A Whole-Brain Scanning System

A novel technique developed by researchers at Cold Spring Harbor Laboratory automates and accelerates histological sectioning for 3-D mapping of the mammalian brain for closer study.


We recently reported on a probe developed by IBM that will allow pathologists to take smaller biopsies. Now there may be a way to perform such histology faster, at least for brain studies. The conventional technique is to freeze a fluorescence-tagged whole brain or fix it in paraffin wax and then proceed to meticulously slice it into hundreds or thousands of micron-wide sections that are then mounted on slides and imaged. This takes huge investments of time and effort, so scientists usually focus on mapping specific regions of interest (e.g. cortex or amygdala). At least one project, the Allen Brain Atlas, emerged in response with the goal to map the entire mouse brain so that all researchers may rely upon it for their work.

Similar atlases may now be created even faster thanks to researchers at Cold Spring Harbor Laboratory, who announced in Nature Methods the development of a novel technique that automates and accelerates histological sectioning for 3-D brain-mapping. Known as serial two-photon (STP) tomography, the technique

...achieves high-throughput fluorescence imaging of whole mouse brains via robotic integration of the two fundamental steps -- tissue sectioning and fluorescence imaging...

A full set of data, including final images, could be obtained by the team in 6.5 to 8.5 hours per brain, depending on the resolution. These sets each were comprised of 260 top-to-bottom, or coronal, slices of mouse brain tissue, which were assembled by computer into three-dimensional renderings themselves capable of a wide range of "warping," i.e., artificial manipulation, to reveal hidden structures and features.

"The technology is a practical one that can be used for scanning at various levels of resolution, ranging from one to two microns to less than a micron," [Professor Pavel] Osten says. Scans at the highest resolution level take about 24 hours to collect. This makes possible an impressive saving of time, Osten says, compared to methods that are now in use. Using these, it would take an experienced technician about a week to collect a set of whole-brain images at high resolution, he noted.

In terms of applications and future work, according to the Nature Methods paper:

STP tomography is particularly well-suited for systematic studies of brain anatomy in genetic mouse models of cognitive disorders, such as autism and schizophrenia. To provide quantitative measurements for such studies, we are now focusing on anatomical registration and the development of computational methods for detection of fluorescence signals in whole-brain datasets generated by STP tomography.

This system, along with other emerging automated brain-scanning techniques, may have the same effect on neuroscience as next generation sequencing technologies had on genetics. It used to be prohibitively expensive to sequence an entire genome (which is why the NIH had to step in for the Human Genome Project), but automated and high-throughput technologies have reduced the time and cost required so researchers can simply sequence an entire sample rather than just a specific region. We hope to see more cool 3-D brain maps, and the discoveries and innovations they inspire, in the near future.

This post also appears on medGadget, an Atlantic partner site.