Nextflow module to use Baysor for cell segmentation in imaging-based spatial-transcriptomics.
To run locally: Nextflow and Docker. Either create the image from the given Dockerfile or pull the image from the repo commented on main.nf. The workflow is currently working using Docker (also printing HTML files with summaries of the segmentation). For creating the Apptainer image one can take the Dockerfile and do the following:
$ docker save -o baysor.tar <name-of-docker-image:tag
and on the HPC build the Apptainer image:
$ apptainer build baysor.sif docker-archive://baysor.tar
Running on the HPC is working but there is currently an issue when saving the output HTML plots, so the -p flag must be silenced.