environment.
apptainer run docker://ghcr.io/tp81/cytopacq
To use one of the defaults configurations, assuming you have an empty directory at "C:\tmp" (you can change it to whatever you please), you can launch cytopack with :
docker run -it -v "C:\tmp:/data" ghcr.io/tp81/cytopacq:master -c /usr/local/config/hl60-release.ini -f /data/im.ics -l /data/lb.ics -e /data/error.log
or with apptainer:
apptainer pull docker://ghcr.io/tp81/cytopacq:master
apptainer run --bind ".:/data" ./cytopacq_master.sif -c /usr/local/config/hl60-release.ini -f /data/im.ics -l /data/lb.ics -e /data/error.log
It'll take a few minutes to process. You should see ywo new images in C:\tmp, im.ics and lb.ics. These will be the image and label component of the simulated output.
The list of available INI files is here:
docker run -it --rm --entrypoint /bin/bash ghcr.io/tp81/cytopacq:master -c "ls /usr/local/config"
or
apptainer exec ./cytopacq_master.sif ls /usr/local/config
You can also create your own by modifying the ones in that directory.
David Svoboda and the CBIA created Cytopacq. Thomas Pengo dockerized it.