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

[via]

References

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

Advertisements

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

  1. Pingback: Watching a brain in motion | neuroecology

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s