Computer Vision Pipeline for Image Analysis for Freeze‐Fracture Electron Microscopy: Rosette Cellulose Synthase Complexes Case

In materials science, plant biology, agriculture, and environmental research, the automated analysis of high‐magnification, complex microscopy images, such as those generated by freeze‐fracture electron microscopy (FF‐TEM), remains a critical challenge that limits the scalability of data interpretation. We present a deep learning computer vision pipeline for high‐throughput detection and morphological characterization analysis of cellulose synthase complexes (CSCs, or rosettes) in FF‐TEM images. The pipeline integrates preprocessing, detection, human‐in‐the‐loop verification, and semantic segmentation to quantify features such as rosette diameter and inter‐lobe spacing. The approach was trained and tested on a curated dataset of high‐resolution FF‐TEM micrographs of Physcomitrium patens , expanded via strategic tiling and augmentation to over 650 images. We compare YOLOv8 and YOLOv9 architectures and demonstrate that YOLOv9 achieves superior performance in both localization accuracy (mAP50‐95 = 0.854) and inference speed. The resulting distributions revealed biological variability consistent with prior manual studies, validating the approach for high‐throughput applications. Our results show that the pipeline achieves human‐expert level accuracy while dramatically reducing analysis time, enabling scalable, reproducible structural characterization of intramembrane protein complexes. The pipeline is broadly applicable to other domains requiring precise interpretation of complex microscopy data and establishes a foundation for future artificial intelligence (AI)‐assisted workflows in biological imaging.