Yes, nip2 has a no-GUI batch mode. You can make a workspace interactively that does some task, then run it with something like: nip2 -bp --set 'Workspaces.pro

Yes, nip2 has a no-GUI batch mode. You can make a workspace interactively that does some task, then run it with something like: nip2 -bp --set 'Workspaces.process.A1=Image_file "fred.jpg"' --set main=Workspaces.process.A10 -o fred2.jpg process.ws -b meaning batch mode, -p meaning send the value of main to the output. That'll load the process.ws workspace, set cell A1 to be the image "fred.jpg", set main (the point of execution) to be cell A10, and save it to fred2.jpg. I made a workspace for medical image analysis (my old job). It finds lungs in a 4D PET-CT scan, then fits a two compartment model per voxel and generates a volume image from k2. It has just over 10,000 cells (!!), 70GB of images, and executes in about 2 minutes using around 1GB of ram. I then used a small bash script to loop over my dataset of 2,000 scans computing an inflammation index. It worked surprisingly well, IMO.