Latest Data Release October 30, 2014

The latest updates to the online public resources available through the Allen Brain Atlas data portal were released on October 30, 2014. These include new data and a new feature debut.

Highlights include:

  • New Data: Mouse retinal projections and additional experiments in the Allen Mouse Brain Connectivity Atlas
    • Two thirds of the planned mouse retinal projection data sets are now available.
    • Thirty Cre driver lines with expression in subsets of retinal ganglion cells were used to map whole brain central projections in a systematic way using the high-throughput pipeline originally set up for the Allen Mouse Brain Connectivity Atlas.
    • For each whole mount retina, fluorescently labeled axons in the corresponding brain are imaged by serial two-photontomography at high throughput, high resolution, and with high sensitivity through the entire brain sampled at 100µm intervals.
    • 282 additional non-retina experiments were added. This includes 16 additional injections in the primary visual area and 266 Cre experiments focusing on projections of neuronal subpopulations.
  • New Feature: Case Studies
    • The new Case Studies feature (available from the brain-map.org homepage and from the Get Started drop-down menu) presents data in a scroll-down format that guides users through the insights available in an interesting data set.
    • The first Case Study presents a heat map of adult human brain differential gene expression by region. The structure and function of the human brain is highly stereotyped, implying a highly conserved molecular program responsible for its development, cellular structure and function. The Case Study walks users through data in the heat map illustrating how gene expression underlies anatomical structure and function of regions in the adult human brain.
  • Paper Publications
    • Allen Developing Mouse Brain Atlas platform paper published in Neuron
    • A description of the high-throughput in situ hybridization (ISH), imaging and data processing pipeline to describe whole brain gene expression patterns in Cre driver mice published in Frontiers in Neural Circuits

Society for Neuroscience Annual Meeting 2014

The Allen Institute for Brain Science will have a presence at the Society for Neuroscience Annual Meeting being held this year in Washington, D.C. on November 15-19, 2014. Come visit us at booth #310 to ask questions, give us feedback and learn more about our online public resources.

Nature Profiles of Two Allen Institute for Brain Science Resources

The Allen Institute for Brain Science published two landmark papers in the April 2nd online edition of the journal Nature, highlighting our groundbreaking work to produce and share the BrainSpan Atlas of the Developing Human Brain prenatal data, and the Allen Mouse Brain Connectivity Atlas.

The publication of these papers coincides with the first anniversary of President Obama's BRAIN Initiative and demonstrates our extensive and successful efforts in bringing big science to neuroscience and in contributing to this exciting public-private partnership.

As with all Allen Institute resources, the data are publicly available through the Allen Brain Atlas portal at http://brain-map.org.

BrainSpan Atlas of the Developing Human Brain

The BrainSpan Atlas of the Developing Human Brain serves as a high-resolution blueprint for how to build a human brain, with detailed maps of where genes are turned on and off during crucial points throughout human development. The first major report from this project focused on the prenatal data set. The data provide insight into diseases like autism that are linked to early brain development, and to the origins of human uniqueness.

The resource comprises de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on laser-microdissected brain regions from two prenatal time points.

For more information, see our press release and read the article in Nature.

Allen Mouse Brain Connectivity Atlas

The Allen Mouse Brain Connectivity Atlas is the first comprehensive, large-scale data set describing how the brain of a mammal is wired, providing a groundbreaking data resource and fresh insights into how the nervous system processes information. The platform paper in Nature describing this invaluable tool to researchers comes on the heels of the last scheduled data release to the Connectivity Atlas in March 2014.

To create the Allen Mouse Brain Connectivity Atlas, scientists used enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections, and high-throughput serial two-photon tomography to image the labeled axons throughout the brain. Data was spatially registered into a common 3D reference space, resulting in a whole-brain, cellular-level, mesoscale connectome for the mouse.

To learn more, read our press release and see the article in Nature. (Be sure to check out the cover of the April 10th print edition, featuring cortical projections from this atlas.)