Looking through the brain with CLARITY!

Imaging single layers of cells is very easy since the light can penetrate the cells quite easily. Imaging a tissue sample of several layers of cells is more difficult, because the passage of light is gradually blocked. To image a whole organ without slicing it was near-impossible, until now.

CLARITY is a new method, developed by the lab of Karl Deisseroth, a neuroscientists from Stanford university and published in the Nature Online. In essence, they took a whole mouse brain, infused it with a hydrogel, which was cross-linked to all the “important” biomolecules (proteins & nucleic acids). They then removed all the lipids and other “non-important” molecules (which were not cross-linked to the hydrogel), with a detergent, SDS.

The result was a transparent mouse brain, that maintained all of it original cellular (and presumably sub-cellular) structure.

Mouse brain before & after CLARITY. Source: Chung, K. et al Nature (2013)

They could then image into the brain, using pre-expressed fluorescent proteins, immunofluorescence (IF) or FISH. Importantly, they claim that one can perform several rounds of IF (and similarly FISH) and they show images to proved that.

They also show that the signal intensity of the IF signal does not diminish when going deeper into the tissue, or using different z-sections.

Structural and molecular phenotyping of a piece of human brain using CLARITY. Source: Chung, K. et al Nature (2013).

Structural and molecular phenotyping of a piece of human brain using CLARITY. Source: Chung, K. et al Nature (2013).

It is my understanding that people in the Neuroscience field have known about CLARITY for quite some time, just waited for it to get published already. It IS very exciting and amazing.

Watch the Clarity Video:

Once CLARITY becomes widespread, we should get immense amount of data on the cellular & molecular structure of many types of whole (unsliced) tissues.  We could follow development, disease and much more.

Perhaps one day even whole animals will be imaged.

ResearchBlogging.orgChung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A., Davidson, T., Mirzabekov, J., Zalocusky, K., Mattis, J., Denisin, A., Pak, S., Bernstein, H., Ramakrishnan, C., Grosenick, L., Gradinaru, V., & Deisseroth, K. (2013). Structural and molecular interrogation of intact biological systems Nature DOI: 10.1038/nature12107

6 responses to “Looking through the brain with CLARITY!

  1. Thought provoking indeed! I’ve said this before and most likely will say it again! Neuroscience is really coming out of its shell…
    Neuroscience is my thing so I’ve been hooked for a while… but it seems like the mainstream are now getting a good glimpse at what we have been excited about for years! I would really like to take a peak at how all of this research plays out in 50 years time or so…


    • Yep. I myself am only just starting to get interested in neuroscience, hoping to start using neurons in my research within a few months (after I establish my system in cells that are more convenient to maintain).
      Hey, we should still be alive in 50 yrs (fingers crossed). Though, I suspect that we wouldn’t need to wait that long for amazing stuff to appear.


      • Hopefully not… have you heard about the Human Brain Project – amazing project but I really can not see it finishing in my lifetime (really hope it does though!)


        • Hey, it took just one decade to get from the human genome to almost completing the 1000 genome project, and there are now real talks about the 1,000,000 genome project. At today’s rate they should be done in less than a decade.
          So I don’t think the Human Brain Project will be much different. Both molecular and imaging techniques are advancing at a fast rate, together with the advancement in computing. We already have the “virtual cell” (http://wp.me/p2jizY-3N) of a bacteria. We should have a mammalian virtual cell within a decade or two. From there we’ll go to the virtual organ/animal…


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