Data Summary

From Whole Brain Catalog

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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.


[edit] Brain Regions

When you open the Whole Brain Catalog environment you will be viewing the Allen Brain Atlas 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.

Allen Brain Atlas
Waxholm Space

[edit] Slides

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.

Dr. Margaret Davis' (NIH/NIAAA) images of a GENSAT mouse hippocampus in the Whole Brain Catalog with the Allen Brain Atlas brain regions.

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.

[edit] Cell Morphologies

The Whole Brain Catalog provides the ability to view cell morphologies. We have already integrated cell morphologies that we grabbed from

Some of the cell types already in the Whole Brain Catalog include...

[edit] Subcellular Reconstructions

Cerebellar subcellular reconstruction within the Whole Brain Catalog.

The Whole Brain Catalog has the capacity to host subcellular reconstructions.

A highlighted data set is in the cerebellum. The subcellular meshes were created from a electron microscopic data set that was traced in Jinx.

We also have some dendrite reconstructions done by Dr. Eric Bushong.

[edit] Neuron Simulations

This was a developer only screenshot taken in the early stages of visualizing the neuron growth and firing.

In the Whole Brain Catalog users can combine neuron morphologies from NeuroMorpho and use NeuroConstruct to accurately show simulation information of neurons.

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!

[edit] Molecular Structures

Potassium channel from Protein Data Bank in the Whole Brain Catalog.

The Whole Brain Catalog can host molecular structures from the Protein Data Bank.

A highlighted molecular structure is the Potassium Channel.

[edit] Fibers

Coming soon!

Fiber tract preview.

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