Two small tools to render the annotation and images of the Allen Mouse Brain Atlas. Both tools take different input files but generate 1304 images of the Mouse Brain (456 sagital, 528 coronal and 320 axial)
Coronal slice 300 created from both tools
This repository contains two projects:
Loads the annotation.raw volume data from the Allen Mouse Brain Atlas and creates images for every slice. Every structure will have a random color.
The raw data is not provided in this repository. You can download the needed data from the Allen Brain Atlas Project:
The Annotation Loader reads the annotation of the structural volume. The data can be found in this zip file. The file in question is annotation.raw. For more information on the format read the documentation.
Compile the code and execute the binary with the following parameters:
AllenMouseBrainAnnotationLoader.exe <path-to-the-annotation.raw> <output-path>
Loads the sagital slices images of the atlas and creates all images of the other axis
The raw data is not provided in this repository. You can download the needed data from the Allen Brain Atlas Project:
The Image Loader uses the image data from the Brain Explorer 2 (an awesome tool, btw.). Download the following zip file and copy the images from zip-file\Spaces\P56\AtlasSlices in a folder.
Compile the code and execute the binary with the following parameters:
AllenMouseBrainAverageImageLoader.exe <path-to-the-image-folder> <output-path>