{"id":1018,"date":"2011-09-15T09:58:13","date_gmt":"2011-09-15T13:58:13","guid":{"rendered":"https:\/\/engineering.jhu.edu\/magazine-archive\/?p=1018"},"modified":"2017-08-02T10:20:39","modified_gmt":"2017-08-02T14:20:39","slug":"mapping-mind","status":"publish","type":"post","link":"https:\/\/engineering.jhu.edu\/magazine-archive\/2011\/09\/mapping-mind\/","title":{"rendered":"Mapping the Mind"},"content":{"rendered":"

\"mapping-the-mind\"<\/a>
\nThe human brain is a masterpiece of circuitry. In a squishy space about the size of an orange, the brain contains 100 billion neurons linked at trillions of critical spots known as synapses that conduct electrical signals to control our bodies, thoughts, and emotions, and make us who we are.<\/p>\n

If scientists could diagram every connection, collectively known as the \u201cconnectome,\u201d they\u2019d have an anatomical map of brain function and, for the first time, a detailed way to understand what mistakes in this biological wiring cause neurological disease and psychiatric disorders. But given that there are more than 100 trillion synapses, well, that\u2019s kind of a lot of work.<\/p>\n

It\u2019s also exactly what the Open Connectome Project<\/a> is making possible. A Web platform that stores and manages 20 terabytes of brain image data, this Hopkins project puts the data online for scientists worldwide to tap and for users\u2014including laypeople\u2014to view and help analyze and annotate. (The project\u2019s motto: \u201cCollectively reverse-engineering the brain one synapse at a time.\u201d)<\/p>\n

\u201cIf you look at data online you can see neural structures, synapses, but it\u2019s just image data,\u201d says Randal Burns, associate professor in the Department of Computer Science<\/a> and director of the Hopkins Storage Systems Labs. \u201cGoing from image data to information about connectivity\u2014that\u2019s the central challenge.\u201d<\/p>\n

An initiative of Hopkins\u2019 Institute for Data Intensive Engineering and Science<\/a> (IDIES) \u2014a partnership of the Krieger School of Arts and Sciences, the Whiting School, and the Sheridan Libraries\u2014the project is one of \u2028several Hopkins efforts aimed at designing computational tools to analyze the unprecedented flood of data collected via digital technologies. Like the Hopkins Sloan Digital Sky Survey, which seeks to map every object in the heavens, the Open Connectome Project leverages crowdsourcing and cloud computing to do large-scale science.<\/p>\n

The project was born on a cocktail napkin when Burns met neuroscientist Josh Vogelstein, \u2028a postdoc in the Whiting School\u2019s Department of Applied Mathematics and Statistics<\/a>, at a dinner in March 2010. \u201cJosh had this vision of an open connectome, and I had experience managing large data\u00adsets\u201d\u2014laying the groundwork for an ideal collaboration, says Burns.<\/p>\n

The data already existed. Most data come from two Harvard laboratories that had collected a mountain of slices of mouse brain that they ran under an electron microscope; more data are expected from such institutions as the Max Planck Institute in Germany. The project also hosts brain data collected from magnetic resonance imaging. Over the past year, Burns and his students built a high-throughput storage system to house the data with Web Services to let users download it. The scientists now are working on making it possible for users to also upload any brain data they want to contribute\u2014and annotate it.<\/p>\n

And they\u2019re developing a tutorial that will enable even laypeople to annotate data.<\/p>\n

Participants will use a tool specifically designed to identify the neuron, bit of neuron, or synapse associated with each pixel in an image. \u201cYou need to know nothing about neuroscience or computers or annotating,\u201d says Vogelstein. They expect to have hundreds of terabytes of data by next year, and petabytes in a few years. Given the scope of the project, the researchers hope many users will contribute the algorithms they write to identify cell boundaries or neurons. This \u201calg-sourcing\u201d is crucial. Because the project is so vast and has so many parts, the researchers expect to use many algorithms together.<\/p>\n

In addition to creating tools for image processing, Vogelstein\u2019s brother, Jacob, a biomedical engineer at Hopkins\u2019 Applied Physics Laboratory<\/a>, is designing modular tools to combine these algorithms.<\/p>\n

Since its launch in March 2011, the site has been getting more than 2,000 hits a month. \u201cThis is a big movement in open science. People anywhere in the world with Internet access can see and contribute to the most-cutting-edge science,\u201d says Vogelstein. \u201cIt takes science out of the ivory tower and makes it available to everyone.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

The Open Connectome Project helps scientists understand neurological diseases.<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[31],"tags":[],"class_list":["post-1018","post","type-post","status-publish","format-standard","hentry","category-big-ideas","issue-fall-2011"],"acf":[],"yoast_head":"\nMapping the Mind - JHU Engineering Magazine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/engineering.jhu.edu\/magazine-archive\/2011\/09\/mapping-mind\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Mapping the Mind - JHU Engineering Magazine\" \/>\n<meta property=\"og:description\" content=\"The Open Connectome Project helps scientists understand neurological diseases.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/engineering.jhu.edu\/magazine-archive\/2011\/09\/mapping-mind\/\" \/>\n<meta property=\"og:site_name\" content=\"JHU Engineering Magazine\" \/>\n<meta property=\"article:published_time\" content=\"2011-09-15T13:58:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-08-02T14:20:39+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/engineering.jhu.edu\/magazine-archive\/wp-content\/uploads\/2014\/06\/mapping-the-mind.jpg\" \/>\n<meta name=\"author\" content=\"Abby Lattes\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Abby Lattes\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/\"},\"author\":{\"name\":\"Abby Lattes\",\"@id\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/#\\\/schema\\\/person\\\/0244393be370fbc3ead8ec26062e9742\"},\"headline\":\"Mapping the Mind\",\"datePublished\":\"2011-09-15T13:58:13+00:00\",\"dateModified\":\"2017-08-02T14:20:39+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/\"},\"wordCount\":661,\"commentCount\":0,\"image\":{\"@id\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/wp-content\\\/uploads\\\/2014\\\/06\\\/mapping-the-mind.jpg\",\"articleSection\":[\"Big Ideas\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/\",\"url\":\"https:\\\/\\\/engineering.jhu.edu\\\/magazine-archive\\\/2011\\\/09\\\/mapping-mind\\\/\",\"name\":\"Mapping the Mind - 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