Workshop organised by the University of Tokyo. Dates: 28 and 29 October 2019
The aim of this workshop is to stress the importance of 3D plant morphology in plant science, and in particular, to address the challenge of modeling plant morphology under field conditions.
The first day of the workshop will give a general introduction on the modelling of 3D plant architecture and its development. We will present the functional-structural plant models (FSPM), the formalisms behind the representation of plant geometry and topology, methods and tools to reconstruct and analysed plant architecture as well as formalisms to simulate plant form and function. We will also present OpenAlea, the open-source software platform dedicated to multiscale modelling of plants. During the second day, you will have the opportunity to develop your own model during hands-on tutorials. This will be the opportunity to simulate your plant of interest.
This workshop will be based on the OpenAlea opensource platform. OpenAlea is a modular platform based on the Python language.
To install OpenAlea, you need first to install the Conda package manager.
Conda is a package manager that can be installed on Linux, Windows, and Mac. If you have not yet installed conda on your computer, follow these instructions:
Conda Installation. Follow instructions for Miniconda.
Conda Download. Use the Python 2.7 based installation.
First copy the file macenv.txt using in a shell using this command:
wget https://gist.githubusercontent.com/pradal/1a7ebb23ba86d980cfae7373517fb5b3/raw/33856ada3c662b34ccd7a9453f16baec073a818d/macenv.txt
If it fails copy the content in a file macenv.txt.
Then, after install of conda, run the following command
conda create -n openalea --file macenv.txt
Activate the environment using
conda activate openalea
Test your installation by running
lpy
Create an environment named openalea: Launch a console (See Anaconda Prompt in Start menu on windows)
conda create -n openalea openalea.plantgl openalea.lpy openalea.mtg pyqglviewer boost=1.66 -c openalea -c anaconda -c openalea/label/unstable
Activate the openalea environment:
conda activate openalea
09:00 - 09:10 Welcome
09:10 - 09:30 Workshop introduction
09:30 - 10:15 Short presentation of the participants
10:30 - 11:30 Introduction to 3D shoot and root plant modelling (Christophe Pradal)
11:30 - 12:00 Discussion
Lunch
13:30 - 14:00 Short Introduction to OpenAlea
14:00 - 14:30 3D Analysis and Reconstruction of Plant Architecture
14:30 - 16:00 Simulation of Plant Architecture using L-Systems
16:30 - 17:00 Light interception on 3D models
Installation of OpenAlea (needed for Tuesday)
Morning (09:00 - 12:00)
Hands-on tutorials : Simulation of shoot or root architecture
Basic tutorials
Simulation of a tree
Simulation of a root system
Afternoon
13:30 - 17:00 Open simulation tutorials based on participants feedback
17:00 - 18:00 Open Discussions and Farewell