From Whole Brain Catalog
The Whole Brain Catalog allows users to integrate data in a common multi-scale spatial framework.
Our environment allows us to view slices through the brain, 3D representations of brain parts as well as cell and molecule models.
We support 2D slice images, 2D tomograms, 3D cell morphologies, 3D EM surface meshes, and 3D EM volumes. Eventually we will allow 2D image segmentation within the environment, but for now you can look into Jinx, our segmentation tool that uses the NIFSTD ontologies.
 Brain Regions
You may change your view to explore the Whole Brain Catalog using the INCF's international standard mouse brain atlas coordinate system for spatial brain mapping, the "Waxholm Space." To switch to this view, under the View menu, choose Waxholm Brain Atlas.
Within the Whole Brain Catalog you may view brain images from serial block imaging, confocal data, microscopic MRI data, and light microscopy images. These images are referred to as slides.
Some featured data sets include:
- Images taken of the hippocampus and striatum of brain slices from GENSAT mice by Dr. Margaret Davis of the National Institute of Alcohol Abuse and Alcoholism.
- Light microscopic astrocyte images taken by Dr. Eric Bushong
- Images of striatal cells
- Retinal data taken by Tom Deerinck
We have also integrated the ability to view images that are gigabytes. In order to explore multiple, massive datasets on your personal computer in a single environment we have implemented a design in which images are broken into tiles. Inspect the highest resolution view via your web browser through links from the Whole Brain Catalog. Learn more about that here.
 Cell Morphologies
Some of the cell types already in the Whole Brain Catalog include...
 Subcellular Reconstructions
The Whole Brain Catalog has the capacity to host subcellular reconstructions.
We also have some dendrite reconstructions done by Dr. Eric Bushong.
 Neuron Simulations
Our first neuron simulation comes from Dr. Rusty Gage's lab at the Salk Institute. Dr. Brad Aimone built a computational model of adult neurogenesis in the dentate gyrus using MatLab. His model evolves through time to show the firing patterns of several cell types in the dentate gyrus, and also specifies the growth and death of neurons over time. Dr. Aimone has published several high profile papers on this model, the most recent in the journal Neuron (Aimone, Wiles, Gage 2009).
Read more about this and other collaborator highlights in the Whole Brain Project blog.
Find out how to make the visualizations of the neuron simulated activity animate!
 Molecular Structures
A highlighted molecular structure is the Potassium Channel.