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Canada Medicine Science

Whole Human Brain Mapped In 3D 99

ananyo writes "An international group of neuroscientists has sliced, imaged and analysed the brain of a 65-year-old woman to create the most detailed map yet of a human brain in its entirety. The atlas, called 'BigBrain,' shows the organization of neurons with microscopic precision, which could help to clarify or even redefine the structure of brain regions obtained from decades-old anatomical studies (abstract). The atlas was compiled from 7,400 brain slices, each thinner than a human hair. Imaging the sections by microscope took a combined 1,000 hours and generated 10 terabytes of data. Supercomputers in Canada and Germany churned away for years reconstructing a three-dimensional volume from the images, and correcting for tears and wrinkles in individual sheets of tissue."
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Whole Human Brain Mapped In 3D

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  • by Lumpy ( 12016 ) on Friday June 21, 2013 @11:01AM (#44070313) Homepage

    After that procedure of mapping her brain, did she recover well? were there any side effects? When will we have the first interviews?

    • by Anonymous Coward on Friday June 21, 2013 @11:30AM (#44070575)

      She seems ok, but she can't stop watching FOX for some reason

    • Well, we replaced it with an electronic brain, a simple one. All it needed to say was "What?" and "Where's the tea?"

      • by Anonymous Coward

        I was thinking the exact same thing:

        "No, no," said Frankie, "it's the brain we want to buy."


        "Well, who would miss it?" inquired Benjy.

        "I thought you said you could just read his brain electronically," protested Ford.

        "Oh yes," said Frankie, "but we'd have to get it out first. It's got to be prepared."

        "Treated," said Benjy.


        "Thank you," shouted Arthur, tipping up his chair and backing away from the table in horror.

        "It could always be replaced," said Benjy reasonably, "if you think it's important

    • Too soon to say. She's really pissed about the whole deal.

    • That is, if the synapses were also preserved in enough detail.
  • to figure out a route between what I want to say and my speech centers
    • In science, Google maps out your brain!

    • to figure out a route between what I want to say and my speech centers

      Interestingly, some studies have found that at least some of the time, you actually say things before you create the "memory" that you want to -- your brain then constructs the memory that you intended to say that after the fact. Spooky stuff.

      However, something else that I'm curious about is this: it's known that male and female brains, while sharing the same generic topography, are actually significantly different, both in use of grey and white matter,, and in density of neurons in various areas and devel

    • by dywolf ( 2673597 )

      no what need is to use it to figure out the route between what i say and my wife's interpretation centers, and back again, so i can figure out how mad she'll be and why about whatever normal innocent thing i say before i say it, and i can properly interpret it when she says "Fine" or "Really?".

  • by lobiusmoop ( 305328 ) on Friday June 21, 2013 @11:05AM (#44070363) Homepage

    10 terabytes? The entropy for the entire human body is about 700 megabytes as per DNA, surely there must be a lower order of complexity than that in the brain?

    • by Anonymous Coward on Friday June 21, 2013 @11:10AM (#44070407)

      The dna is just the code. The brain represents the running state of that code following 65 years worth of exogenous and endogenous inputs.

    • Re: (Score:2, Insightful)

      by Anonymous Coward

      No? DNA is instructions; if you run a 700 mb program for 65 years, subject to an entire world of input, it will probably generate a lot more than 10 tb of data. The data, in the case of the brain, is the way the neurons connect to each other. Were that complexity limited by DNA we wouldn't be able to remember anything that wasn't already hardcoded into our DNA; we would be non-learning beasts of pure instinct.

    • Re: (Score:3, Insightful)

      by Anonymous Coward

      Fractals are very complex structures produced by very simple equations. The data needed to store a fractal image is much greater than the data needed to store the equation that can generate it.

      Same deal here between DNA and the structures that get built from it.

      • by HiThere ( 15173 )

        That's a decent analogy, but it leaves out that a bunch of the structure of the brain is driven by environmental stimuli.

    • by cdrudge ( 68377 )

      Why is a SVG-based image a much smaller filesize than a identical raster-based image? Because the SVG-based image tells HOW to build the image while the raster-based image just described each and every pixel.

      Same thing applies to this case. The human genome may be 700 MB as you state, but that only describes HOW to build a human so to speak, not what it looks like after it's finished. Human DNA doesn't say that a particular spot of an organ should be this color, and a adjacent spot a slightly different co

    • The blueprints for a house are a few MBs. A 3D Scan of the house down to the texture of the wood would be petabytes.

      • by Creepy ( 93888 )

        For raw data, of course, but since the house is mostly planar surfaces you most likely could massively reduce the data using octrees, kd-trees, or other methods.

      • If you want to understand how houses in general work though, it's better to study those blueprints than the color of the counter-tops in the kitchen.

  • Maybe this will help fix some of our wetware bugs.
  • Now someone needs to boot a simulation of that brain up on a super computer and see what it does.
    • Ethics (Score:4, Interesting)

      by Picass0 ( 147474 ) on Friday June 21, 2013 @11:33AM (#44070601) Homepage Journal

      Consider for a moment that were possible. Probably not today, at some point if driver software could be written to run this digital model. If by some long shot it were possible would it be ethically right? What if there were some sense of awareness, personality, fear of the strange circumstances she now finds herself in? She would be without her senses and without any level of input from the outside that she would relate to as a normal person.

      And then consider: Is it right to turn such a system on and off like any other computer?

      • Re: (Score:3, Interesting)

        by Tighe_L ( 642122 )
        It was mostly in jest, but being that it is a simulation, is it real at all. Will it have a soul? I would think that in a few decades that computers would be able to run such a simulation.
        • A soul? Probably not. But then I've never seen any evidence for souls, so my best bet is that I'm as soulless as an average brick. It wouldn't be fair of me to look down on her for lacking something I don't possess myself.

          Now, the question of if she's real is an interesting one, which has been discussed to death by various philosophers. The discussion usually goes something like:

          Imagine that the test subject has a wholly human brain. There's no question whether the subject is real or not. Now, replace a sin

          • by Tighe_L ( 642122 )
   [] "Dr. Bashir, on the orders of Bareil, gave him an experimental drug that let him function for a few days. However, the drug did irreversible damage to the vedek's organs, eventually destroying part of his brain. At Kira's urging, Bashir replaced the damaged brain region with an artificial positronic implant, so that Bareil could continue to advise Winn. Soon after the peace treaty was signed, the remainder of Bareil's brain was destroyed. Kira and Bashir decided
        • by end15 ( 607595 )

          What do you mean by the term "Soul"? It seems so broad that it loses meaning quickly.

          • by Tighe_L ( 642122 )
            Something intangible. The spark of life. Hey do you remember that 80s thriller drama where a father is diagnosed with a terminal disease and is frozen. He is thawed years later (his son is now close in age to the father) but when he was reanimated he was soulless/evil?
            • by end15 ( 607595 )

              "Something intangible."

              See that makes it very difficult to discuss. Maybe there's another way to get at what your suggesting other than the term "soul".

      • Re:Ethics (Score:4, Interesting)

        by SuricouRaven ( 1897204 ) on Friday June 21, 2013 @11:41AM (#44070669)

        On her, no way it's possible. The brain went too long between death and digitisation - no oxygen means rapid and extreme damage. Even if the scan were good enough to get synapse-level tracing (It isn't), it wouldn't run.

        Give it a few more decades though, maybe as much as a century. There's nothing scientifically impossible about it - it's just an engineering challenge. I imagine you'd need to resort to either nondestructive living readout (Future super-MRI?) or some sort of preservation process (Cryonic or chemical).

        Senses can be simulated too. Just wire up to a robot, or a simulated environment.

        • by Tighe_L ( 642122 )
          The map is there, with the layout of the neurons, in the simulation you just replace the damaged neurons with simulations of healthy ones.
      • by cfulton ( 543949 )

        Consider for a moment that were possible. Probably not today, at some point if driver software could be written to run this digital model. If by some long shot it were possible would it be ethically right?

        You clearly don't read enough science fiction. Of course it would be ethical. Then we could all retire to a computerized wonderland of drugs and sex with no side effects. Trillions of lives could be encoded with out the crazy need for real food, clothing and shelter. If it could be done it would be Nirvana/Heaven/Wonderland/Paradise come true!!! Rock on supercomputers. I wanna be your first upload.

        • I wanna be your first upload.

          Oh really? You want to be a beta tester for that? Me, I'm waiting for rev 3, at least.


        • by Tighe_L ( 642122 )
          Ahh, but it wouldn't be you, as you are dead. It would be a simulation of you. I would imagine that the brain simulations would be done in the future for ability to retain knowledge of the previous generations. The alive people wouldn't maintain those computer systems for simulations of past generations to have fun. Most likely they would boot you up, consult with you for some fact or advice the put you in sleep mode until next time you are needed.
    • Aren't we all inside a big simulation already?
  • Surprise! (Score:5, Funny)

    by Sperbels ( 1008585 ) on Friday June 21, 2013 @11:08AM (#44070387)
    Boy is she going to be surprised once she wakes up inside of a full brain emulation program.
    • by Anonymous Coward on Friday June 21, 2013 @11:23AM (#44070533)

      Thus begins the next Cylon revolution. Not from a transplanted girl dealing with the emotional stress of knowing that her fleshy self has died, but starting from an elderly lady who now has the army of combat drones to successfully force everyone 'off her lawn.'

  • Should have this wrapped up in a few centuries.
  • by GeekWithAKnife ( 2717871 ) on Friday June 21, 2013 @11:19AM (#44070489)

    I always worry when such notions arise. After all, everyone has a slightly different brain. some people have entire regions and functions mapped to areas we thought were science fiction just a decade or two ago. (typically the result of serious childhood brain trauma)
    For all we know her brain might differ from the norm, or her regional background might produce a similar anomaly. We'll need many thousands more of such scans.

    While this is and should be a celebrated achievement we must keep in mind that microscopically accurate scans will most likely be required on a per individual basis.
    Perhaps in the future we'll all carry our own 10PB brain map in our sub-dermal biochips.
    • by dywolf ( 2673597 )

      but if we can learnt o understand hers, we can learn to understand others. eventually a methodology to map and understand the brain in a living person, without surgery, could be the norm. alzheimers beings to set in? No problem. Step into the BRI machine for a few a hours, doc reads the results, then they apply a small implant to the precise relevant location of your unique brain to repair the malfunctioning communication relay.

  • Now that they got the procedure I hope they do that with Einstein's brain and, after that, let it rest in peace with the rest of the body. That is assuming that the cellular structure is still intact after half a century inside a jar. Then delete IBM watson and instead install the observed model along side an appropriate bio-physic-chemical engine on the hardware and we can finally enjoy the new age of singularity and no need to think anymore.
    • Yeah, and Einstein's brain in a computer does nothing all day but bemoan his lack of arms to play the violin and ears to listen to music. He was more than a theoretical physicist.
    • No, the cellular structure isn't intact. And it's not intact for the brain mentioned in TFA. A quick glimpse of the sections indicates that they were stained in a variant of the hemotoxylin / eosin stain - one use commonly in light microscopy but one that doesn't even preserve structure at electron microscopy levels, much less biochemically useful levels of detail.

      Remember, the process is something like this: Dead person - checked two or three times to make sure they're dead. No brain function. Drain b

  • It would be just as or even more useful to have this 3D tool available for the commonly used animal models in research. Given the cost to do just one single brain, it won't be feasible to analyze healthy brains vs brain suffering from disease X. Even if it was feasible, identifying anatomical abnormalities in disease provides limited insight into the mechanism of the disease... these things are sorted out with other techniques that require the use of animal models. I think this is a nice teaching tool for
    • by HiThere ( 15173 )

      Don't expect the cost to stay constant. Even the next time could be a lot cheaper, as the software has been written, and computers have gotten faster and cheaper.

      OTOH, there are probably limits as to how cheap it can get. I'd be really surprised if it got cheaper than $500,000 during this century, unless there was MASSIVE deflation. That would additionally require robotic surgeons doing and examining the slices, as well as better algorithms (probably rewritten to be more extensively parallel) running on

  • ...who else is hungry for cold cuts?

    Anyone? Anyone?

    Just me, then.

  • MineCraft map. Just add some viruses, white and red blood cells, and a little submarine.
  • ... after running it through gzip?

  • > 7,400 slices
    > 1,000 hours
    > 10 terabytes of data
    > Supercomputers churned away for years
    > BigBrain is part of the Human Brain Project, a 10-year,
    > €1-billion European initiative to create a supercomputer
    > simulation of the human brain

    "Done! Wait, hang on. Please tell me this wasn't a murderer's brain?"

    "No, this person died in a hospital. 'Abby-someone'."


  • The original publication is here: []
    And the database is here: []

Time to take stock. Go home with some office supplies.