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Institute for Plant Sciences Update 8.29.17

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The Institute for Plant Sciences gave a college-wide update on the progress it's made on the goals outlined in 2013 as part of Purdue Moves.

If you have any questions, please contact plantspl@purdue.edu.

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Institute for Plant Sciences Update 8.29.17

  1. 1. Plant Sciences Update Tuesday, August 29, 2017 11:00 a.m. – 12:00 p.m. PFEN 241 (Deans Auditorium)
  2. 2. Introduction Karen Plaut Interim Dean, College of Agriculture Mitch Tuinstra, Scientific Director, Institute for Plant Sciences
  3. 3. About • Component of Purdue Moves, a series of university initiatives announced by President Mitch Daniels in 2013 • More than $20M invested in plant sciences since fall 2013 • Brings together multidisciplinary research and education • Developing phenotyping technology to enhance research, teaching, extension • Renamed the Institute for Plant Sciences to align with the other Life Science Institutes 3
  4. 4. Pipeline • Expand basic plant biology • Automate phenotyping to link genes with observable traits • Integrate data streams using robust analytic platform • Move technology from research to commercialization 4
  5. 5. Center for Plant Biology Clint Chapple Director, Center for Plant Biology
  6. 6. Center for Plant Biology Update Expanding research and education in basic plant biology
  7. 7. What is CPB? • Established through Purdue Moves to expand research and education in basic plant biology • Interdepartmental community of 32 faculty who share an interest in basic plant biology • Enhance graduate student training in basic plant sciences • Support research of participating members through collaboration, mentoring, and discussion • Renamed from Center for Molecular Agriculture to CPB to reflect its mission within the Institute for Plant Sciences 7
  8. 8. New Hires • 10 new faculty members – seven on campus, two arriving this semester, and one arriving January 2018 • Six – Department of Botany and Plant Pathology • Three – Department of Biochemistry • One – joint appointment in Department of Entomology and Department of Forestry and Natural Resources 8
  9. 9. Membership • Finalized membership agreements and faculty applications • 32 faculty from seven departments and two colleges • 10 members hired under Institute for Plant Sciences 9
  10. 10. Progress • Biweekly faculty meetings to discuss next steps and future initiatives • CPB Symposium associated with the Midwest ASPB meeting • Web presence and graduate student recruitment material being developed • Reduced rates for CPB faculty – Bindley Bioscience Center • CPB Seminar Series co-hosted with departments – starting in September • CPB Seed Grant program – proposals due in September and funding announcements in October 10
  11. 11. Molecular Agriculture Summer Institutes and Educational Initiatives Amy Jones Plant Sciences Recruitment and Outreach Coordinator
  12. 12. 12 Undergraduate MASI Communication Mentorship 7 8 9 8 2014 2015 2016 2017 Participants Funding for 10 students Funding Breakdown 1/3 1/3 1/3 Office of Academic Programs Faculty Home Dept. Faculty Funds Other Programmatic Costs: OAP $4,800 total stipend ● $1,600 per entity Research and Communication 5communication lunches 2Poster Presentations 40research hrs. weekly
  13. 13. 13 Pre-College MASI 13 16 18 2015 2016 2017 Participants 4 6 8 2015 2016 2017 Mentors Future: 25 students 47 TOTAL Future: Sustain 8 Mentors Increase involvement 4Departments Representing College Decisions 22 College-age 18 Applied to Purdue 15 Purdue Students 8 (50%+) in Ag 4 (25%+) in Engineering 3 in other Colleges Discovery Mentorship Belonging
  14. 14. Other Initiatives and Looking to the Future Pre-College Funding Questions Amy Jones jones176@purdue.edu Teaching Lab SpacesLearning Community Student Participation Undergraduate
  15. 15. Controlled Environment Phenotyping Facility (CEPF) Julie Hickman Plant Sciences Project Manager Chris Hoagland CEPF Facility Manager
  16. 16. Controlled Environment Phenotyping Facility (CEPF) • End of September 2017 – building shell construction complete • Fall 2017 – equipment delivered • Approx. 7 different vendors • Week of August 21 – Conviron large growth chamber arrived; assembly over next few weeks • Late September – conveyors and camera imaging systems arrive from Netherlands • February 2018 – equipment installation and initial testing complete 16
  17. 17. CEPF features • Conviron Growth House • 256 plant capacity Growth House with precise environmental controls • Automated conveyors for plant growth and randomization • Argus Multi-feed Nutrient Injection • Fully automated precise weight-based water dosing and water to saturation options • Single nutrient limitation with gradient control • Imaging System for plants up to 4m high • RGB – high throughput morphology, geometry, biomass, plant size, and color • Top-view and multiple side-view cameras • Segmentation: chlorophyll fluorescence to detect plant tissues • Up to 150 plants per hour • Hyperspectral • Color, vegetative indices, physiological status, and pigmentation • Up to 70 plants per hour 17
  18. 18. CEPF equipment factory acceptance 18 • The equipment for the CEPF is custom made. In August, we inspected and verified the conveying and camera equipment was correct for the facility.
  19. 19. ISAL software demonstration at Netherlands Grower 19 • Equipment review included a sneak peak of the ISAL software being developed to image and move our plants. • This software will enable the different vendors to communicate opening doors, watering, and imaging plants. • The software will enable us to capture images and will work with other packages, including the ones were are developing here at Purdue for data graphs and analysis.
  20. 20. Aris TopView Multispectral Imager
  21. 21. Potential Applications • Seedlings to mid sized plants • Genotype performance • Fertility and water responses • Herbicide damage • Soil contaminants • Soil microbes 21
  22. 22. TopView Imager 22 • Imaging cabinet for basic phenotyping • Captures eight spectral bands • Stitches Red, Green, and Blue bands to form a RGB image • Automatically segments data into parameters and histograms • Starting point for digital phenotyping
  23. 23. Time Lapse Image Data and Leaf Count 23 Channel Color Wavelength (nm) 0 Deep blue 450 1 green 520 2 yellow 590 3 amber 634 4 red 660 5 hyper red 730 6 infra red 870 7 white 400-700 Leaf count
  24. 24. Parameter Data plant nr length (mm) width (mm) center x center y grid row grid col plant area (mm2) plant convex hull area (mm2) longest radial (mm) roundness avg hue avg sat avg val plant 1 140.46 619.419 1442 224 0 0 218778 367050 387.243 232.997 65.485 8.11198 124.632 plant 2 213.285 619.419 1646 407 0 0 469879 614042 358.576 67.0578 58.9705 8.94594 115.557 plant 3 163.005 619.419 1544 277 0 0 297110 443456 371.716 166.096 57.8946 8.69574 121.652 plant 4 20.6042 55.4963 1358 1781 0 0 3451.65 4591.14 36.9934 36.3893 30.8044 69.3358 60.5648 plant 5 77.1741 91.8922 1701 1859 0 0 12079.4 34709.3 65.5914 256.655 29.874 63.5456 64.4642 plant 6 25.8489 46.5033 2052 1592 0 0 3935.48 5922.76 28.9074 53.5608 28.3247 71.6823 71.8321 24 • Automatically segments masked image • Plant characteristic data for each plant • Calculates a mean for each Hue Saturation and Value (HSV) • Histogram for HSV and gray scale • Provides repeatable objective measurements • User friendly interface Segmented data from Topview imager
  25. 25. Indiana Corn and Soybean Innovation Center Jason Adams Advance Phenotyping & Plant Processing Facility Manager
  26. 26. ICSC Users • Approx. 40 different labs or groups have used the facility • During the winter and spring the seed processing areas became very active • Threshing and shelling • Plant and seed grinding • Seed treating • Seed counting and weighing • Root washing and scanning • Summer has brought in higher numbers to the imaging and sensor development areas • Pilot work area • PhenoRover development • Break room for ICSC and ACRE users • Meeting space for labs or groups 26
  27. 27. ICSC Tours 27 180 individual tours with a total of over 3300 guests • Over 40 groups were student groups, including Bourlaug Scholars, MASI, FFA, 4-H, Mandela Washington Fellows and Ivy Tech • Individuals or groups from over 20 countries have walked through ICSC
  28. 28. New and Donated Equipment 28 • Ear Photometry Box with the capability to make approximately 30 different ear and kernel measurements • 2 Root washing stations for washing root samples down prior to measurements • 1 large ice machine for research use • 2 Li-COR 6400 Portable Photosynthesis System
  29. 29. Meeting and Classroom Space 29 • Student Innovation Hub now has projector and large screen • Three small conference rooms equipped with phones; one also equipped with a monitor • Data command converted into dual purpose room; now equipped with projector, large screen, and 22 classroom seats
  30. 30. Indiana Corn and Soybean Endowment Innovation Grants - 2017 • Development of a Plant Tattoo for Managing Crop Stress – d development of chromatic biosensors for heat stress and ABA content • Chongli Yuan, Chemical Engineering, Alexander Wei, Chemistry • Development of a Universal Method for High-Throughput Automated Root Phenotyping to Identify Root Traits in Soybean • Gordon McNickle and Anjali Iyer-Pascuzzi - Botany and Plant Pathology, Jian Jin- Ag and Biological Engineering 30
  31. 31. 2017 Precision Measurement Zone & Contracted Flights Rick Westerman Data Analyst Bioinformatics Specialist
  32. 32. First full year • Flights from May 2017 through the present • Our own 5-band multispectral camera (RedEdge) • Our own flying platforms 32 3DR Solo
  33. 33. Contracted flights • ~100 acres • All maize • Bi-weekly flights • Low cost 33 RGB NDVI (false color) Close up (brown areas are Bare spots between plots)
  34. 34. PMZ (Precision Measurement Zone) • ~25 acres • Wheat, sorghum, soybean, maize • Weekly flights • Some ground measurements included • No cost 34 Wheat (late season) Sorghum & Maize Soybean
  35. 35. Data delivery • Atlas for first pass • Rectified to GCP (ground control points) • Plot-level NDVI extraction if feasible 35
  36. 36. Plot NDVI extraction 36 Plot Treatment 2017-06-25 2017-07-09 2017-07-28 303 45 0.40 0.67 0.72 304 23 0.38 0.70 0.75 2017-06-25 2017-07-09 2017-07-28 (NDVI – near infared versus red)
  37. 37. Experiences and further work • Remainder of 2017 More flights More plot-level data Ground truthing – own, researcher, ARPA-E! Further development of data delivery methods • 2018 Same camera and flight platforms Anticipate more serving more researchers 37
  38. 38. Ag-Celerator Tim Peoples Managing Director, Purdue Foundry
  39. 39. Foster Entrepreneurship • Ag-celerator Summary • 28 involved in Launchbox excluding students • 2 rounds, 4 companies funded – Phicrobe, HyroGrow, Akanocure, Vinsense Phicrobe -designed to enhance food safety in plant based products
  40. 40. Round 2 – Ag-Celerator winners Akanocure - Bioinspired molecule development for agrochemicals Vinsense – decision making tool for water use in crops
  41. 41. Ag-Celerator Fall 2017 Timeline Sept 14 Sept 28 Oct 5 Oct 12 Oct 16- Nov 22 Nov 26 Nov 27 Dec 18 Dec 19 Questions to pvinfo@prf.org Callout Application Deadline Semi-finalists Announced Mandatory Semi-finalist Meeting Firestarter Training at the Foundry Final Materials Upload Deadline Finalists Announced Demo Day Awards Announced
  42. 42. ASPIRE Internship Nathan Mosier Professor, Agricultural & Biological Engineering Chair, ISA Soybean New Uses
  43. 43. 26 Years of ISA Student Soybean Product Innovation Competition • 16 Teams completed the 2016-2017 competition, 5 provisional patents • 50 students • Representing 20 different majors from the Colleges of Agriculture, Engineering, Pharmacy, Science, and Business (5) • Focuses on generating product ideas and proofs of concept with preliminary market analysis
  44. 44. Execution • Pilot program Summer of 2017 • Students who completed the contest invited to apply • 6 Student interns selected to work on 5 projects • Projects = product ideas from competition (provisional patents, other vetted concepts) • Partnership between Purdue Foundry and Laboratory of Renewable Resources Engineering/ABE for student mentoring and oversight Funding • Purdue Ag-celerator Program ASPIRE Ag Soy Product Innovation Realization and Entrepreneurship Internship Program
  45. 45. ASPIRE Program • FIRESTARTER: “Bootcamp” • Customer DiscoveryEntrepreneurship • Business Plan Development • Networking and Entrepreneur-in-Residence Mentoring Micky Creech Competition and ASPIRE Coordinator 2017 ASPIRE Interns
  46. 46. ASPIRE Ag-Celerator Demo Day • 6 Teams pitched their companies to the Ag-Celerator Selection Committee on August 18, 2017. • Recommendations for funding were made (official announcements forthcoming) NeoSeed SoyaMein Absoybeancy Soy Metal Adsorbent SoyPoofession FiltraSoy
  47. 47. Questions? 47

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