Brain heatmap

Create custom brain heatmaps

Use this page to generate brain heatmaps ontop of the Allen Brain Atlas. You can generate heatmaps for the human brain (such as this ) or for the mouse brain (such as this). This is done by editing a google spreadsheet template and publishing it to the web.

* If you are more comfortable using matlab you can find the source code on my github page .

Customize the brain heatmaps in four steps

1. Make your own copy of the spreadsheet template: From google spreadsheet menu press File -> make a copy
   • For the mouse brain use this template .
   • For the human brain use this template .
   • For the compact human brain use this template .
2. Edit your new spreadsheet: For each brain region that interest you provide a numeric value. It is possible to remove the unused regions (rows). The region names follow the ontology used in the Allen Mouse Reference Atlas and in the Human Brain Reference Atlas .
   Here is an example of spreadsheet for the mouse and for the human.
3. Publish your google spreadsheet to the web: From google spreadsheet menu press File -> publish to the web -> start publishing then copy the link.
4. Fill the rest of this form:
   • Place the link to your google docs here:
     .
   • choose the atlas: human human (compact display) mouse
   • (optional) provide a minimum and a maximum values for the color scale.
   • Generate heatmap ⇒

Examples

• The expression of the gene HTR1B in the adult human brain (the spreadsheet used).
• The expression of the gene HTR1B in the adult human brain compact display (the spreadsheet used).
• Example of usage in the mouse brain (the spreadsheet used).

Special thanks

I would like the thanks The Allen Institute for the hard work they put in creating the reference atlases and for making them publicly available online.