Online workshop: intro and user training workshop, 6-7 March

PHENOMICS DATA PLATFORMS – INTRODUCTION & USER TRAINING WORKSHOP, Online: Monday March 6, 2023 – Tuesday March 7, 2023
with optionally on site in Helsinki: Wednesday March 8, 2023

The program is found below. Please indicate your interest here and your will be contacted by Kristiina Himanen at University of Helsinki.

Background of the workshop:

In March 6-7 2023, The EGI-ACE use case project “PHIS deployment on EGI cloud” is organizing a workshop on plant “Phenomics data platforms – introduction and user training workshop”.

The aim of the workshop is to support image-data users to adopt FAIR data management practices and to support the implementation of a dedicated phenomics information system PHIS. The other part of the formation will focus on data processing tools and methods in EGI platforms.


The workshop programme:

DAY 1:

central European time

09:00 – 09:15 Opening of the workshop [Kristiina Himanen, NordPlant, UH]

09:15 – 10:00  Introduction to NaPPI phenomics platform and DMP [Sylvain Poque, UH]    

10:00 – 10:30 Coffee break

10:30 – 11:15  EGI-ACE Phenomics use case project 2021-2023 [Vincent Negre, INRAE]            

11:15 – 12:00  Imaging for Horticulture and Phenotyping at University of Angers [David Rousseau, UA]

12:00 – 13:00 Lunch break

13:00 – 13:45  Deep Learning in plant phenomics [David Rousseau, UA]

13:45 – 16:00  Phenomics data user showcase session: Deep Learning demo [Herearii Metuarea, UA]

  1. Questions/Answers about the video material on image segmentation and classification
  2. Showcase of image segmentation

DAY 2:

central European time

09:00 – 10:00 Introduction to EGI service platforms [Andrea Manzi, EGI]

10:00 – 10:30 Coffee break

10:30 – 11:15 Introduction to data management information systems [Pascal Neveu, INRAE]

11:15 – 12:00 Introduction to Phenotyping Hybrid Information System (PHIS) [Isabelle Alic, INRAE]

12:00 – 13:00 Lunch break

13:00 – 16:00 Phenomics data user showcase session:

  1. R, Phyton and JMP tools in phenomics data analysis [Sylvain Poque, UH]
  2. Practical showcase on PHIS database structure and function: data insertion, visualization, extraction and exploitation [Isabelle Alic, INRAE]


Optional on-site DAY 3: 

  1. Optional hands on/consultation event for NaPPI and other data owners on how to use JMP and/or R for image-based data processing.
  2. Optional hands-on event for Phenomics data owners on PHIS information system and how to define own provenances, variables and other aspects of Data Management Plans. Practical construction of shared variables between the different participants.