MORPHA: Morphology-Constrained Training and the Limits of Cross-Acquisition Transfer in Low-Resource Malaria Microscopy

Automated malaria diagnosis from thin blood-smear microscopy could meaningfully reduce the burden on under-resourced laboratories, but a model that maximises accuracy on clean laboratory images fails badly the moment an inexpensive smartphone camera introduces sensor noise. This paper introduces MalariaCascade, a two-stage inference system in which a lightweight MobileNetV2 sentinel (2,225,153 parameters) makes confident classifications at low compute cost and escalates uncertain cases to an EfficientNet-B3 expert (10,697,769 parameters) that sees only clean, standardised images regardless of how corrupted the incoming frame is. Structural isolation of the expert stage, not learned robustness, is the mechanism. The sentinel is trained under a safety-score objective that places an explicit floor on Recall(Parasitised) (>=0.95) and Recall(Uninfected) (>=0.40) before precision is optimised, ensuring the checkpoint satisfies clinical safety constraints by construction. On the NIH Malaria Cell Images Dataset (27,558 cells), the cascade reaches Accuracy=0.9736, Recall(Parasitised)=0.9570, Precision(Parasitised)=0.9912, F1=0.9738, and AUROC=0.9955 on the clean test set. Under Gaussian sensor noise at full severity, cascade Recall(Parasitised) degrades by only 2.4 pp (0.9570 to 0.9329), while the flat single-model baseline collapses by 63.0 pp (0.9584 to 0.3281). McNemar's test confirms the cascade improvement is statistically significant (chi^2=11.14, p=0.00085). An ablation isolating the structural property shows that routing clean images to the expert is responsible for a 16.8 pp Recall(Parasitised) advantage under sensor noise relative to a cascade where the expert also sees corrupted inputs.

Automated malaria diagnosis from blood smear microscopy is a critical challenge in global health AI; in resource-limited settings, the scarcity of expert microscopists remains the primary bottleneck to timely and accurate diagnosis. Three compounding failure modes prevent reliable clinical deployment of existing deep learning systems. First, end-to-end detectors treat unannotated cells as background during training, producing recall figures that are strongly influenced by annotation completeness rather than reflecting true cell recovery. Second, Non-Maximum Suppression tends to suppress valid detections in dense smear regions where infection counts matter most. Third, existing whole-slide detection pipelines lack per-cell spatial evidence for clinical audit, despite image-level explainability methods such as Grad-CAM having been applied to malaria image classification tasks. We present MalariAI, a two-stage decoupled framework that addresses all three failure modes in a unified pipeline. Stage 1 applies an annotation-agnostic distance-transform guided watershed algorithm to isolate every cell in a full 1600x1200 blood smear image, recovering 75.95% of ground-truth cells by centroid localisation across the 120-image NIH BBBC041 test set without any ground-truth input. Stage 2 fine-tunes EfficientNet-B0 with Focal Loss (gamma = 2.0, per-class inverse-frequency weights) on 64x64 crops, achieving 98.36% overall classification accuracy with 87.5% and 75.0% per-class accuracy on the rare schizont and gametocyte stages, compared to only 24.57% and 25.95% AP for a Faster R-CNN baseline on the same classes. Grad-CAM++ heatmaps generated per detected cell provide instance-level spatial evidence for clinical audit, enabling microscopists to verify model predictions at the individual parasite level without sacrificing classification performance.

Malaria remains a leading cause of mortality in resource-limited settings, where expert microscopists are scarce. Automated diagnosis based on microscopy images thus has strong potential to improve care delivery. But for an algorithm to deploy, a necessary requirement is that it meet a suite of non-obvious (from a machine learning (ML) perspective) clinical constraints. Therefore, in close consultation with a national health center we developed a malaria diagnosis pipeline which addresses key requirements listed by the health care center but typically ignored in the ML malaria literature. In particular, it includes: (i) stopping criteria (to reduce image acquisition and time-to-result); (ii) human-in-the-loop functionality (for review and accountability); (iii) multi-species discrimination (since treatment varies by species); (iv) thick film detection (standard for microscopy); (v) computationally-efficient uncertainty calculations (to aid clinician review); and (vi) an edge device platform (since internet can be spotty in this catchment area). The mobile system performs all inference on-device using YOLOv13n deployed via TensorFlow Lite. It detects four species and white blood cells from Giemsa-stained thick blood smear images, aggregating per-image detections into slide-level parasitemia with World Health Organization (WHO)-standard quantification. This paper highlights these various clinical constraints and offers methods to address them. Evaluated on 2,739 annotated images across all four species, the system achieves [email protected] of 0.863, per-image parasite count correlation of r = 0.812, slide-level r = 0.951 (soft counting, 10 images/slide), and runs entirely offline with a pipeline time of 10.27 +- 1.65 s per image.