Open RGB Imaging Workflow for Morphological and Morphometric Analysis

Overview

This repository provides an open-source implementation of the RGB imaging workflow for morphological and morphometric analysis of fruits and seeds.

Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits and Seeds using AI: A Case Study on Almonds.

Fruit Breeding Group, Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura - Spanish Research Council (CEBAS-CSIC), Campus Universitario Espinardo, E-30100 Murcia, Spain.

Features

• Open-source RGB imaging workflow.
• AI-based morphological and morphometric analysis.
• Automated image processing for fruit and seed characterization.
• Reproducible methodology for research applications.

Installation

To use this workflow, you can either clone the repository to work locally or access it online via Google Colab.

Clone for local use:

git clone https://github.com/jorgemasgomez/almondcv2
cd your-repository-name
pip install -r requirements.txt

Work online in Google Colab:

Install dependencies with:

pip install -r requirements.txt

Videotutorial

Example Images

Disclaimer: The picture files in the "images" folder are not covered by the same GPL-3.0 license as the source code. These data files are dedicated to the public domain under CC-by-4.0 Creative Commons Attribution 4.0 International.

Almond processed by the workflow

Mas-Gómez, J., Rubio, M., Dicenta, F., & Martínez-García, P. J. 2025. Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using AI: A Case Study on Almonds.

Strawberry processed by the workflow

Mitchell J Feldmann, Michael A Hardigan, Randi A Famula, Cindy M López, Amy Tabb, Glenn S Cole, Steven J Knapp, Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry, GigaScience, Volume 9, Issue 5, May 2020, giaa030, https://doi.org/10.1093/gigascience/giaa030

Apple processed by the workflow

Beat Keller, Michaela Jung, Simone Bühlmann-Schütz, Marius Hodel, Bruno Studer, Giovanni A L Broggini, Andrea Patocchi, The genetic basis of apple shape and size unraveled by digital phenotyping, G3 Genes|Genomes|Genetics, Volume 14, Issue 5, May 2024, jkae045, https://doi.org/10.1093/g3journal/jkae045

Citation

If you use this workflow in your research, please cite:

Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using AI: A Case Study on Almonds Mas-Gómez Jorge, Rubio Manuel, Dicenta Federico, Martínez-García Pedro José bioRxiv 2025.05.05.652179; doi: https://doi.org/10.1101/2025.05.05.652179

License

This project is licensed under the GNU GPL v3

CVAT INSTALL

https://www.cvat.ai/ https://docs.cvat.ai/docs/administration/basics/installation/ https://www.cvat.ai/resources/blog/facebook-segment-anything-model-in-cvat https://docs.cvat.ai/docs/administration/advanced/installation_automatic_annotation/ https://www.youtube.com/watch?v=xopaChA1xn0

YOLO

https://docs.ultralytics.com/es/tasks/segment/ https://docs.ultralytics.com/es/modes/train/#train-settings https://docs.ultralytics.com/es/tasks/segment/#models

ZENODO REPOSITORY ALMOND

https://doi.org/10.5281/zenodo.15423562

WORKFLOWHUB

https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1731.1