I loons proclaim size of the completed the data imagesthe into asingle 3D volume. The bal tists took about three months to assemble developed by institute’s the computer scien each just 40 nanometres thick. Then, software images of 25,000 slices of mouse cortex, visual months, more collecting than 100 million roughly of size the a grain of sand. millimetre of mouse — a sample that’s tions, or synapses, inacubic them between 100,000 and one billion the connec latest milestone inan effort to map each of the ebrate institute’s the researchers reaching the are bobbing around. The are balloons to cel tron microscopes, three shiny balloons party BY SARAH DEWEERDT volumes ofdata accumulate, researchers must find ways to make them useful. Efforts to chart the brain, synapse by synapse, are coming to the fore. But asthe massive connections Deep The synapsebetweentwoneurons (retinal ganglioncell,blue;amacrineyellow)inamouseretina reconstructed forneuron-mapping gameEyewire. S6 | NATURE | S6 VOL | JULY 571| 25 2019 The microscopes ran continuously for five a room containing five transmission elec Brain in Seattle, Science Washington. In t’s April 2019at Institute Allen the for - - - - - has 10 has brain — is along still way off. The connectomenanoscale of awhole human direct behaviour — in short, how work. how circuits neural information encode and give unparalleledefforts them will insights into level detail. that think these diagram of system nervous the with synapse- to map a nanoscale — a wiring just one attempts of several invarious species WilliamEnglish poet Blake. neurobiologist at Institute, Allen the quoting “a world inagrain of sand”, says Clay Reid, a which makes mouse-brain the images almost missions, up take only about 1.3 petabytes, lite images by collected Landsat the of Earth, and silver letters. More than 30years of satel is equivalent to 2 million gigabytes) in blue spelling outset, “2PB” (2 petabytes, which The ultimate achievement area — a inthis The mouse-brain cubic-millimetre project is ©

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A l l r i g h t s r e s e r v e d . - progress continues, computational inboth leveltic might inconceivable. seem But if steady “Today, mapping human the brain at synap the brain is becoming alegitimate long-term goal. ade. And doing for so much the larger human volume — might possible next be inthe dec mouse brain — about 500cubic millimetres in researchers now that think mapping entire the ing about acubic millimetre,” says. Reid Many years ago, it felt overly ambitious think to be that involved. has even those surprised “Five of field the connectomics forwards at a pace algorithms for image analysis, have propelled and computers powerful more of development required for such an endeavour. thousands of years just data the to collect of microscopes, working around clock, the rent imaging technology, it would dozens take Milkythe Way, around 100 billion. Using cur same number of neurons as there are stars in But advances inmicroscopy, as well as the - - - -

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capabilities and scientific techniques, another to be released represents a one cubic millimetre in volume, but to capture factor of 1,000 is not out of the question.” roughly 100-micrometre cube of mouse the full thickness of the human cortex, the containing around 1,000 neurons and sample is shaped like a slab, rather than a cube. ALL THE SMALL THINGS 250,000 synapses. Denk, now director of the Denk and his colleagues are mapping Nanoscale connectomes have been completed Max Planck Institute of Neurobiology in portions of the connectome in the zebra finch in two species: the Caenorhabditis Martinsried, Germany, and his collabora- (Taeniopygia guttata), a small bird whose pro- elegans1, in 1986, and the larva of a marine tor Moritz Helmstaedter, co-director of the cess of song learning can yield insights into organism known as Ciona intestinalis2, in 2016. Max Planck Institute for Brain Research in human speech. And Kasthuri has a number These neural maps are a powerful winnowing Frankfurt, Germany, published the analysis4 of projects in progress. “Now that there is a lot tool. “There are a lot of hypotheses that have in 2013. But the mouse-brain cubic-millimetre of data available on the circuitry of the mouse been refuted by the C. elegans wiring dia- project will be looking at 100,000 neurons, and brain, I think the best way to do it is to either gram,” says Bobby Kasthuri, a other, similar programmes are also under way. look across species or look across develop- at Argonne National Laboratory in Lemont, “A cubic millimetre is a size that seems to be ment,” he says. “The best information will come Illinois. If an observation about the worm’s sufficient, at least for the neurons in the centre of from comparing that diagram to other things.” or behaviour can be easily that grain of sand, to get most of their local con- To that end, Kasthuri aims to map the visual explained by the wiring diagram, there’s no need nections,” says Nuno da Costa, a neuroscientist part of the brain in non-human primates, as for further experiments; researchers can move at the Allen Institute. The mouse-brain project well as in an octopus (Octopus bimaculoides). on to more fruitful lines of inquiry. But when will therefore enable scientists to explore com- “It’s probably the creature that is the most alien the connectome doesn’t offer a ready expla- plete local circuits, rather than single neurons to us that’s still smart,” he says, of the octopus. nation for results, it can indicate productive with a sparse network of connections. The work “So, I’m interested in comparing the wiring of directions of research for scientists to explore. being conducted at the Allen Institute is part of a that brain to the wiring of the mouse brain.” Some researchers do question the focus collaboration with researchers at Baylor College Kasthuri is also working on the full on nanoscale connectomes. The enormous of Medicine in Houston, Texas, Princeton connectomes of young mice and octopuses; amount of time, effort and money that goes University in New Jersey and Harvard Univer- comparing these immature connectomes to into such projects might be overkill, says sity in Cambridge, Massachusetts, known as those of adult animals could offer insights into Anthony Movshon, a neuroscientist at New Machine Intelligence from Cortical Networks, how the brain learns from experience. Owing York University in New York City who studies which is funded by the US government. to its small size, he hopes to map the young- the visual system. When it comes to complex Its progress has led some to predict that the octopus connectome in about one year. brains such as those of mice or humans, “I nanoscale connectome of a complete mouse don’t need to know the precise details of the brain — likely to produce around one exabyte AI SPY wiring of each cell and each synapse in each of (one billion gigabytes) of data — could be Now that the researchers at the Allen Institute those brains,” Movshon says. “What I need to mapped in the next decade. “It would require have finished imaging their cubic millimetre know, instead, is the organizational principles many laboratories,” says Jeff Lichtman, a of mouse brain, they have passed on the data that wire them together.” This, he suggests, can neuroscientist at Harvard University. “But it’s to , a neuroscientist and com- be gleaned with a coarser level of resolution. doable,” he says, “and that’s exciting.” puter scientist at Princeton University. Seung’s Yet the nanoscale connectome is a goal that Others remain cautious. “There are so many lab will align the resulting images, and then captures the imaginations of many scientists. logistic challenges” to a project of that size, annotate the synapses and trace, or segment, They say that this work could help to unravel says Stephen Plaza, a computer scientist at the estimated four kilometres of nerve fibre that the origins of mental-health conditions and the Howard Hughes are contained within the volume. lead to more informed treatments, as well as Medical Institute “We’re still in Segmentation has long been the rate-limiting have applications in a host of fields, includ- Janelia Research step in connectomics. It can take weeks to trace ing (see page S15) and Campus in Ashburn, the training- by hand the path of a single through a energy-efficient computation. Virginia. He thinks wheels stage of stack of electron micrographs. But now, arti- that the field should connectomics.” ficial intelligence is getting involved. Seung’s PROJECT PROLIFERATION target intermediary- team has developed a machine-learning algo- To map the nanoscale connectome of scale projects before tackling something as rithm that can evaluate images pixel by pixel to C. elegans, in the 1980s, researchers led by complex as the mouse brain. “We’re still in the determine the location of neurons. biologist Sydney Brenner at the University of training-wheels stage of connectomics,” he says. Computers can perform segmentation faster Cambridge, UK, thinly sliced the millimetre- Plaza manages one such project. Called than the human , which cuts down the time long worms and photographed each slice FlyEM, it aims to produce a connectome of it takes to trace neurons to a matter of minutes using a film camera mounted to an electron the central nervous system of the fruit fly or hours. But they aren’t as accurate: algorithms microscope. In the resulting images, they then melanogaster. His team expects can miss out bits of neuron or incorrectly merge painstakingly traced by hand the pathways of to release data on roughly one-third of the two neurons into one. People are therefore still neurons and the connections between them. D. melanogaster brain in early 2020. Plaza needed to check the reconstruction. Seung is But C. elegans has a mere 302 neurons and expects that the connectome of the entire tackling this requirement through crowdsourc- around 7,600 synapses. The methods used to central nervous system — composed of about ing and, specifically, an online game called produce its connectome simply weren’t practical 100,000 neurons and 100 million connections Eyewire, in which players are challenged to to use in larger nervous systems. Researchers in the fly’s brain alone, plus a similar number correct mistakes in the rough draft of a connec- did not think seriously about embarking on of neurons and synapses in the ventral nerve tome. Launched in 2012, Eyewire has 290,000 considerably larger projects until 2004, when cord (roughly equivalent to the spinal cord of registered users who have collectively put in physicist Winfried Denk and neuroanatomist vertebrates) — will follow a few years later. an effort that is equivalent to 32 people work- Heinz Horstmann, then both at the Max Planck Meanwhile, Lichtman is working on the ing full time for 7 years, says Amy Robinson Institute for Medical Research in Heidelberg, zebrafish (Danio rerio) connectome, as well as Sterling, executive director of Eyewire. Germany, proposed using an automated micro- analysing a small piece of the human brain — a So far, players have been tracing cells in scope to slice and image the brain and software sample of the medial temporal gyrus obtained the mouse retina. They’ve contributed to the to stack and align the resulting images3. from a person who was undergoing brain sur- discovery of six types of neuron, which play- One of the largest complete nanoscale gery for epilepsy. That piece is also roughly ers chose to name after ancient Greek deities.

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adds. “That’s agreat place to be.” not able to keep up with them,” he team can imaging collect data. “We’re is able to neurons trace faster than his says of result, the noting that algorithm the labsthe of and Denk Lichtman. Campus. areThey working also with data from imaged by another team at Janelia Research draft connectome of brain awhole fly that was to FlyEM data and has constructed a rough- Jain says. His team is applying technique the a human would colour inacolouring book,” neurons at once. “It’s alittle bit like way the to boundaries the define than of trying all structures from apoint inan image, rather network, which builds a flood-filling called has designed a machine-learning algorithm AI,inMountainat Google View, California, neuron segmentation. Ateam by led Viren Jain to data. visualize connectome-mapping program the use efforts 3Dforestcolourful of neurons. Many nanoscale black-and-whiteflat, electron micrographs as a program developed that by visualizes Google with mouse the used visual-cortex data set. version of game, the Neo, called that be will Sterling and her team are preparing a new volume imaged to be by method. this FlyEM sample represents first substantial the surface, and process the then is repeated. The capturesscope an image of freshly the exposed away layer athin of atissue sample. The micro tions that images. the make to align it difficult cutting sample the inevitably results indistor Butneeded. no matter how precisely it is done, sample and is preserved re-imaged, can be if onto a reel — through film microscope. the result — whichthe remarkably looks similar mount slices the tape on and a specialized feed tion of the thickness of a human hair. then They in plastic, and cut it into slices that are afrac microscopy. Researchers tissue neural embed microscopy electron known as serial-section copy in connectomics of is a type electron of large, mammalian brains. ontaking nanoscale the connectomes much quicker pace, in anticipation of sharper, more-detailed images at a microscopy techniques to produce Meanwhile, scientists are honing CLOSE LOOK human checking that is required. keep feasible amount the of to become more accurate to have algorithms segmentation tists on take ever larger projects, note, and points out that as scien SEM), of abeam uses charged ions to shave scanningbeam electron microscopy (FIB- S8 | NATURE | S8 VOL | JULY 571| 25 2019 OUTLOOK A newer approach, ion known as focused The advantage of is this method that the The conventional approach to micros Jain amore strikes cautious “It’s beautiful to truly look at,” Lichtman developed an has algorithm also forGoogle Neo’s interface on Neuroglancer, is based a THE BRAIN - - - - - nanoscale connectome projects are rapidly But creates speed its own problems. Now that MAKE ITMEANINGFUL gigapixel of second. imaging data every way,the which might eventually capture a microscopes with hundreds of beams are on has oneDenk with 91 beams. And electron duced by Carlthat Zeiss has 61 beams, and second.per Lichtman is using amachine pro toscope capture hundreds of millions of pixels imaging nervefibres inthebrains of newborns. The DevelopingHumanConnectomeProject is at same the time, which enables micro the tion. Numerous electron beams asample scan researchers up image speed hope will acquisi with multibeam electron microscopes, which in imaging larger brains. of view, which makes it more feasible for use Campus, works similarly but has alarger field Hayworth, aneuroscientist at Janelia Research copy (GCIB-SEM), developed by Kenneth cluster ion scanning beam electron micros into gas chunks.) smaller called Amethod size ofthe apoppy has chopped to seed, be ples. (Even brain, fruit-fly the which is roughly which makes to apply it difficult to larger sam cess. In addition, small, of field the is very view once, are they because vaporized pro inthe axis. However, samples imaged can be only rather than coarser being along vertical the produced three is same the dimensions, inall FIB-SEM is that resolution the of images the GCIB-SEM more might be also compatible Although it one lacks speed, advantage of ©

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A l l r i g h t s r e s e r v e d . ------5. 4. 3. 2. 1. Washington. Seattle, DeWeerdtSarah as well as those of both full-term andas well of premature as full-term those both brainsthe of hundreds of fetuses womb, inthe Project, which is wrapping up its effort to scan ofpart Developing the Human Connectome neonatologist at Kings London. College He is macroconnectome. the of brain. the The result was a map known as fibres ofwide tracts nerve that connect regions of about 1,200 people to millimetre- define magnetic resonance imaging to brains the scan . That effort used large-scale projects such as the connectome data with that produced by other than we could possibly hire.” cover things new on data Many this set. more large number of scientists could routinely dis processed data at our fingertips,” says. Reid “A how to make of sense it “We all. have much so producing data, another challenge is looming: says, going “is one to be of next the frontiers.” synaptomethe with connectome,” the Grant the problemthe of scale,” says David Edwards, a microscale, great things beingdone at popula macroscale,the great things being done at the babies. are “There great things being done at connections that make. they “Marrying up to match begun also subtypes the with the variousacterize brain regions. The team has and to identify patterns of subtypes that char basisthe of protein content, size and shape, which enabled tothem 37 subtypes define on synapses across whole the mouse brain “The biggest“The problem inneuroscience is There issue the is also of nanoscale- linking Zhu, F. etal. (2013). Helmstaedter, M.etal. (2004). Denk. W.&Horstmann,H.PLoS Biol. e16962 (2016). Ryan, K.,Lu, Z.&Meinertzhagen,I.A.eLife (1986). Brenner, S.Philos.Trans. R.Soc.Lond. B White, J.G.,Southgate,E.,Thomson,N. & Grant and his team catalogued one billion tion level,” Edwards says. “But there are very few ways of together.” those linking brain function. Enter synaptome. the In a2018paper, how evolution and genetics govern some ways, even more detailed Fresh sources of data that are, in will be essential for be will working out than the nanoscale connectome, connectome, nanoscale the than genomic insights, Grant suggests, are emerging. also For example, way to .” the And those Neuron the connectome only provides provides only connectome the bridge it, you don’t your find of Edinburgh, UK.“If you can’t neuroscientist at University the location the about information says Seth Grant,says Seth amolecular a gap that bridged,” to needs be lar composition. “I that see as of synapses, not molecu their is ascience is writer based in 99, 781–799(2018). Nature , 168–174 500, 168–174 2 , e329 , e329 , 1–340 314, 1–340 5 , 5 ■ - - - - ,

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