Training school: Phenotyping Practice, Machine Learning and Industry Insights

TRAVEL GRANT:

 
  We are grateful for a Travel Grant of the  Wheat Phenotyping to Support Wheat Improvement Expert Working Group (->Phenotyping EWG) and the Wheat Initiative (WI) for  paticipants of the training school and the EPPS

The training school is designed to introduce the participants to the fundamentals of Machine Learning and Deep Learning and it will provide you with hands-on experience and insights from industry experts on the use of the latest technology.

The Program:

Day 1, Friday 05.09., Online preparatory workshop

The online workshop aims to deliver biological basics as well as basics in different sensing technologies. The afternoon lectures will include brief introductions to four hands-on exercises in python which we will work on Friday 12.09. 

All times: CEST - UTC+2

08:30-8:45 

Welcome (Andreas Hund, ETH Zurich/ Roland Pieruschka, FZJ) 

08:45-9:00 

Introduction Wheat Initiative (Nicola Pecchioni, CREA) 

09:00-09:45

Basics on imaging for plant sciences (Achim Walter, ETH Zurich) 

09:45-10:30

Basics in deep learning and machine learning (David Rousseau, U. Angers) 

 Break

 

10:45-11:30

Quantifying leaf chlorophyll fluorescence in the field (Onno Muller, FZJ) 

 Break

 

13:15-14:30

Semantic segmentation of plant organs using the example of Global Wheat  (Zijian Wang, U.  Queensland) 

14:30-15:15

Basics in radiometric calibration and its importance (Raul Lopez-Lozano, INRAe). 

 Break

 

 15:30-16:15

Extraction and use of 3D information from binocular imaging of complex canopies and sensor fusion using RGB and NIRS image for the literal (Benoit de Solan, Arvalis) 

16:15-17:00

Hyperspectral imaging  (Gerit Polder, WUR) 

Day 2, Friday 12.09., hands on in data processing 

Hands-on in python around the topic of workflows to quantify organs and measure reflectance in complex canopies 

Location:  

Institute of Geodesy and Geoinformation 
Seminar II, room 2.001 (second floor) 
Nußallee 17,  
53115 Bonn 
https://www.openstreetmap.org/way/54135346 

09:00 - 9:15

Welcome  (Andreas Hund, ETH Zurich / Josef Peller, WUR / Roland Pieruschka, FZJ) 

09:15 - 11:15

Extract plant organs from complex wheat canopies using the global wheat full  
semantic segmentation model  (Zijian Wang, U. Queensland/Andreas Hund, ETH  
Zurich) 

 Break

 

11:30-12:45

Extraction of 3D information from binocular images (Samuel Thomas, Arvalis)

12:45-13:30

Lunch (University canteen, 5 minutes walk) 

13:30-15:00

Radiometric calibration (Raul Lopez-Lozano, INRAe
1. Estimation of reflectance from digital number using the empirical line 
2. Examples on the stability of radiometric correction during a drone flight.

 Braek

 

 15:15-17:00

Practical exercise on feature extraction from hyperspectral images (Joseph Peller,  
Gerrit  Polder, WUR) 

Day 3, Saturday 13.09, Excursion to local sites  

Bus pick up at 9:00 am local time, Carl-Troll-Straße 31, 53115 Bonn (next to LIMES building).  

https://www.openstreetmap.org/way/128133018 

Please arrive on time to allow for a relaxed bus boarding process.  

Visits of regional sites on the way towards bio-based economy, led by Uli Schurr, FZJ 

  • AgriPV experimental site: AgriPV  
  • Lunch at a local restaurant: Teuterhof (included) 
  • Return in Bonn at around 17:00 pm 

Day 4, Monday 15.09., hands-on device (Campus Klein-Altendorf - Forum) 

Bus pick up at 7:45 am local time, Carl-Troll-Straße 31, 53115 Bonn (next to LIMES building).  

https://www.openstreetmap.org/way/128133018 

Please arrive on time to allow a relaxed bus boarding process.  The bus will depart at 8:00 a.m.

07:45 - 08:45

Bus transfer to the Campus Klein-Altendorf

09:00 - 09:10       

Welcome ( Roland Pieruschka, FZJ) 

09:10 - 10:30

 Introduction to the methods and technology

  • Martina Lazzarin, PHENOSPEX 
  • Priscilla Malcolm, PhenoVation 
  • Alexandra Bürgy, Hiphen 
  • Onno Muller (FZJ)/Beat Keller (ETH Zurich), LIFT/FLOX 

 Break

  

11:00 - 16:30

 Hands on excercises: four different stations in small groups: 

​Time / Station  

​PHENOSPEX 

​Hiphen 

​PhenoVation 

​LIFT / FLOX 

​11:00 - 12:00 

​Group 1 

​Group 2 

​Group 3 

​Group 4 

​12:00 - 13:00 Lunch 

​13:00 - 14:00 

​Group 4 

​Group 1 

​Group 2 

​Group 3 

​14:00 - 15:00 

​Group 3 

​Group 4 

​Group 1 

​Group 2 

​Break 

​15:30 - 16:30 

​Group 2 

​Group 3 

​Group 4 

​Group 1​  

16:45 - 17:30

  Discussion / Conclusion Trainers and Organizers
17:30 - 18:00

  Return to Carl-Troll-Straße 31, 53115 Bonn

 

 Supported by: