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Neuroscience Waves to the Crowd Vivien Marx Researchers Scale up How to Crowdsource the Mapping of Neural Circuits

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Neuroscience Waves to the Crowd Vivien Marx Researchers Scale up How to Crowdsource the Mapping of Neural Circuits TECHNOLOGY FEATURE Finding the crowd 1070 Testing, gaming 1072 Folding as play 1073 Neuroscience waves to the crowd Vivien Marx Researchers scale up how to crowdsource the mapping of neural circuits. These projects entice crowds by tapping into their spirit of play. Nonscientists can help with sophisticated ahead for now. “Unusual means may get us images of brain slices and to turn the two- neurobiology challenges. Researchers will- to some really cool goals,” he says. dimensional (2D) image information into ing to follow in the tracks of labs pioneer- Being ‘bold’ and ‘ambitious’ is now fash- connectivity maps of how the neurons run, ing this approach need to know that work- ionable in neuroscience, as illustrated by branch and connect throughout a section of ing with crowds means more than sharing large-scale efforts to map the human brain the brain. EyeWire is the father of crowd- neuroscience and computing knowledge. and accelerate technology development sourcing in this field, a gaming project initi- Initiating and managing peopled projects in neuroscience—such as the Brain ated by Seung and the first to “crowdsource takes stamina, management the connectome,” he says. expertise, unconventional The online project invites recruiting methods and slight- volunteers to compete against ly more-than-healthy amounts one another to map the neu- of pizza and caffeinated soft rons in a region of the mouse drinks. retina. The goal is to better In 2009, when neurosci- understand how visual infor- ence crowdsourcing ventures mation is processed in the began, skepticism reigned brain and to help train com- about the prospect of map- puters to get better at this kind ping neurons of entire cir- of tracing. cuits; crowdsourcing this chal- Around 82,000 partici- © 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature lenge to interested volunteers pants, who are almost all seemed to arouse even more citizen scientists as opposed skepticism. “That is a good to formally trained scientists, sign. If you’re doing something have played the game so far. npg new, there should be measured As EyeWire’s creative direc- skepticism—otherwise it is Neurobiology MPI for tor Amy Robinson says, their not new enough”, says Moritz Neuroscientist Moritz Helmstaedter (middle) and Brainflight programmers want surveys show that ‘EyeWirers’ Helmstaedter, a neuroscien- crowdsourced neuroscience to be fun. range from high school stu- tist at the Max Planck Institute dents to retirees and hail (MPI) of Neurobiology. He from basically all walks of life. and Sebastian Seung, a computational Research through Advancing Innovative Some players are researchers, but they are neuroscientist at Massachusetts Institute Neurotechnologies Initiative launched by mainly just people interested in science, says of Technology (MIT), and a few other neu- US President Barack Obama. Anatomical Seung. The top players, he says, are a mix roscientists are crowdsourcing in connec- mapping of the brain’s connections is one of of men and women. There is even a slight tomics, a field in which researchers seek to the initiative’s top priorities as described in skew toward more female players among generate and analyze detailed anatomical the first report recently issued to the direc- EyeWirers. “It’s pretty hard to predict who maps of entire nervous systems. tor of the US National Institutes of Health. will like this game.” As projects have drawn crowds and gen- Separately, scientists have found that The project takes two long-standing neu- erated publications, researchers now face crowdsourcing is a promising way to analyze roscience traditions of manual labor into the challenges in scaling up the ways crowds increasingly large data sets generated in labs realm of computer games. One of these is follow neurons through a stack of electron that perform neuroanatomical mapping. skeletonization, in which researchers trace microscopy (EM) images. The ability to per- the likely paths of neurons through stacks form this tracing is “a key bottleneck right EyeWire of EM images, he says. The other is one in now in connectomics,” says Helmstaedter. Crowds in neuroscience are already helping which scientists trace and render the neu- Crowdsourcing is the only way to move researchers to analyze high-resolution EM rons and their paths in three dimensions, NATURE METHODS | VOL.10 NO.11 | NOVEMBER 2013 | 1069 TECHNOLOGY FEATURE precisely outlining every neuron’s contour Seung is happy about the success of the and curve. project thus far in garnering so many par- Performed with “human intelligence,” ticipants for the game and the competitions. both these tasks done manually are pains- He acknowledges that his project’s players takingly slow, says are far fewer than the millions of players Seung. His idea has reached with games unrelated to science. been to accelerate Laughing, he points out that the game the process with Angry Birds has 2 billion downloads across many volunteers all platforms. “If you compare EyeWire with competing with a commercial game, it looks kind of pathet- one another and ic,” he says. “It needs to be much more fun, by harnessing arti- and that’s a challenge.” K. Krug/PopTech ficial intelligence. It is hard to recruit game developers to Sebastian Seung’s In the lab, his work on neuroscience. Helmstaedter—who EyeWire is the father team uses software is also trying to use gaming to grow the scale of crowdsourcing in called Omni to of neural circuit tracing in his lab—takes connectomics. render neurons in unusual approaches to recruiting potential three dimensions. programmers. EyeWire uses a slightly simplified version of Omni that lets players see one 3D and Finding the crowd one 2D view. In 2009, Helmstaedter and some students There is also a trained convolutional neural positioned themselves at the bottom of network at the heart of EyeWire, the code for the staircase leading to the cafeteria of the which is part of the paper Seung coauthored University of Heidelberg. A large projec- with Helmstaedter and others, in which the tion screen showed what one student was team presented a connectomic reconstruc- doing on a computer: tracing neurons in tion of a layer of the mouse retina1. EyeWire EM images. taps into the crowd to follow the path of neu- “It got so much attention,” Helmstaedter rons and perform volume reconstruction says of the recruiting session for his neuron- of neurons and the circuits to which they tracing project. People stopped, asked ques- belong. “It’s like coloring in a neuron with the tions, picked up flyers. Excitement mount- help of the computer,” Seung says. ed, and the crowd of his volunteers grew its Separately, he and his team also run algo- ranks to the list of 224 names that accom- rithm development competitions. “We put a pany his latest Nature paper, completed with © 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature data set online, and we let people try to sub- Seung, Winfried Denk from the Max Planck mit their algorithms to reconstruct from it, Institute for Medical Research and research- and we score them and we see who the win- ers in the UK, Germany and the USA1. ner is,” Seung says. The plan for the future is The recruited crowd was made up of npg to feed this algorithmic knowledge gained paid undergraduate and graduate students. back into EyeWire. Applying a software tool called KNOSSOS2 EyeWire, MIT/Seung lab MIT/Seung EyeWire, Around 82,000 participants have played EyeWire thus far. 1070 | VOL.10 NO.11 | NOVEMBER 2013 | NATURE METHODS TECHNOLOGY FEATURE members. After ing company, in which he learned to fos- some training ses- ter an environment with a group “driven sions, the crowds set by the goal, not by hierarchies,” he says. out to establish con- Helmstaedter then switched back to science nectivity between and completed an MD-PhD; he has conse- neurons and anno- quently brought his management experi- tate the microscopy ence to neuroscience crowdsourcing. data. With the skel- For the volunteers to begin their neu- etons, Helmstaedter ral reconstruction tasks, scientists pre- was then able to selected points in the EM images where apply the machine the volunteers were to start tracing. Then, EyeWire, MIT/Seung lab MIT/Seung EyeWire, learning algorithm Helmstaedter says, the volunteers followed used in EyeWire to a neurite for as long as they could, and the Volunteers compete to map and reconstruct neurons in EyeWire. “blow up the skel- results were returned to the research team etons into full vol- for evaluation. umes,” says Seung. Scientists could developed at the MPI, they helped to recon- Helmstaedter believes that anyone can cross-check the struct the circuit of 950 neurons in a layer of run a crowdsourcing project, but the project delivered results the mouse retina called the inner plexiform leaders will need to fully embrace it. After because multiple that had been imaged through serial block- finishing his master’s degree in physics, students were face EM. “KNOSSOS is made to ‘fly along’ Helmstaedter spent a few months working assigned the same neurites” to reconstruct skeletons of neurons, for a consulting company, which offered neuron, he says. Helmstaedter says. “EyeWire ‘paints’ neu- “great experience in how to manage very MPI Neurobiology More than 20,000 rons,” generating volume reconstructions. large teams, how to motivate people,” he says. “A lot of pizza was annotator hours He distributed hard disks of EM data sets Frequent meetings and benchmarking involved,” says Moritz led to 2.6 meters of Helmstaedter. and the KNOSSOS software to all the team were part of the project for the consult- skeleton. © 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature npg NATURE METHODS | VOL.10 NO.11 | NOVEMBER 2013 | 1071 TECHNOLOGY FEATURE Testing, gaming Dominic Bräunlein is testing several games—all in the prototype stage—that are intended to help annotate neurosci- ence data.
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