Recording thousands of cells like it’s nobody’s business

Is this what the world is now? Recording thousands of cells per paper? After the 14000 neuron magnum opus from Markram, comes a paper from Jiang et al recording 11000 neurons. When your paper is tossing off bombs like:

We performed simultaneous octuple whole-cell recordings in acute slices prepared from the primary visual cortex (area V1)

and figures like:

octuple recordings

you know you are doing something right. How much do you think this cost compared to the Blue Brain project? (Seriously: I have no sense of the scale of the costs for BBP, nor this.)

I will try to read this more closely later, but I will leave you with the abstract and some neural network candy for now:

Since the work of Ramón y Cajal in the late 19th and early 20th centuries, neuroscientists have speculated that a complete understanding of neuronal cell types and their connections is key to explaining complex brain functions. However, a complete census of the constituent cell types and their wiring diagram in mature neocortex remains elusive. By combining octuple whole-cell recordings with an optimized avidin-biotin-peroxidase staining technique, we carried out a morphological and electrophysiological census of neuronal types in layers 1, 2/3, and 5 of mature neocortex and mapped the connectivity between more than 11,000 pairs of identified neurons. We categorized 15 types of interneurons, and each exhibited a characteristic pattern of connectivity with other interneuron types and pyramidal cells. The essential connectivity structure of the neocortical microcircuit could be captured by only a few connectivity motifs.

NN candy

Read it here.

Watching a brain in motion

And science steadily advances. It was only last July that I posted a video showing the activity of all the neurons in a brain. But that animal was stuck in place – not moving freely (though it was in virtual reality).

Jeffrey Nguyen and Andrew Leifer just uploaded their manuscript detailing their work imaging the whole brain of an animal that is freely moving. The animal is just locomoting around like nobody is their boss. That’s important as a lot of evidence points to neural activity being different when an animal is restrained and when it is allowed to move of its own volition. This technical feat is particularly exciting because the animal is C. elegans, which means that we know how all of the neurons are connected (we have the connectome). Here’s a video:

What you are seeing is a wormlike animal bend its nose from right to left (see the green lines moving out from the center mass? Those are processes sent to the sensory receptors at the very tip of the nose of the animal). I assume the animal is moving during this, but the whole image is stabilized.

There is a smoother/faster version hereHere is another videoHere’s a description of the work from Technology Review.


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