MouseAtlas

Tool to interactively create a Mouse Brain Atlas.

You need Matlab (tested on v. 2016) and SPM12.

Installation

Copy the files to a location of your choice. Make sure that you included your SPM12 path in Matlab. Open the application by 'ms_gui_mouseAtlas'

Creating an atlas

On the left, there is a tree selection (starting with 'root'). From there you can explore the atlas.
To 'select' a region right click its name in the tree selection. Selected regions are getting a bold green font.
For a visual presentation you can click 'Update'. The axis on the right is updated. The color of a region of interest (ROI) is the same as indicated in the selection tree.
Click 'Create Atlas'. After creation you can inspect the result (a figure opens automatically). In total, the app will create 4 files:
- the annotation atlas (matching the Allen avg template)
- a txt file linking the numbers with the names of regions
- the Allen atlas average template
- an annotation file in paxinos space (suffix '_inPax')

Manual

A manual can be found in the doc folder.

Example

You can find an usage example in the example folder. This example extracts ROI time courses from a 4D nifty file and calculates a correlation matrix. The used atlas was created with this application. Make sure to unzip 'data.zip' before usage!

Citation