BioIMA: a one-click desktop tool for standardized extraction of phenotypic traits from biological images
Standardized extraction of quantitative phenotypes from images is increasingly important across plant biology, from ecological and evolutionary studies to genetics, breeding, and functional genomics. However, as large image datasets are increasingly used for trait analysis, many biologically relevant traits, including size, shape, color, and spatial patterning, are still measured manually or…
Research introduces BioIMA, a desktop tool designed to streamline the standardized extraction of phenotypic traits from biological images. This tool merges foundation model-driven segmentation with automated trait computation, enabling rapid and accurate quantitative measurements without the need for model training. BioIMA simplifies the process by offering an intuitive graphical interface, thus enhancing throughput, reproducibility, and accessibility—especially for researchers lacking computational skills.
The effectiveness of BioIMA was demonstrated by quantifying knot morphological traits in two Populus species, where automatic measurements exhibited a high degree of agreement with manual ImageJ-based measurements (R2 = 0.95) while cutting processing time significantly, from around 15 seconds to just 4 seconds per image. The tool's utility was further tested on diverse plant datasets such as Helianthus and Rhododendron images, showcasing its adaptability to various morphologies and background conditions.
Though primarily tailored for plant phenotyping, BioIMA holds potential for broader applications across other biological samples where traits like size, shape, and color are relevant. By providing a lightweight, local application that combines ease of use with standardization, BioIMA serves as a valuable community resource for image-based phenotyping in ecological and evolutionary research.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
