my question is to know whether there is a way in Caret that would allow
me to see labeled cells that are initially 'below' the surface of the
brain at the surface of the brain.
This is why:
Initially, I plot section outlines and labeled cells using a computer
based charting system.Software written in our lab allows me then to
reconstruct 2D maps showing the location of labeled cells in the
cerebral cortex.
For the purpose of 3D reconstruction of brains in Caret, this customized
software also allows me to draw a 'fictive' layer IV in each section of
a dataset that will be converted in files readable in Caret.I draw the
'fictive' layer IV between layer III and layer V.
In Caret, once I have reconstructed the contours into surface, I can
only see labeled cells that are located in supra-granular layers
('above' the fictive layer IV, namely labeling in layers 2 and 3) at the
surface of the brain.In order to see labeled cells located in
infra-granular layers ('below' the fictive layer IV, namely labeling in
layers 5 and 6), I need to decrease the opacity of the brain.
Thank you for your help in this matter-- Isabelle.
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