Read An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

mleiwe / PathologyRegistrationPipeline

A Project for the Merbl lab at Cornell. The aim is to create a registration pipeline whereby large .bif files of histological sections can be put in registration with an MRI template in order to view the anatomy in high resolution.

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Sadly the answer is that it won't be as easy as I hoped. It can register large.bif files but, they have to be of the same plane.

We can do this if the MRI plane we obtain is exactly the same as the plane of sectioning
- This can be overcome if the MRI gets rotated to the same angle of sectioning.
- We still need to stitch sections across multiple cassettes too.
The precision doesn't need to be perfect, i.e. if there is a bit of jitter we'll be fine. The issue is I don't know how much jitter there will be
Need to see if the differences in resolution will be a problem

mleiwe / PathologyRegistrationPipeline

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