I am interested in extracting 3D map of MOG (myelin oligodendrocyte glycoprotein) gene available here (ISH Data :: Allen Brain Atlas: Mouse Brain).
I want to download whole mouse brain map of MOG gene as 3D and convert to nifti file (.nii). Is there anyway I can do that?
I also found spatial transcriptomics data at here (AWS S3 Explorer). Here the files are in .h5ad format. I tried to convert to nifti. However, it does not work. I am a beginner in this area of allen gene/cell atlas. I would highly appreciate if I find some help from the experts to solve this issue. Thanks.
Mamun
Indiana University
I can speak to the spatial transcriptomics data. There is currently no way to download a 3D map of individual gene locations. What you can do is plot the cell centroids of cells registered to the CCF and plot the expression level for MOG of each cell. There are ways on how to convert that information into an image but we currently have no automated way to do it.
Thanks for the reply.
Well, could you please tell me a bit more on how to register cell to the CCF and plot the expression level for MOG? I am excited to know more about this.
You can find a data table where each cell is assigned to a CCF structure at different ontology levels here:
It also has columns for the CCF coordinates.
Michael