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Activity of Whole Fish Brains Mapped Second To Second

Soulskill posted about a year and a half ago | from the pretty-pictures dept.

Science 56

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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First (0)

Anonymous Coward | about a year and a half ago | (#43220481)

Well, this is a first.

Fish's last thought recorded (5, Funny)

Grayhand (2610049) | about a year and a half ago | (#43220487)

"Oh look, a hook!"

Re:Fish's last thought recorded (1)

girlinatrainingbra (2738457) | about a year and a half ago | (#43220525)

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...)

Re:Fish's last thought recorded (2)

fustakrakich (1673220) | about a year and a half ago | (#43220591)

...fish thinking deep thoughts...

Why do the caterpillar and the ant have to be enemies? One eats leaves, and the other eats caterpillars. Oh, I see now.

Re:Fish's last thought recorded (1)

the_Bionic_lemming (446569) | about a year and a half ago | (#43220635)

You forgot about carpenter ants...

Re:Fish's last thought recorded (4, Funny)

Anonymous Coward | about a year and a half ago | (#43220937)

in case someone thinks i'm serious about fish thinking deep thoughts

Admittedly lab aquariums are pretty shallow, but some fish live and think a kilometre below sea level. Those are some pretty deep thoughts.

Re:Fish's last thought recorded (0)

Anonymous Coward | about a year and a half ago | (#43220743)

First after thought: "F*ck!"

Re:Fish's last thought recorded (0)

Anonymous Coward | about a year and a half ago | (#43220975)

More like "why is this worm so sharp?!"

Re:Fish's last thought recorded (1)

Wolfrider (856) | about a year and a half ago | (#43236747)

--The mind of a fish:

waterwaterswimcoldwater,warmwater,swimwaterwater,PREDATORFLEEfastwater
morewater,darknesslight,coralwaterwater,wasthatashark?hmmswimwater,plankton
wigglysquirmything,investigatechompbite
OHSHI--NO CARRIER

Amazing! 4513 bytes per neuron (5, Informative)

girlinatrainingbra (2738457) | about a year and a half ago | (#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.

Re:Amazing! 4513 bytes per neuron (0)

Anonymous Coward | about a year and a half ago | (#43221377)

That sounds really high. The data must be actual photos or something. Seems like they can safely discard most of it after being processed.

cube with edge 16.5 pixels=4513 bytes per neuron (1)

girlinatrainingbra (2738457) | about a year and a half ago | (#43222033)

It's not just photos (2-d) but three-dimensional volumetric acquisition, so if it's got the same resolution in all three dimensions, then each three-dimensional slab acquired every 1.3 seconds is 361MB ( = 1.2 TB / 2769.23 slabs acquired per hour) [ which is also = 1.2 TB / (3600 seconds / 1.3 seconds per slab acquisition) ].
.
Then, 361 MB per slab / 80Kneurons per slab ~= 4512.5 (the original result was 361,111,111 / 80k ~= 4513.88888763503 from perl -e "print 1e12/(2769.23077)/(.8*1e5)"; echo. Then, since it's a 3-d volume acquisition, take the cube root of 4513.888 to get 16.525 for the edge of the cube for monochromatic 8-bit depth data.
.
So on average, each neuronal body occupies a cube in the 3-d slab of approximately 16.5 pixels $\times$ 16.5 pixels $\times$ 16.5 pixels, if the volume acquisition is done with a single monochromatic laser using a single byte to encode intensity. If the images for the 3-d slab are acquired as an RGB dataset with three different colored lasers (which is not what is going on, i believe) then take 4513 per neuron per slab acquired and divided by three is 1504.27ish, take the cube root of that and get 11.45 pixels for the cube edge length (again assuming pixel intensity is one byte per RGB color channel). Smaller again if colors are encoded using more than one byte per color channel. Arithmetic done. (or /arithmetic or /arithmegeek, to use slashdot-speak) ;>)

Progress, but not totally there yet (5, Interesting)

girlintraining (1395911) | about a year and a half ago | (#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...

Re:Progress, but not totally there yet (1)

Nyder (754090) | about a year and a half ago | (#43220571)

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:Progress, but not totally there yet (3, Interesting)

Anonymous Coward | about a year and a half ago | (#43220587)

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.

Re:Progress, but not totally there yet (1)

Anonymous Coward | about a year and a half ago | (#43222015)

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.

Re:Progress, but not totally there yet (1)

Anonymous Coward | about a year and a half ago | (#43220615)

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.

Re:Progress, but not totally there yet (0)

Anonymous Coward | about a year and a half ago | (#43220717)

I'm reminded of the anecdote of the police officer beating the man who rolled through the stop sign. "Now, do you want me to stop or slow down?"

Re:Progress, but not totally there yet (0)

Anonymous Coward | about a year and a half ago | (#43220763)

Actually it is nothing like that.

Re:Progress, but not totally there yet (1)

bill_mcgonigle (4333) | about a year and a half ago | (#43223967)

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."

Obviously.. (1)

blackicye (760472) | about a year and a half ago | (#43220557)

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!!!

Re:Obviously.. (1)

cheater512 (783349) | about a year and a half ago | (#43220759)

Bonus points for lasers being involved in step 1.

Re:Obviously.. (3, Funny)

MachDelta (704883) | about a year and a half ago | (#43221237)

Let me guess... Linux user? [xkcd.com]

Feedback? (2)

LiavK (2867503) | about a year and a half ago | (#43220567)

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?

Re:Feedback? (1)

TWX (665546) | about a year and a half ago | (#43220723)

Are you speculating that the fish was thinking, "ooooh, pretty colors!" the whole time?

Re:Feedback? (1)

LiavK (2867503) | about a year and a half ago | (#43220767)

Probably more likely: "I wish I could figure out how to eat/fuck that thing over there.."

Re:Feedback? (1)

eyrieowl (881195) | about a year and a half ago | (#43223529)

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:Feedback? (2, Informative)

Anonymous Coward | about a year and a half ago | (#43220995)

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 (4, Interesting)

dwywit (1109409) | about a year and a half ago | (#43220575)

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

Re:Reminds me of (2)

webmistressrachel (903577) | about a year and a half ago | (#43220883)

That's beautiful. Thank you.

They achieved cellular resolution! (5, Interesting)

wisebabo (638845) | about a year and a half ago | (#43220693)

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.

Re:They achieved cellular resolution! (3, Informative)

ldobehardcore (1738858) | about a year and a half ago | (#43220895)

Interesting fact: neural activity can be modulated by shining light on the neurons. Here's a video of a mouse forced to RUN when a blue light is shone onto it's motor cortex [youtube.com]

Re:They achieved cellular resolution! (1)

LongearedBat (1665481) | about a year and a half ago | (#43220959)

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.

mouse forced to RUN when a blue light is shone onto it's motor cortex

So, said artist would need to wear a hat to not run around uncontrollably. Trying to work out if wearing a transparent skull would be a bright idea. !-)

Re:They achieved cellular resolution! (1)

sFurbo (1361249) | about a year and a half ago | (#43221599)

By the way, are there any transparent plastics that are suitable for 3D printing? Biocompatible?

PLA, which is on of the most used plastics for 3D printing, is transparent and biocompatible to the degree of being biodegradable. It is used for making implantable "molds" that are slowly replaced with tissue as they break down (OK, not really what you want as a skull).

Re:They achieved cellular resolution! (1)

tehcyder (746570) | about a year and a half ago | (#43224709)

I can see a time when some really crazy performance artist replaces his/her skull with a transparent one.

You appear to have misspelled "retard".

Neurons in human brain (4, Insightful)

neurophys (13737) | about a year and a half ago | (#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.

Re:Neurons in human brain (0)

Anonymous Coward | about a year and a half ago | (#43223385)

Well, you could start with nacny pelosi's brain. That'll cut it back an order of magnitude. Provided she's not talking.
After all, we have to agree to do the experiment before we find out what is actually in there.

One step toward the singularity. (0)

Anonymous Coward | about a year and a half ago | (#43229183)

One small step toward the technological singularity, but I don't think it will be parabolic advancement forever. It will end in a dissapointing wimper when it turns into an s-curve at some distant point in the future long before the heat death of the universe. But then again a hundred years or so ago someone said, "Everything that can be invented already has been invented". SO SINGULARITY, HEAR WE COME let us wait and see! http://rawcell.com [rawcell.com]

Brain Activity of a Goldfish (1)

Solo-Malee (618168) | about a year and a half ago | (#43221239)

Castle, Rock, Castle, Rock, Cat Whoaa!, Castle, Rock, Cat Whoaaa! ...

Re:Brain Activity of a Goldfish (2)

wonkey_monkey (2592601) | about a year and a half ago | (#43221661)

And the cat:

Huh. Forcefield. Huh. Forcefield. Huh. Forcefield? Huh! Forcefield. [youtube.com]

Re:Brain Activity of a Goldfish (1)

MessageApprovalMan (2871053) | about a year and a half ago | (#43223693)

Finally, it doesn't matter that they can't talk... you can ask a fish head anything you want to!

ultimate goal (1)

rickyslashdot (2870609) | about a year and a half ago | (#43221427)

DARPA will throw money at this - if details can be refined, and RECORDED, then IMPOSING the recorded patterns onto another brain equals INSTANT CONDITIONING !

Re:ultimate goal (1)

wonkey_monkey (2592601) | about a year and a half ago | (#43221663)

I hear the trials involve making people capitalise words for no apparent reason.

Re:ultimate goal (0)

Anonymous Coward | about a year and a half ago | (#43223417)

DOH !

Re:ultimate goal (0)

Anonymous Coward | about a year and a half ago | (#43221841)

The ONLY way to SAFETY is to MASTURBATE! That's WHY I MASTURBATE three times a DAY. If YOU think THAT is EXCESSIVE than I FEAR for YOUR safety. THEY MAY ALREADY have gotten to you. The GOVERNMENT the UN and the CORPORATIONS! It's a GRAND conspiracy. The ONLY way TO be SAFE is to MASTURBATE!

When you MASTURBATE you TRIGGER certain NEURONS that CANNOT be OVERRIDDEN! That PROTECTS you from the CONDITIONING!

SEX also WORKS but Slashdotters aren't getting any are you. I know I'm not. Life is pain.

Re:ultimate goal (0)

Anonymous Coward | about a year and a half ago | (#43224683)

> but Slashdotters aren't getting any are you. I know I'm not. Life is pain.

Conditioning attempt detected

Uploading lobsters (1)

magic maverick (2615475) | about a year and a half ago | (#43221831)

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!

Re:Uploading lobsters (0)

Anonymous Coward | about a year and a half ago | (#43226029)

Il make sure to not file away any emails I get from KGB.ru

Fish brain (1)

Blaskowicz (634489) | about a year and a half ago | (#43221949)

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

Strobed stimulation would be interesting... (1)

DoctorBonzo (2646833) | about a year and a half ago | (#43222993)

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.

Beware JFRC (0)

Anonymous Coward | about a year and a half ago | (#43224629)

I read the article and the work seems pretty good. It's important to bring up that this is a new facility and scientists there (mostly post-docs) are kept in an isolated environment and expected to work 80+ hour weeks. They've had several suicides in the last few years by these post-docs. Their director, Gerry Rubin, has acknowledged that the environment they have created will not allow many scientists to "thrive" (his word).

Fish Brain Model (1)

Graydyn Young (2835695) | about a year and a half ago | (#43225183)

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?

Re:Fish Brain Model (0)

Anonymous Coward | about a year and a half ago | (#43225537)

Connectivity.

Re:Fish Brain Model (1)

geekoid (135745) | about a year and a half ago | (#43228763)

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

Fish Brains (0)

Anonymous Coward | about a year and a half ago | (#43226037)

Will it prove the goldfishes' memory span ?

Re:Fish Brains (0)

Anonymous Coward | about a year and a half ago | (#43226167)

This works in zebrafish because they are transparent when measured and there are genetic tools to do this experiment for this species (which would take years of effort to get to work in goldfish, if it's even possible).

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