I’d be really curious what software/pipelines are being used by anyone out there who is doing -nonlinear- whole scanned slide alignment. I know Visiopharm and Halo should do this in one form or another but I wonder if anyone has an open source approach they are happy with. The topic came up here: Automatically align and rotate images but I thought applications requiring nonlinear alignment could use the visibility of its own thread. I outline my application and what I’ve been tinkering with below but would love to hear about any relevant experiences.
The goal is to generate a merged aligned tiff for visual inspection of multiple scans superimposed (of the same slide restained primarily, rather than adjacent sections) as well as co-localization quantitation at the single cell level across multiple restainings (done in say QuPath).
With the same tissue restained, things seem to be linear locally and you could export and analyze ROI this way but this is awkward and globally, with re staining and drying out, things seem to creep around a good bit at the scale of the whole tissue slice requiring a nonlinear alignment. Though there aren’t necessarily shared channels, there should always be at least similar nuclear information in each scan.
So far, I’ve computed a cruddy warping on a low res images in Elastix just for testing purposes. I did this trying to map DAPI to one channel of color deconvolved IHC and applied this transformation to a high resolution tiff of one channel of the whole slide. I think I could get the alignment right with deeper study of Elastix parameters and though I don’t have much experience with these big images I imagine I could build script to semi-automate this and assemble all the resulting .raw files into a QuPath readable tiff. It looks from the literature like various folks have used a process like this, but so far I can’t find a real protocol. I am really curious however if anyone has an approach that is working for them, rather than reinventing the wheel since getting even this far as a test has taken quite a bit of time tinkering.