3dCAP

This project aims at reconstructing plant canopy structures by 2D images of plants and plant organs, and calculating canopy photosynthesis with further measurement of leaves nitrogen content and photosynthetic light response curves.

View the Project on GitHub rootchang/3dCAP

README for 3dCAP (1.0)

Introduction

In the current rice breeding programs, morphological parameters e.g., plant height, leaf length and width, leaf angle, panicle architecture and tiller number during the grain filling stage are used as major selection targets. However, so far, there is no robust approach to quantitatively define the optimal parameter combinations that can lead to increased canopy radiation use efficiency (RUE) and grain yield. Here we develop a 3D canopy photosynthesis model (3dCAP), which effectively combines 3D canopy architecture, canopy vertical nitrogen distribution, ray tracing algorithm and leaf photosynthesis model. For the sake of users to perform basic canopy structure and canopy photosynthesis simulation, optimization of planting spacing and tiller number, optimization of plant architecture and etc, we develop a GUI for this model, i.e. RCDS. Concurrently, we developed an efficient workflow for parameterization of 3dCAP, i.e. the 3dPlant. Briefly, 3dCAP can predict daily canopy RUE for different rice cultivars under different weather. Using 3dCAP, one can explore the influence of canopy structural parameters, e.g., planting spacing, tiller number, tiller angle, leaf angle, leaf area index and plant height on canopy RUE. Overall, this new model has a potential to be used in rice ideotype design for improved canopy RUE.

Install

  1. Installation of MATLAB compiler runtime 9.1 (http://ssd.mathworks.com/supportfiles/downloads/R2016b/deployment_files/R2016b/installers/win64/MCR_R2016b_win64_installer.exe).
  2. Download and run the .exe files following the users manuals provided in the corresponding directories.

Usage of RCDS

A detailed user manual is provided in ./3dCAP/RCDS/

Usage of 3dPlant

A detailed user manual is provided in ./3dCAP/3dPlant/

Support or Contact

Any bug is welcomed to report to changtiangen@gmail.com