NSF Advisory Committee 2016 Table of Contents Click Page to Navigate • Analysis of Genes AffectingPlant Regeneration and Transformation in Poplarby Steve Strauss………........................................................................................Page 4 • High Throughput Culture and Image Plans by Anna Magnuson.………………………………………………............................................................................................Page 42 • High Throughput Fluorescence Imagingby Chris Draves.………………………………………………………………………………………………………......................................Page 81 • Culture Medium and Transformation Plans by Amy Klocko, Cathleen Ma, & Michael Nagle……………………….............................................................................Page 105 • Epigenetic Regulators of Regeneration and Transformation (RT) For Expanding the Reach of GWASby Michael Nagle…………………………………………………...Page 146 • PGRP Outreach and Social Science by Troy Hall & Jay Well…………………………………….…………....………………………………………………………………………….........Page 157 • Automatic Explants Segmentation From Images by Fuxin Li, Zheng Zhou, & JialinYuan…...…………..........................................................................................Page 200 • Data Visualization and Statistical Analysis by Yuan Jiang…………………………………………………………………………………………………………………………………….….Page 253 • Genome-Wide Association Mapping Studies (GWAS) for Identifying Mutations Underlying Tissue Regeneration by Wellington Muchero…………………………..Page 298 Home Meeting Agenda Tuesday, December 20th • 8:30-9:30am “Analysis of genes affecting plant regeneration and transformation in poplar” (Steve Strauss) • 9:30-10:00am “High throughput culture and imaging plans” (Anna Magnuson) • 10:00-10:30am “High throughput fluorescence imaging” (Chris Draves of Middleton Spectral Vision) BREAK • 11:00-11:45am “Culture medium and transformation plans” (Amy Klockolead, with Cathleen Ma and Steve Strauss) • 11:45-12:00pm “Epigenetic regulators of regeneration and transformation (RT) for expanding the reach of GWAS” (Michael Nagle) • 12:00-1:00pm “Social science and education/outreach plans” (Troy Hall lead, with Jay Well) Thursday, December 22nd • 8:30-9:30am “Analysis of genes affecting plant regeneration and transformation in poplar” (Steve Strauss, repeat presentation) • 9:30-10:30am “Image analysis system plans” (Fuxin Li) BREAK • 11:00-12:00pm “Data visualization and statistical analysis” (Yuan Jiang) • 12:00-1:00pm “GWAS approach, experience, plans” Directed by Wellington Muchero 3 Home Steve Strauss presents… “Analysis of Genes Affecting Plant Regeneration and Transformation in Poplar” 4 Analysis of genes affecting plant regeneration and transformation in poplar Steve Strauss, PI Kickoff Advisory Meeting / December 2016 5 Agenda Check-in, introductions and logistics • Advisory meeting goals and agenda review • Science goals • People and organizational plans • Work flow and budget overview • Major near-term activities underway and planned • Risk analysis • 6 Meeting goals To present and discuss our plans, and solicit critiques and • suggestions for improvement To discuss emerging opportunities, new technologies, and new • ideas prior to project initiation Output: Summary report of criticisms, suggestions, planned • actions 7 Advisory committee meeting agenda Tuesday, December 20th • 8:30-9:30am “Grant introduction and overview of plans, • organization” (Steve Strauss) 9:30-10:30am “High throughput culture and imaging plans” • (Anna Magnuson lead, Middleton Spectral) BREAK 11:00-12:00am “Culture medium and transformation plans” • (Amy Klocko lead, with Cathleen Ma, Michael Nagle and Steve Strauss) 12:00-1:00pm “Social science and education/outreach plans” • (Troy Hall lead, with Jay Well) 8 Advisory committee meeting agenda Thursday, December 22nd • 8:30-9:30am “Grant introduction and overview of plans, • organization” (Steve Strauss)—for those of you who did not attend the first presentation 9:30-10:30am “Image analysis system plans” (Fuxin Li) • BREAK 11:00-12:00pm “Data visualization and statistical analysis” (Yuan • Jiang) 12:00-1:00pm “GWAS approach, experience, plans” (Wellington • Muchero) 9 Agenda Check-in, introductions and logistics • Advisory meeting goals and agenda review • Science goals • People and organizational plans • Work flow and budget overview • Major near-term activities underway and planned • Risk analysis • 10