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McGill Plant Phenomics Platform - MP3

Explore the McGill Plant Phenomics Platform (MP3) tools such as LemnaTec Scanalyzer 3D and HTS for data collection and analysis. Learn about methods like Arsenic Tolerance Assay and how data is collected and processed.

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McGill Plant Phenomics Platform - MP3

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  1. McGill Plant Phenomics Platform - MP3 Emilio Vello

  2. Overview • What tools do we use to get the phenotyping data? • Greenhouse • LemnaTec Scanalyzer 3D • LemnaTec HTS • How do we collect and analyze? • Arsenic Tolerance Assay

  3. McGill University - MP3 Location Montreal Greenhouse McGill Biology Building Montreal Weather http://blogs.mcgill.ca/iss/category/winter/ http://www.hrviews.ca -40°C 40°C

  4. Lemnatec Scanalyzer 3D Plant Phenomics 2.3 m 3.0 m Conveyor- Plants Cars “parking” 3.8 m Cameras Watering and weighing station Working Area – Load station

  5. 3D-Components Features: • Top and Side views • Angles from 0° to 360°. • Automatic Watering and weighting system • Small and big plants. • Near Infrared Scanning for water content • Infrared Scanning for temperature • RGB scanning for plant architecture. • Max. height for a plant 900 mm • Max. width 600 mm • Max. width if all pots are filled: 240 mm NIR VIS Weighing station IR Watering station

  6. 3D – Pots, support and Identification 3D pot registration screen Plant pot support adapters Medium Small Large

  7. Lemnatec Scanalyzer HTS – high-throughput screening Sensor arm Growth chambers 1.10 m 3.00m 1.95 m Close to minimize plant movements Growth chambers

  8. HTS-Sensors

  9. HTS-Plant supports Pot support / Free format support Capacity: 96 small pots Plate support Capacity: 60 square petri dishes

  10. HTS - Lights • Near infrared light • Fluorescent light • Ring light • Top visible light • Bottom visible light Camera Bottom light

  11. HTS – sample identification system Mutant / tray Replicate / set Barcode reader Assay ID

  12. How do we collect and analyze data? An example: arsenic tolerance assay

  13. Arsenic Tolerance Experimental design • Arabidopsis thaliana • 136 DNA targets / mutant lines (T-DNA knockout genes) • 3 replicates • 1 square petri dish per line • 36 seeds per petri dish • 750 µM arsenic • 408 plates in total • 14688 seeds/seedlings (Without counting the concentration tests) Objective: Identification of DNA target candidates showing a significant resistance or sensitivity to high concentration of arsenic. Bioinformatics Analysis. Proxy of germination

  14. Arsenic – Safety • The plates covers can't be removed because of the arsenic toxicity following the rule of the EHS. (McGill Environmental Health and Safety Office) • The covers fog because of the water condensation • High reflection due to the cover and water. Will we be able to classify the seeds?

  15. Arsenic – Image acquisition configuration Fluorescent light 1 frame 1 plate Visible bottom light 4 frames 1 plates 2448 images in total. Visible bottom light 1 frame 1 plate

  16. Arsenic – Image Analysis Pipeline RGB selection raw object list creation McGill development using java, ImageJ libraries and R Object size > 10 px Object circularity > 0.099 d(centroid,squareCenter)<130 Big Object HUE(HSB) 16 colour classification Object properties / features

  17. Arsenic - Clustering 1 2 3 Hierarchical cluster Ward's minimum variance method Euclidean distance matrix Group 2 Group 1 4

  18. Arsenic – Cluster Interpretation 103 Group 2 = Sensitive = Non Germination WT 152 Group 1 = Resistant = Germination

  19. Arsenic - Results 103 152 WT

  20. Arsenic Mutant 152 Mutant 152 = ARS5 is the strongest arsenic resistant mutant identified by Sung et al.

  21. Conclusion • Integrationand contribution of people from different domains have been a key for the success of the MP3. • Integration is also true for the different tools use in the digital phenotyping including hardware, software. • we need to findnew metricsfrom different kind of sensors to increase the spectrum of phenotypes.

  22. Acknowledgements • Prof. Thomas Bureau • Amadou Oury Diallo • Zoe Joly-Lopez • Ewa Forczek • Akiko Tomita • Douglas Hoen • CFI – Canada Foundation for Innovation • Genome Canada • Genome Quebec • Prof. Daniel Schoen • LemnaTec • Mark Romer

  23. HTS – sample identification system Mutant / tray Replicate / set Assay id Bar Code columns (0,0) Bar code reader (6,1) rows

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