A 50-terabyte database of brain maps

A 50-terabyte database of brain maps

Summary: If you want to compare images from human brains with the ones of monkeys, dogs, cats, mice or birds, you should visit the BrainMaps.org website at UC Davis. It contains over 50 terabytes of brain image data directly available online. The researchers have found a way to transform sections of brain mounted on microscope slides into brain maps with a resolution of half a micrometer per pixel, or 55,000 dots per inch. With such a resolution, all the images are fully zoomable. You start with a single section of a brain and you explore it like if you had a virtual microscope. And the site also provides free downloadable tools to see the images in 3-D. Be warned: you might spend lots of time exploring this site.

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If you want to compare images from human brains with the ones of monkeys, dogs, cats, mice or birds, you should visit the BrainMaps.org website at UC Davis. It contains over 50 terabytes of brain image data directly available online. The researchers have found a way to transform sections of brain mounted on microscope slides into brain maps with a resolution of half a micrometer per pixel, or 55,000 dots per inch. With such a resolution, all the images are fully zoomable. You start with a single section of a brain and you explore it like if you had a virtual microscope. And the site also provides free downloadable tools to see the images in 3-D. Be warned: you might spend lots of time exploring this site.

In "Brain maps online," UC Davis gives a short description of the project which was initiated by researchers at its Center for Neuroscience.

BrainMaps.org features the highest resolution whole-brain atlases ever constructed, with over 50 terabytes of brain image data directly accessible online. Users can explore the brains of humans and a variety of other species at an unprecedented level of detail, from a broad view of the brain to the fine details of nerves and connections. The website also includes a suite of free, downloadable tools for navigating and analyzing brain data.

The figure below describes an example of navigation through virtual slides at BrainMaps.org using the African green monkey Nissl data set (Credit for images and caption: BrainMaps.org). "All images are actual screen shots from a Web browser and are what a visitor to brainmaps.org would see. (a) An array of virtual slides for the data set, shown as clickable thumbnails that, when clicked on, launch a new browser window allowing navigation through the high-resolution image (b). The image in panel b is 95,040×74,711 pixels and 20 gigabytes in size. The thumbnail in the upper left is for navigation purposes. Shown also are overlying labels of brain areas that may be toggled on and off. (c) Zooming in on the slide in panel b. The red box in panel b corresponds to panel c. (d) Zooming in to full resolution in panel c, showing details of individual neurons in the insula. The red box in panel c corresponds to panel d."

An example of navigation at at BrainMaps.org

There are many species present here, from primates, such as humans and monkeys, to rodents, and from cats to dogs. There is even a bird, the Tyto alba (barn owl). Below are two pictures of one owl and a section of its brain (Credit: BrainMaps.org). You'll find more sections of the owl's brain on this page (the one below is section 25).

A barn owl and its brain

And how such maps are done?

To make the maps, the researchers started with sections of brain mounted on microscope slides. Those slides were scanned to create image files or "virtual slides," and assembled like tiles into composite images. The maps have a resolution of better than half a micrometer per pixel, or 55,000 dots per inch, with virtual slides approaching 30 gigabytes in size each.

The latest research work about this project has been published by the journal NeuroImage under the name "Internet-enabled high-resolution brain mapping and virtual microscopy" (Volume 35, Issue 1, Pages 9-15, March 2007). Here are two links to the abstract and to the full paper (PDF format, 7 pages, 890 KB) from which the top image in this post has been picked. Here are some additional details about this project from the introduction of this paper.

Virtual microscopy involves the conversion of histological sections mounted on glass microscope slides to high-resolution digital images. Virtual microscopy offers several advantages over traditional microscopy, including remote viewing and data sharing, annotation, and various forms of data mining.
We describe a method utilizing virtual microscopy for generation of internet-enabled, high-resolution brain maps and atlases. Virtual microscopy-based digital brain atlases have resolutions approaching 100,000 dpi, which exceeds by three or more orders of magnitude resolutions obtainable in conventional print atlases, MRI, and flat-bed scanning. Virtual microscopy-based digital brain atlases are superior to conventional print atlases in five respects: (1) resolution, (2) annotation, (3) interaction, (4) data integration, and (5) data mining.

For more information about how these maps were built, please read the full paper.

A final note: the website contains several downloadable tools to visualize these brain maps in 3-D. And it also contains lots of brain maps. So be warned: you might spend a long time browsing this addictive site.

Sources: University of California, Davis, February 27, 2007; and various other websites

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