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A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.

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DeepRootGen

DeepRootGen

pre-commit Code style: black Tests Documentation Build

Website: DeepRootGen

A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.

Table of contents

Introduction

This repository contains an implementation of a simulation model for generating a synthetic root system architecture, for the estimation of root parameters as informed by observational data collected from the field.

Data Schema

The primary purpose of DeepRootGen is to output a synthetic root system into a tabular data format. The tabular data are composed of several columns:

Column Type Description
id Discrete A unique ID for each row.
plant_id Discrete A unique ID for each plant.
organ_id Discrete A unique ID for each root.
order Discrete The plant order. A first order root grows from the plant base, second order roots emerge from first order roots, third order roots emerge from second order roots, and so on.
root_type Discrete The root type classification. Can be one of 1 = Structural Root or 2 = Fine Root.
segment_rank Discrete The rank number for each root segment. A small rank refers to segments that are close to the root base, while a large rank refers to roots that are near the root apex.
parent Discrete The parent organ of the root segment. The parent node of the organ within the GroIMP graph. Used by the XEG reader to recursively import the synthetic root data.
coordinates Continuous The combined 3D coordinates (x, y, and z) of each root segment.
diameter Continuous The root segment diameter.
length Continuous The root segment length.
x Continuous The x coordinate of the root segment.
y Continuous The y coordinate of the root segment.
z Continuous The z coordinate of the root segment.

Contacts

  • DeepRootGen Developer: James Bristow
  • DeepRootGen Project Supervisor: Junqi Zhu
  • Crop System Modeller: Xiumei Yang