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https://github.com/jbris/deep-root-gen
A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.
https://github.com/jbris/deep-root-gen
3d-modelling 3d-models approximate-bayesian-computation bayesian-inference bayesian-statistics crop-model crop-modeling dash-app dash-plotly deep-learning generative-neural-network likelihood-free-inference normalising-flows normalizing-flows optuna root-system root-system-architecture sequential-monte-carlo simulation-based-inference simulation-modeling
Last synced: 3 days ago
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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.
- Host: GitHub
- URL: https://github.com/jbris/deep-root-gen
- Owner: JBris
- License: gpl-3.0
- Created: 2024-08-16T07:48:48.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2024-09-18T14:51:08.000Z (about 2 months ago)
- Last Synced: 2024-09-18T15:08:49.613Z (about 2 months ago)
- Topics: 3d-modelling, 3d-models, approximate-bayesian-computation, bayesian-inference, bayesian-statistics, crop-model, crop-modeling, dash-app, dash-plotly, deep-learning, generative-neural-network, likelihood-free-inference, normalising-flows, normalizing-flows, optuna, root-system, root-system-architecture, sequential-monte-carlo, simulation-based-inference, simulation-modeling
- Language: Python
- Homepage: https://jbris.github.io/deep-root-gen/
- Size: 3.44 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# DeepRootGen
[](https://github.com/pre-commit/pre-commit)
[](https://github.com/psf/black)
[](https://github.com/JBris/deep-root-gen/actions/workflows/tests.yaml)
[](https://github.com/JBris/deep-root-gen/actions/workflows/docs.yaml)
[](https://github.com/JBris/deep-root-gen/actions/workflows/docker-build.yaml)
Website: [DeepRootGen](https://jbris.github.io/deep-root-gen/)
*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
- [DeepRootGen](#deeprootgen)
- [Table of contents](#table-of-contents)
- [Introduction](#introduction)
- [Data Schema](#data-schema)
- [Contacts](#contacts)
# 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