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Science

Activity of Whole Fish Brains Mapped Second To Second 56

Posted by Soulskill
from the pretty-pictures dept.
ananyo writes "Researchers have imaged an entire vertebrate brain at the level of single neurons for the first time. A team of scientists based at the Janelia Farm Research Campus in Ashburn, Virginia, were able to record activity across the whole brain of a fish embryo almost every second, detecting 80% of its 100,000 neurons. The work is a first step towards mapping the activity of a whole human brain — which contains about 85,000 times more neurons than the zebrafish brain. The imaging system relies on a genetically engineered zebrafish (Danio rerio). The fish's neurons make a protein that fluoresces in response to fluctuations in the concentration of calcium ions, which occur when nerve cells fire. A microscope sends sheets of light rather than a conventional beam through the fish's brain, and a detector captures the signals like a viewer watching a cinema screen. The system records activity from the full brain every 1.3 seconds."
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Activity of Whole Fish Brains Mapped Second To Second

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  • by Grayhand (2610049) on Tuesday March 19, 2013 @11:22PM (#43220487)
    "Oh look, a hook!"
    • Re: Fish's last thought recorded... Oh look, a hook!"
      .
      Ha ha ha! No, they were zebra-fish embryos still in development. No need to hook them; the scientists already had them ensnared. And they probably had not developed up to the "thinking" stage! (jk, jk, just in case someone thinks i'm serious about fish thinking deep thoughts...)
  • by girlinatrainingbra (2738457) on Tuesday March 19, 2013 @11:27PM (#43220513)
    That's amazing! I hope that there will be good data that can be pulled out of the large dataset. I wonder if the 1.3 seconds per frame time is enough resolution to capture some of the key activities since there are many neurons that can fire more than once per second.
    .
    Each hour-long experiment generated 1 terabyte of data and they were able to detect 80% of the 100k neurons in the fish's brain. So that works out to
    1 terabyte $\div$ 1 hour * (3600 seconds/hour) / (1.3 seconds / data item) / (80000 neurons) = 4513 bytes per neuron in the dataset.

    Run that as

    perl -e "print 1e12/(2769.23077)/(.8*1e5)"; echo 4513.88888763503

    I wonder how much faster the ata really needs to be captured in order to get as much resolution as needed to understand what's going on.

  • by girlintraining (1395911) on Tuesday March 19, 2013 @11:35PM (#43220547)

    This is like taking slices of 80% of a computer's memory once a second. Sure, you might be able to get an idea of what's going on, but until you can see the whole picture, a lot of things are not going to make sense...

    • by Nyder (754090)

      This is like taking slices of 80% of a computer's memory once a second. Sure, you might be able to get an idea of what's going on, but until you can see the whole picture, a lot of things are not going to make sense...

      Yep, but dang, that is really cool they got this far.

      Fish heads, fish heads,
      Rolly-polly fish heads,
      Fish heads, fish heads,
      Eat them up, yum!

    • Re: (Score:3, Interesting)

      by Anonymous Coward

      This is like taking slices of 80% of a computer's memory once a second. Sure, you might be able to get an idea of what's going on, but until you can see the whole picture, a lot of things are not going to make sense...

      Not really. The indicator they are using can be deconvolved to near action potential resolution.

      • by Anonymous Coward

        Look up Nyquist on Wikipedia, 1 second sampling is not sufficient to resolve the frequency of an action potential. Deconvolution
        does not change anything about that, they would still need faster sampling to be able to do that.

    • by Anonymous Coward

      80% of a core file at every second leading up to a crash could be useful...

      Of course, 100% would be better but this is still an impressive improvement.

    • IMO, TFA is completely. fucking. amazing. This comment is like people telling Watson, Crick, and Franklin, "yeah, but you don't have a complete working model of human genetics."

  • The next steps are fairly obvious..
    1) Figure out how to write data to said mapped brain.
    2) Attach USB Interface to organic storage unit.
    3) Profit!!!

  • Since these techniques rely on bio luminescence, can the light generated from the neural activity travel to and stimulate the retinal cells? Can the animal... see itself thinking?
    • by TWX (665546)
      Are you speculating that the fish was thinking, "ooooh, pretty colors!" the whole time?
      • by LiavK (2867503)
        Probably more likely: "I wish I could figure out how to eat/fuck that thing over there.."
        • by eyrieowl (881195)
          Well, maybe a little more than that... "Scary large thing! Hide! ... Hm, is this food? Scary large thing! Hide! Hm, is this food? THIS IS MY TERRITORY! Hm, is this food? I SAID THIS IS MY TERRITORY! Hm, this must be food. THIS IS oh, what a nice cloaca you have! Scary large thing! Hide!"
    • Re: (Score:2, Informative)

      by Anonymous Coward

      The technique relies on fluorescence, not bioluminescence.

      Here is a breakdown of an earlier version of the molecular biology side of the technology.

      http://brainwindows.wordpress.com/2009/11/09/three-cheers-for-gcamp/

  • Reminds me of (Score:5, Interesting)

    by dwywit (1109409) on Tuesday March 19, 2013 @11:41PM (#43220575)

    http://www.visual6502.org/JSSim/ [visual6502.org] in action.

  • by wisebabo (638845) on Wednesday March 20, 2013 @12:06AM (#43220693) Journal

    Not apparent from the (cool) video they linked to is that according to the paper in Nature (yes I RTFA and I followed a link) they say they achieved cellular resolution (the video must be a down-sampled version). This would explain them collecting 1TB of data for each 1 hour "run". Another neat thing to notice is that their data is 3D, they are collecting volumetric data (as you can see from the video "slice") and explained in a previous paper. Impressive! Now if only they could increase the temporal resolution (multiple parallel scanning beams?) we could really see how a fish thinks!

    They say they could collect data from (currently small) sections of mammalian brains but it would require surgery. I wonder how soon until we see monkeys with their skulls replaced with transparent plastic or glass? Maybe they could use (a very advanced version of this) on patients undergoing brain surgery.

    By the way, are there any transparent plastics that are suitable for 3D printing? Biocompatible? I can see a time when some really crazy performance artist replaces his/her skull with a transparent one. I guess they would have to wear a hat whenever they went out into the sun though.

  • by neurophys (13737) on Wednesday March 20, 2013 @12:35AM (#43220835)

    Nice work. I look forward to see the 1 millisecond time reolution. The researchers state that the human brain contain 85000*100000 -> 8.5 billion neurons. Most textbooks says the human brain has about 100 billion neurons. There are also papers out telling that the neocortex of a young male contain about 22.8 billion neurons (Pakkenberg). So the human brain is much more complex than stated.

  • Castle, Rock, Castle, Rock, Cat Whoaa!, Castle, Rock, Cat Whoaaa! ...
  • DARPA will throw money at this - if details can be refined, and RECORDED, then IMPOSING the recorded patterns onto another brain equals INSTANT CONDITIONING !
  • This is obviously the first step to being able to upload. First it will be fish (e.g. lobsters), then kittens, and sooner or later, humans. But we should make sure we get the ethics and legal aspects sorted out first, I wouldn't want to die, and then wake up a slave to someone else.

    A bright new trans and/or post human future awaits us!

  • I'm sure recording fish brain is awesome, but I can't comment on it. I've forgotten what the news blurb said.

  • Maybe two decades or so ago, I recall seeing movies of scanning electron micrographs (SEM) of microchips (CMOS?) strobed with periodic inputs of fairly high frequency. By making slight changes in the input frequency, it was possible to see individual signals (electron charges) travel across the traces on the chip. I've been waiting to see this sort of visualization technique available for biological neural networks. The temporal resolution isn't quite there yet, but it appears to be coming.
  • Assuming that we could get the positions and synaptic weights from this data, what's to stop us from making a neural network to reproduce the function of this fish brain?
    • by geekoid (135745)

      Nothing.
      Ans in the lab tiny, tiny, samples of simulate brain begin to act like a brain.

      So if there is a very real possibility that simulating the brain may be enough to create what we would unmistakably call intelligence

We warn the reader in advance that the proof presented here depends on a clever but highly unmotivated trick. -- Howard Anton, "Elementary Linear Algebra"

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