Sorting the brain's cells

January 8, 2016

As part of our goal to understand the cellular building blocks of the brain, scientists at the Allen Institute for Brain Science are using gene expression information from single cells to help identify the different types of brain cells. Their work, published in Nature Neuroscience, identifies 49 distinct cell types in the mouse visual cortex in a detailed taxonomy.

The data and taxonomy are also available in an interactive, visual format as part of our Science Vignettes series on

“Studying any system requires knowing what the system is made of,” says Bosiljka Tasic, Ph.D., Assistant Investigator at the Allen Institute for Brain Science. “There are many ways to define the brain’s cellular building blocks. Our approach was to look at all the genes that are expressed in individual cells in the mouse visual cortex and use that information to classify the cells.”

Since each cell expresses thousands of genes, classifying numerous cells by their gene expression is an enormous computational undertaking.

“Initially, the problem of classifying cells is like sorting Skittles in the dark,” says Vilas Menon, Scientist II at the Allen Institute for Brain Science. “With single-cell gene expression data, we get the equivalent of color, or type, information, but we still have to extract it from the large-scale data set. Ultimately, we wanted to figure out how many types there were in an unbiased, data-driven way.”

For more information, watch the animation above, view the full interactive vignette and read our press release.

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