Core-level registration across 9 IHC biomarkers using outputs from QuPath

Hi guys, I have 10 TMAs and I’d like to perform image registration for each core.
My current workflow is, for each TMA, export the core as jpg images at the highest resolution, this gives me 10 images at each position:


Then I choose H&E as the fixed image, others as moving image and then use the Registration Estimator App within Matlab to perform the registration. This step gives a transformation matrix.
Now the problem is, how to use this matrix to transform the cell coordinates within each core? To answer this question I need to know how QuPath generate such image for each core so that I can first accurately map those cells to the images and then perform the registration.
Any ideas? Thank you!