Hello brain mapping community,
I am looking to register IHC expression data from coronal sections to a P14 (3D) reference atlas. I would like to use stereotaxic coordinates so I can also register my images to the Mouse Brain Connectivity Atlas/expression data. Has anyone attempted to do this either of these things with success? As the Allen Developing mouse atlas has only an unannotated coronal P14 nissl atlas I was thinking of attempting to register the P14 nissl coronal sections to the P56 coronal atlas or the 3D atlas to create an annotated coronal P14 reference space/atlas. Has anyone tried this before?
I quite like the WholeBrain registration platform as I am comfortable coding in R, but very new/not savvy at python/python notebooks. I fear I may need to learn quickly to perform the above tasks. Any help or direction would be very much appreciated.