@Clarence Mah Your pipeline diagram looks a lot like our (non-nf-core) EASI-FISH pipeline but with TIFF files instead of N5 😁 Ultimately, I think neither of these formats is the ideal interchange format for reusable pipeline modules: TIFF doesn't support large images and N5 doesn't have wide adoption. They may be fine as a stop-gap measure for now, and I'm certainly moving forward with N5 in my nf-core pipeline for the time being, but it would be ideal to standardize on an input/output format that we can use across many microscopy pipelines. Some folks on image.sc are organizing a hackathon in November around using next generation file formats (i.e. OME-NGFF) for image workflows. I'll be at the hackathon because I think this approach holds a lot of promise. If we can agree on the input/output format for workflow modules that deal with images, then we will be able to easily re-arrange the modules into new pipelines and get a lot more out of each module. None of that is meant to dissuade you from forging ahead with what you have! I think a switch to NGFF will take some time, especially since the tools are still catching up. But if you're interested in supporting very large images, TIFF might be an issue eventually.

darn that hackathon is quite far for me, i'm excited to hear how it goes!