Watch ALL the neurons in a brain: Ahrens and Freeman continue their reign of terror

Okay, not quite all of them. But it looks like Misha Ahrens and Jeremy Freeman are going to continue their reign of terror, imaging the whole zebrafish brain as if it’s no big deal. Yeah they’ve got almost every neuron of a vertebrate, so what?

Besides figuring out that not shooting light at the eyes might be a good idea (I think it may have been a little more complicated than that…), they released software for analysis of these kind of big data sets. Beyond Ahrens and Freeman, I know of at least two other labs using the same type of microscope to image all of the fly and can count five labs doing the same in worms. And that’s probably both a huge undercount, as well as the tip of the iceberg that will be a coming tidal wave of massively-large neural data sets. This is something that is so important, DARPA is throwing huge amounts of money at it (or at least wants to).

Their software, called thunder, is freely available and open-sourced, and available at a really slick website. It has a really great tutorial to analyze data and make sweet figures. This kind of openness is really Science Done Right.

Seriously, look at these bad boys:

running mice make neurons go fast

Mice running make mice neurons go fast

neurons in phase space


Neural activity floats around in their own not-so-metaphorical dimensions.the whole brain of the zebrafish is tuned for direction


Neurons are tuned for motion, with different colors representing different motions.ze brafish



Freeman, J., Vladimirov, N., Kawashima, T., Mu, Y., Sofroniew, N., Bennett, D., Rosen, J., Yang, C., Looger, L., & Ahrens, M. (2014). Mapping brain activity at scale with cluster computing Nature Methods DOI: 10.1038/nmeth.3041

Vladimirov, N., Mu, Y., Kawashima, T., Bennett, D., Yang, C., Looger, L., Keller, P., Freeman, J., & Ahrens, M. (2014). Light-sheet functional imaging in fictively behaving zebrafish Nature Methods DOI: 10.1038/nmeth.3040

Image ALL the neurons!

So you want to image every neuron in the brain of a vertebrate?  What kind of crazy man are you?  Misha B. Ahrens, that’s who.

In what can only be described as a “crazy awesome” experiment, Ahrens used a technique that’s been recently emerging called light sheet microscopy to image the activity of (nearly) every neuron in the zebrafish brain simultaneously.  The whole method faces a slight problem in that neurons are active on the order of milliseconds whereas Ahrens can only image the whole brain every 1.3 seconds.  Still, it seems reasonable that most behaviorally relevant activity can be captured at that speed.  A larger problem is that they might be activating neural activity by shining light at the zebrafish’s eyes.

This is only a methods paper which I’m guessing means that they’re presenting a ‘weak’ result, with a super awesome result to come in 6-12 months in Nature.  Their weak result still showcases the power of their method: by looking at single unit activity, they are able to find previously unknown coupling across different regions as well as specific subpopulations that are linked in distinct ways.

Awesome things are coming from the Ahrens lab.  I foresee it.


Ahrens, M., & Keller, P. (2013). Whole-brain functional imaging at cellular resolution using light-sheet microscopy Nature Methods DOI: 10.1038/nmeth.2434