We have added over two hundred Allen Atlas brain regions to the latest version of the Whole Brain Catalog. These changes haven’t been incorporated into the main release yet, but they are ready to be evaluated. The addition of the Allen Atlas brain regions gives a more a detailed and elegant view of the mouse brain, but visualizing over 200 brain meshes at once has proven to be challenging. The following post intends to elaborate on this new feature and the challenges we have come across during the implementation phase.
A Whole Brain Catalog user has the option of visualizing all brain regions at once or each individually, but for the purpose of simplicity only five brain regions are visible by default at program startup. In order to display all the brain regions in the scene, we first have to download the corresponding data files from our server. Once we have downloaded the data files, we create objects (Tangibles) for all the brain regions using a geometry mesh called “TriMesh”, which is available to us through the game engine platform JMonkeyEngine. As of this version we are using “.obj” files to store the brain region’s data, but we also have access to these files in Collada format which we intend to use in future releases.
Once we have finished downloading the data files and creating the objects (Tangibles) we need to render them on the scene. In order to do this we use the objects we previously created and make spatials (TangibleViews) out of them. A spatial is created by attaching the object (Tangible) to a JmonkeyEngine graph scene node called a Node. When all spatials have been created, we attach them to the 3D scene and this is how we are able to visualize the entire Allen Atlas brain inside the Whole Brain Catalog. One of the challenges we have come across while implementing this feature is the high amount of video card resources it takes to render over 200 meshes at the same time. Each brain region is represented by a mesh and each mesh can be represented by hundreds of verticies which can make the 3D scene really crowded. The more crowded the scene, the less performance we get from the application. For future releases, we will explore different rendering techniques to increase the performance of the application when the entire Allen Atlas brain is visible.
Be sure to visit our developer documentation for more information or post to our google groups mailing list if you have questions.
[...] of the mouse brain, but visualizing over 200 brain meshes at once has proven to be challenging. Take a look at a post from Jesus Martinez, who has been tackling this challenging problem on the developers blog if you would like to learn [...]