Cortical Box method


  • In situ hybridization technique can generate a vast amount of data with rich information about the neuroanatomical basis for gene expression regulation.  How can we analyze such complex datasets?  

  • Cortical box method was developed by Dr. Junya Hirokawa in our lab to map c-fos immunoreactivity in the rat cortex (ref 15).  This method was now applied to analyze the in situ data (ref 16). 

  • Here is the preview of what "cortical box" looks like.
  • For more details, visit our cortical box website.

What is cortical box method?

This is the original image.

Image of RORbeta

Cortical region is taken out and transformed...

RORbeta transformed

and then, normalized....

ROR beta transformed 3

You do this to a set of coronal sections of a rat cortex

Serial sections

Then, the cortex becomes a box.....
You can now slice the cortical box at desired lamina positions for layer maps

Cortical box

Want to know more about this method?

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