Dharmendra S. Modha

My Work and Thoughts.

Archives for 2009

A Conceptual Cortical Surface Atlas

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Today, the journal PLoS ONE published a paper entitled “A Conceptual Cortical Surface Atlas” that I authored. The paper should be useful to neuro-anatomically-challenged lay people (“dummies”) seeking a bird’s eye view of cortical surface atlas. The key contribution is encapsulated in Figure S1. You can download the atlas in excel format here.

Abstract:

Volumetric, slice-based, 3-D atlases are invaluable tools for understanding complex cortical convolutions. We present a simple scheme to convert a slice-based atlas to a conceptual surface atlas that is easier to visualize and understand. The key idea is to unfold each slice into a one-dimensional vector, and concatenate a succession of these vectors – while maintaining as much spatial contiguity as possible – into a 2-D matrix. We illustrate our methodology using a coronal slice-based atlas of the Rhesus Monkey cortex. The conceptual surface-based atlases provide a useful complement to slice-based atlases for the purposes of indexing and browsing.

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The key idea is to take slices in a stereotaxic atlas (for example, Paxinos G, Huang XF, Petrides M, Toga AW (2009) The Rhesus Monkey Brain in Stereotaxic Coordinates. Elsevier Science & Technology) and then convert each slice into a one-dimensional vector. The 1D vectors are then concatenated together to create a 2D representation.

The process of creating 1D vectors is hown below for Slices 23 and 22, respectively.

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AGEA: Anatomic Gene Expression Atlas

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Nature Neuroscience recently published a breakthrough paper from Allen Institute for Brain Science and several collaborating institutions. The study was led by Michael Hawrylycz who is a mathematician by training (advisor: late famed Gian-Carlo Rota).

TITLE: An anatomic gene expression atlas of the adult mouse brain

ABSTRACT: Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of genome-scale in situ hybridization datasets enables new possibilities for understanding brain organization based on gene expression patterns. The Anatomic Gene Expression Atlas (AGEA) is a new relational atlas revealing the genetic architecture of the adult C57Bl/6J mouse brain based on spatial correlations across expression data for thousands of genes in the Allen Brain Atlas (ABA). The AGEA includes three discovery tools for examining neuroanatomical relationships and boundaries: (1) three dimensional expression-based correlation maps, (2) a hierarchical transcriptome-based parcellation of the brain and (3) a facility to retrieve from the ABA specific genes showing enriched expression in local correlated domains. The utility of this atlas is illustrated by analysis of genetic organization in the thalamus, striatum and cerebral cortex. The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea).

The paper brings structure-function together at previously unprecendented scale of 200 micron x 200 micron x 200 micron grid cells.

Humor: Theory of Intelligence from Cheers!

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"Well, you see, Norm, it’s like this. A herd of buffalo can only move as fast as the slowest buffalo. And when the herd is hunted, it’s the slowest and weakest ones at the back that are killed first. This natural selection is good for the herd as a whole, because the general speed and health of the whole group keeps improving by the regular killing of the weakest members.

In much the same way, the human brain can only operate as fast as the slowest brain cells. Now, as we know, excessive intake of alcohol kills brain cells. But naturally, it attacks the slowest and weakest brain cells first. In this way, regular consumption of beer eliminates the weaker brain cells, making the brain a faster and more efficient machine.

And that, Norm, is why you always feel smarter after a few beers."