Supporting data for "Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using Deep Learning: A Case Study on Almonds."

High-throughput phenotyping is addressing the current bottleneck in phenotyping within breeding programs. Imaging tools are becoming the primary resource for improving the efficiency of phenotyping processes and providing large datasets for genomic selection approaches. The advent of AI brings new advantages by enhancing phenotyping methods using imaging, making them more accessible to breeding programs. In this context, we have developed an open Python workflow for analyzing morphology, colour and morphometric traits using AI, which can be applied to fruits and other plant organs.<br>The workflow was implemented in almond (<i>Prunus dulcis</i> (Mill.) D. A. Webb), a species where breeding efficiency is critical due to its long breeding cycle. Over 25,000 kernels, more than 20,000 nuts, and over 600 individuals were phenotyped, making this the largest morphological study conducted in almond so far. The best segmentation and reconstruction approaches achieved error rates below 1%. Weight and area variables enabled accurate estimation of kernel thickness, with a root mean squared error (RMSE) of 0.47. Fifty-five heritable morphological, morphometric and colour traits were identified, highlighting their potential as target traits in breeding programs.<br>The proposed workflow demonstrated robust performance across diverse datasets and being effective with limited training data for fine-tuning. Its compatibility with the output of AI-based labelling tools allows users to fully leverage the advantages of these technologies-reducing manual effort, accelerating dataset preparation, and streamlining the fine-tuning process of segmentation models. This flexibility enhances the scalability and practical applicability of the workflow in real-world phenotyping scenarios, especially in the context of breeding programs.