{"id":13499,"date":"2017-04-19T16:00:02","date_gmt":"2017-04-19T15:00:02","guid":{"rendered":"https:\/\/blogs.nature.com\/naturejobs\/?p=13499"},"modified":"2017-07-12T20:34:17","modified_gmt":"2017-07-12T19:34:17","slug":"techblog-need-an-instrument-build-it","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/naturejobs\/2017\/04\/19\/techblog-need-an-instrument-build-it\/","title":{"rendered":"TechBlog: Need an instrument? Build it!"},"content":{"rendered":"

The 6 April issue of Nature<\/em> included a Toolbox feature on the growing use of DIY electronics<\/a> in scientific research.<\/p>\n

Daniel Cressey writes:<\/p>\n

Arduinos and similar devices, such as the Raspberry Pi, pack considerable power on their diminutive boards, providing tremendous opportunities for automation, networking and data collection and analysis. For researchers, those features can translate into benefits both economic and practical. Users can shoehorn the systems into tiny spaces, deploy them without monitors or keyboards, buy them in bulk, and pack them into autonomous devices that need to be taken to (and transmit data from) remote field locations. All it takes is a little ingenuity.<\/em><\/p><\/blockquote>\n

A recent article <\/a>on the bioRxiv preprint server provides a case in point.<\/p>\n

<\/p>\n

\"The<\/a>

The FlyPi in fluorescence mode.{credit}Tom Baden{\/credit}<\/p><\/div>\n

In 2011, Tom Baden<\/a>, a neuroscientist at the University of Sussex in the UK, who then was at the University of T\u00fcbingen, Germany, cofounded a non-governmental organization dedicated to scientific education in Africa, called TReND in Africa<\/a>. The organization runs multiday workshops in which experts from around the world travel to Africa to teach undergraduate and graduate students scientific concepts, with a focus on open-source instrumentation and software.<\/p>\n

Baden himself sometimes ran those courses, and in 2014, he and TReND cofounder Lucia Prieto, were in Tanzania when Prieto suggested trying to build a neuroscience instrumentation platform that would support so-called thermogenetics, a heat-regulated genetic control system akin to optogenetics, which can be used to control fruit fly behavior. To build it, they worked with another TReND in Africa volunteer, Andr\u00e9 Maia Chagas.<\/p>\n

Chagas, a graduate student at the University of T\u00fcbingen, who happened to work on the same hallway as Baden prior to Baden\u2019s move to the UK, had set up a web site dedicated to open-source neuroscience projects, called OpenNeuroscience<\/a>. In 2013, Baden stumbled across the web site, and encouraged Chagas to join his organization.<\/p>\n

The team started with a simple Arduino-controlled Peltier element \u2013 basically a ceramic wafer that heats and cools when an electrical current is applied. From there, the system slowly evolved to include high-intensity LEDs for illumination and optogenetic stimulation, a servo motor to control focus, a camera, micromanipulators, and a 3D-printed frame. To tie it all together, they added a Raspberry Pi computer and developed a graphical user interface that runs on the Linux-based Raspberry Pi operating system, Raspbian.<\/p>\n

The fully tricked-out system, called FlyPi, can be built for under 200 euro, Baden says \u2013 orders of magnitude less than some commercial implementations; the base configuration, comprising the frame and camera, costs just half that \u2013 a \u201c100 \u20ac lab,\u201d as the preprint dubs it.<\/p>\n

In their preprint, the authors \u2013 Chagas, Prieto, Baden, and Aristides Arrenberg, also at T\u00fcbingen \u2013 put the FlyPi through its paces in zebrafish, fruit flies, and nematodes. But there\u2019s still room for improvement, Baden notes. The system has relatively poor spatial and z-axis resolution compared to commercial microscopes, for instance, and limited fluorescence capabilities. Planned improvements include a universal mount that can accommodate any microscope objective a researcher happens to have on hand, and a broader palette of fluorescent channels. Another possible upgrade, he says, would be adding a small screen and batteries so the FlyPi could become portable for use in the field.<\/p>\n

\u201cThe big hope is that \u2026 people will latch onto this and come up with, well, hopefully better ideas than ours and sort of develop it from there,\u201d Baden says.<\/p>\n

That open-source strategy dovetails nicely with the TReND in Africa project itself. According to Chagas, TReND aims not to teach students how to build one particular device, but to empower them to address whatever needs may arise in their research. One former student leveraged the course to automate a behavioral task for rodent studies; another developed a method to automate mushroom farming.<\/p>\n

Riffing on an old adage that says \u2018give a man to fish, feed him for a day; teach a man to fish, feed him for a lifetime,\u2019 Chagas says of TReND, \u201cIt\u2019s a little bit [like] not teaching people how to fish, but teaching people how to make fishing rods. The fishing rod that they need depends on where they\u2019re trying to fish, basically.\u201d<\/p>\n

 <\/p>\n

Jeffrey Perkel <\/em><\/strong>is Technology Editor, <\/em>Nature.<\/em><\/p>\n

 <\/p>\n

Suggested posts<\/strong><\/p>\n

My digital toolbox: Lorena Barba<\/a><\/p>\n

JOSS<\/em> gives computational scientists their academic due<\/a><\/p>\n

My digital toolbox: Santiago Perez De Rosso on Git, reimagined<\/a><\/p>\n

Genome editing meets version control<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

The 6 April issue of Nature included a Toolbox feature on the growing use of DIY electronics in scientific research.  Read more<\/a> Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":104777,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[192,200],"tags":[326,6575563,6575561,5945961,6575565,6677357,75,6575567],"class_list":["post-13499","post","type-post","status-publish","format-standard","hentry","category-blog-2","category-technology-2","tag-africa","tag-arduino","tag-flypi","tag-jeffrey-perkel","tag-raspberry-pi","tag-techblog","tag-technology","tag-tom-baden"],"_links":{"self":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts\/13499","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/users\/104777"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/comments?post=13499"}],"version-history":[{"count":0,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts\/13499\/revisions"}],"wp:attachment":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/media?parent=13499"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/categories?post=13499"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/tags?post=13499"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}