Hello! I am trying to do something very simple but not having much luck. I want to use the adult mouse brain atlas to get average depths / thicknesses of cortical layers to use in a modeling project. Is there a simple way to do this? And is this information available in the human atlas as well?
Hi @bmarsh,
Sorry, our applications and services does not currently support cortical thickness calculations.
Hello @bmarsh , are you looking for depths/thicknesses as a proportion (percent) of total cortical thickness, or in terms of raw measurements? If the former, the solution to Laplace’s equation within the isocortex (http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/cortical_coordinates/ccf_2017/laplacian_10.nrrd) can be used in conjunction with the atlas labels. If you’re looking for depth in physical units, I have generated streamlines for a previous project over which thickness can be computed. Happy to share those resources + code if you want.
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Hello @yyee, thank you for the input! I am also trying to accomplish this, if by chance you still monitor this. I am just looking for approximate depths that can define each layer, (layer 4 begins at depth x, layer 5 begins at depth x, etc.). I am not sure how to use the file you linked, but if you can, any help is greatly appreciated!
For the purposes of cortical analysis, our morphology pipelines have used these values as an average value of hand drawn layer boundaries done on dapi stain images. This isn’t derived from the CCF though, so there may be slight differences, and this project was focused on visual cortex, so there are differences by area.
{
“4”: 333.4658190171,
“5”: 453.6227158132,
“2/3”: 115.1112491335,
“6a”: 687.6482650269,
“6b”: 883.1308910545,
“wm”: 922.5861720311
}
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