Decoupling Detection and Classification to Improve Morphological Phenotype Analysis of Sickle Red Blood Cells in Full-Scope Microscopy

Abstract Microscopy-based analysis of red blood cell (RBC) morphology is widely used to study phenotypes in sickle cell disease (SCD). Although AI models have been developed to automate classification, most are trained on pre-cropped single-cell images and thus struggle with full-scope microscopic images containing densely packed cells and diverse morphologies, which require both accurate detection and fine-grained classification. We propose an end-to-end computational framework to identify individual RBCs in full-scope microscopy images and classify them into five morphological categories: discocytes (DO), echinocytes (E), elongated and sickle-shaped cells (ES), granular cells (G), and reticulocytes (R). We first evaluate advanced detection-classification models, including You Only Look Once (YOLO) and Detection Transformers (DETR), and demonstrate that while these models effectively detect cells, their classification performance falls short of specialized classifiers trained on single-cell images, particularly for minority phenotypes. To address this limitation, we introduce a two-step framework in which a YOLO-based detector localizes and crops individual cells from full-scope images, followed by a fine-tuned DenseNet121 ensemble classifier that assigns each cell to one of the five morphological categories. The proposed framework achieves a detection-level F1-score of 0.9661 and a weighted-average classification F1-score of 0.9708, with an overall classification accuracy of 97.06%. Compared with the single-step YOLO26n baseline, the two-step pipeline yields a macro-average F1-score improvement of +0.1675, with particularly substantial gains for minority classes (E: +0.1623; G: +0.2774; R: +0.2603). Overall, this hybrid framework demonstrates a practical strategy for adapting fast, general-purpose detection models to domain-specific biomedical tasks by combining them with specialized classifiers, delivering both efficiency and high accuracy for scientific and clinical image analysis. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵* he.li3{at}uga.edu