Website: DeepRootGen
A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.
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.
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. |
- DeepRootGen Developer: James Bristow
- DeepRootGen Project Supervisor: Junqi Zhu
- Crop System Modeller: Xiumei Yang