{"470091":{"#nid":"470091","#data":{"type":"news","title":"iPlant Hosts Platform for Field-Based Imaging of Root Traits","body":[{"value":"\u003Cp\u003EBy Shelley Littin, iPlant Collaborative\u003Cbr \/\u003EOriginal Story: \u003Ca href=\u0022http:\/\/www.iplantcollaborative.org\/blog\/news\/iplant-hosts-platform-field-based-imaging-root-traits\u0022 title=\u0022http:\/\/www.iplantcollaborative.org\/blog\/news\/iplant-hosts-platform-field-based-imaging-root-traits\u0022\u003Ehttp:\/\/www.iplantcollaborative.org\/blog\/news\/iplant-hosts-platform-field...\u003C\/a\u003E\u003C\/p\u003E\u003Cp\u003EResearchers led by a team at the \u003Ca href=\u0022http:\/\/www.gatech.edu\u0022\u003E\u003Cstrong\u003EGeorgia Institute of Technology\u003C\/strong\u003E\u003C\/a\u003E (Georgia Tech) have developed an online platform that enables plant scientists to obtain quantitative phenotype information on the root systems of plants imaged in the field.\u003C\/p\u003E\u003Cp\u003EThe platform, called \u003Ca href=\u0022http:\/\/dirt.iplantcollaborative.org\u0022\u003E\u003Cstrong\u003EDigital Imaging of Root Traits\u003C\/strong\u003E\u003C\/a\u003E (DIRT), is now hosted by the \u003Ca href=\u0022http:\/\/www.iplantcollaborative.org\u0022\u003E\u003Cstrong\u003EiPlant Collaborative\u003C\/strong\u003E\u003C\/a\u003E\u2019s computational infrastructure, as described in a \u003Ca href=\u0022http:\/\/www.plantmethods.com\/content\/11\/1\/51\u0022\u003E\u003Cstrong\u003Erecent publication\u003C\/strong\u003E\u003C\/a\u003E in the journal \u003Ca href=\u0022http:\/\/www.plantmethods.com\u0022\u003E\u003Cstrong\u003EPlant Methods\u003C\/strong\u003E\u003C\/a\u003E. Researchers anywhere in the world with an Internet connection can access the program by logging into an iPlant account.\u003C\/p\u003E\u003Cp\u003EThe idea is to expedite and simplify the process of collecting measurements of plant roots in the field, said \u003Ca href=\u0022http:\/\/www.bucksch.nl\u0022\u003E\u003Cstrong\u003EAlexander Bucksch\u003C\/strong\u003E\u003C\/a\u003E, a research scientist in \u003Ca href=\u0022http:\/\/ecotheory.biology.gatech.edu\u0022\u003E\u003Cstrong\u003EJoshua Weitz\u0027s group\u003C\/strong\u003E\u003C\/a\u003E at Georgia Tech, and corresponding author on the paper. \u201cVisual phenotypes of a plant can be computed reproducibly with imaging, including features impractical to measure by hand,\u201d Bucksch explained.\u003C\/p\u003E\u003Cp\u003EThe research team spent three years collecting plant root samples at field stations in the United States and South Africa and manually measuring dozens of traits including root density, angles, surface area, number of roots, and many more. They then configured calculations based upon these standardized measurements, to produce a program capable of giving highly accurate measurements for root traits based upon a photograph of roots.\u003C\/p\u003E\u003Cp\u003ETo use the platform, a scientist need only lay out the roots next to a marker for scale and take a photograph, and the program will provide many dozens of phenotype measurements. \u201cDIRT provides a pipeline to move from a field-based image to quantitative data as part of studies by academics and breeders alike,\u201d said Joshua Weitz, associate professor of biology and director of the \u003Cstrong\u003E\u003Ca href=\u0022http:\/\/qbios.gatech.edu\u0022\u003EQuantitative Biosciences Graduate Program\u003C\/a\u003E\u003C\/strong\u003E at Georgia Tech.\u003C\/p\u003E\u003Cp\u003EIn response to broad interest in using DIRT in the field, Bucksch and his colleagues approached iPlant to host the platform and make it freely available to researchers anywhere. Through iPlant, a user\u2019s data are secure, so that only the account owner and their collaborators may see the results. This makes DIRT a secure, open-access, time saving tool for botanists everywhere.\u003C\/p\u003E\u003Cp\u003E\u201cField-based measurements are vital for quantifying traits,\u201d said \u003Cstrong\u003E\u003Ca href=\u0022http:\/\/www.bio5.org\/about\/scientists\/nirav-merchant\u0022\u003ENirav Merchant\u003C\/a\u003E\u003C\/strong\u003E, co-principal investigator of the iPlant Collaborative at the \u003Cstrong\u003E\u003Ca href=\u0022http:\/\/www.arizona.edu\u0022\u003EUniversity of Arizona\u003C\/a\u003E\u003C\/strong\u003E\u2019s \u003Cstrong\u003E\u003Ca href=\u0022http:\/\/www.bio5.org\u0022\u003EBIO5 Institute\u003C\/a\u003E\u003C\/strong\u003E, and director of Biocomputing at \u003Cstrong\u003E\u003Ca href=\u0022http:\/\/www.arl.arizona.edu\u0022\u003EArizona Research Laboratories\u003C\/a\u003E\u003C\/strong\u003E. \u201cAutomating these methods is essential to support the high throughput nature of analysis. For scientists in the field, DIRT elegantly facilitates the analysis and management of image-based phenotype data by connecting them with scalable cyberinfrastructure and their global community of collaborators.\u201d\u003C\/p\u003E\u003Cp\u003E\u201cManually,\u201d Bucksch said, \u201cyou cannot measure many dozens of traits in just five minutes, as you can with DIRT.\u201d\u003C\/p\u003E\u003Cp\u003EThe program currently works for nearly all plant root systems. \u201cThere are certain traits that only work on monocots or dicots, and we are currently exploring more about this,\u201d Bucksch said, explaining that slight differences in the algorithms account for variation in the plant species.\u003C\/p\u003E\u003Cp\u003EAlready the platform has a substantial user base, with several scientists regularly using it for their root measurements. \u201cUndergraduate students are using DIRT, a \u003Ca href=\u0022https:\/\/groups.google.com\/forum\/#%21forum\/dirt-users\u0022\u003E\u003Cstrong\u003EGoogle group\u003C\/strong\u003E\u003C\/a\u003E is providing user-to-user support, and at least one citizen scientist is currently using it,\u201d said Bucksch.\u003C\/p\u003E\u003Cp\u003E\u0022DIRT seems especially useful in my work because a plant is a lot like an iceberg: Most of it is totally hidden beneath the surface,\u0022 said Tim Zebo, a recently retired electronics engineer turned hydroponics and aeroponics systems researcher. Dr. Zebo is analyzing the roots of plants grown in liquid nutrients because, in this era of rapid climate change and major droughts, those plants require less than 10 percent of the water needed for soil-grown plants.\u0026nbsp; He plans to use DIRT to better understand root system architectures to increase production and reduce time to harvest.\u003C\/p\u003E\u003Cp\u003EFor plant scientists and breeders, Bucksch said, root traits are key. \u201cThe root is important to nutrient uptake,\u201d he said, continuing \u201cand understanding how environmental and growth factors influence root traits is vital to developing crops capable of surviving climate change.\u003C\/p\u003E\u003Cp\u003EIncreased food availability and resilience is necessary to accommodate accommodate rapidly increasing global populations. Plant scientists must work together to understand how plant traits \u2013 including root structure and function \u2013 affect crop survivability and adaptability. Bucksch and co-authors have developed DIRT with this objective in mind and to enhance the science of root systems.\u003C\/p\u003E\u003Cp\u003ETheir work was supported, in part, by grants from Georgia Tech, the \u003Ca href=\u0022http:\/\/www.nsf.gov\u0022\u003E\u003Cstrong\u003ENational Science Foundation\u003C\/strong\u003E\u003C\/a\u003E, the \u003Ca href=\u0022http:\/\/www.thehowardgbuffettfoundation.org\u0022\u003E\u003Cstrong\u003EHoward G. Buffett Foundation\u003C\/strong\u003E\u003C\/a\u003E and the \u003Ca href=\u0022http:\/\/www.bwfund.org\u0022\u003E\u003Cstrong\u003EBurroughs Wellcome Fund\u003C\/strong\u003E\u003C\/a\u003E. Bucksch also thanks iPlant co-principal investigator Nirav Merchant and iPlant senior projects coordinator Martha Narro for their assistance integrating DIRT on iPlant infrastructure. Abhiram Das, a graduate student studying under Bucksch and Joshua Weitz at the Georgia Institute of Technology, led the effort to develop DIRT prior to receiving his doctorate in Bioinformatics earlier this year.\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EResearchers led by a team at the \u003Ca href=\u0022http:\/\/www.gatech.edu\u0022\u003E\u003Cstrong\u003EGeorgia Institute of Technology\u003C\/strong\u003E\u003C\/a\u003E (Georgia Tech) have developed an online platform that enables plant scientists to obtain quantitative phenotype information on the root systems of plants imaged in the field.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Researchers led by a team at the Georgia Institute of Technology (Georgia Tech) have developed an online platform that enables plant scientists to obtain quantitative phenotype information on the root systems of plants imaged in the field."}],"uid":"27245","created_gmt":"2015-11-16 13:00:29","changed_gmt":"2016-10-08 03:19:58","author":"Troy Hilley","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2015-11-16T00:00:00-05:00","iso_date":"2015-11-16T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"470081":{"id":"470081","type":"image","title":"Alexander Bucksch","body":null,"created":"1449257160","gmt_created":"2015-12-04 19:26:00","changed":"1475895218","gmt_changed":"2016-10-08 02:53:38","alt":"Alexander Bucksch","file":{"fid":"203878","name":"roots.jpg","image_path":"\/sites\/default\/files\/images\/roots_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/roots_0.jpg","mime":"image\/jpeg","size":327433,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/roots_0.jpg?itok=XXZrXAd1"}}},"media_ids":["470081"],"groups":[{"id":"1275","name":"School of Biological Sciences"}],"categories":[{"id":"146","name":"Life Sciences and Biology"}],"keywords":[{"id":"147971","name":"Alexander Bucksch"},{"id":"11599","name":"Joshua Weitz"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EBy Shelley Littin, iPlant Collaborative\u003C\/p\u003E","format":"limited_html"}],"email":[],"slides":[],"orientation":[],"userdata":""}}}