Computer-assisted algorithms have become a mainstay of biomedical applications to improve accuracy and reproducibility of repetitive tasks like manual segmentation and annotation. We propose a novel pipeline for red blood cell detection and counting in thin blood smear microscopy images, named RBCNet, using a dual deep learning architecture. RBCNet consists of a U-Net first stage for cell-cluster or superpixel segmentation, followed by a second refinement stage Faster R-CNN for detecting small cell objects within the connected component clusters. RBCNet uses cell clustering instead of region proposals, which is robust to cell fragmentation, is highly scalable for detecting small objects or fine scale morphological structures in very large images, can be trained using non-overlapping tiles, and during inference is adaptive to the scale of cell-clusters with a low memory footprint. We tested our method on an archived collection of human malaria smears with nearly 200,000 labeled cells across 965 images from 193 patients, acquired in Bangladesh, with each patient contributing five images. Cell detection accuracy using RBCNet was higher than 97%. The novel dual cascade RBCNet architecture provides more accurate cell detections because the foreground cell-cluster masks from U-Net adaptively guide the Manuscript

We propose a new framework, PlasmodiumVF-Net, to analyze thick smear microscopy images for a malaria diagnosis on both image and patient-level. Our framework detects whether a patient is infected, and in case of a malarial infection, reports whether the patient is infected by Plasmodium falciparum or Plasmodium vivax. PlasmodiumVF-Net first detects candidates for Plasmodium parasites using a Mask Regional-Convolutional Neural Network (Mask R-CNN), filters out false positives using a ResNet50 classifier, and then follows a new approach to recognize parasite species based on a score obtained from the number of detected patches and their aggregated probabilities for all of the patient images. Reporting a patient-level decision is highly challenging, and therefore reported less often in the literature, due to the small size of detected parasites, the similarity to staining artifacts, the similarity of species in different development stages, and illumination or color variations on patient-level. We use a manually annotated dataset consisting of 350 patients, with about 6000 images, which we make publicly available together with this manuscript. Our framework achieves an overall accuracy above 90% on image and patient-level.

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