Automated detection and staging of malaria parasites from cytological smears using convolutional neural networks
Authors: Davidson Mira S. , Yahiya Sabrina , Chmielewski Jill , O’Donnell Aidan J. , Gurung Pratima , Jeninga Myriam , Prommana Parichat , Andrew Dean , Petter Michaela , Uthaipibull Chairat , Boyle Michelle , Ashdown George W. , Dvorin Jeffrey D. , Reece Sarah E. , Wilson Danny W. , Ando D. Michael , Dimon Michelle , Baum Jake 
Published: January 2021

AbstractMicroscopic examination of blood smears remains the gold standard for diagnosis and laboratory studies with malaria. Inspection of smears is, however, a tedious manual process dependent on trained microscopists with results varying in accuracy between individuals, given the heterogeneity of parasite cell form and disagreement on nomenclature. To address this, we sought to develop an automated image analysis method that improves accuracy and standardisation of cytological smear inspection but retains the capacity for expert confirmation and archiving of images. Here we present a machine-learning method that achieves red blood cell (RBC) detection, differentiation between infected and uninfected RBCs and parasite life stage categorisation from raw, unprocessed heterogeneous images of thin blood films. The method uses a pre-trained Faster Region-Based Convolutional Neural Networks (R-CNN) model for RBC detection that performs accurately, with an average precision of 0.99 at an intersection-over-union threshold of 0.5. A residual neural network (ResNet)-50 model applied to detect infection in segmented RBCs also performs accurately, with an area under the receiver operating characteristic curve of 0.98. Lastly, using a regression model our method successfully recapitulates intra-erythrocytic developmental cycle (IDC) stages with accurate categorisation (ring, trophozoite, schizont), as well as differentiating asexual stages from gametocytes. To accelerate our method’s utility, we have developed a mobile-friendly web-based interface, PlasmoCount, which is capable of automated detection and staging of malaria parasites from uploaded heterogeneous input images of Giemsa-stained thin blood smears. Results gained using either laboratory or phone-based images permit rapid navigation through and review of results for quality assurance. By standardising the assessment of parasite development from microscopic blood smears, PlasmoCount markedly improves user consistency and reproducibility and thereby presents a realistic route to automating the gold standard of field-based malaria diagnosis.Significance StatementMicroscopy inspection of Giemsa-stained thin blood smears on glass slides has been used in the diagnosis of malaria and monitoring of malaria cultures in laboratory settings for >100 years. Manual evaluation is, however, time-consuming, error-prone and subjective with no currently available tool that permits reliable automated counting and archiving of Giemsa-stained images. Here, we present a machine learning method for automated detection and staging of parasite infected red cells from heterogeneous smears. Our method calculates parasitaemia and frequency data on the malaria parasite intraerythrocytic development cycle directly from raw images, standardizing smear assessment and providing reproducible and archivable results. Developed into a web tool, PlasmoCount, this method provides improved standardisation of smear inspection for malaria research and potentially field diagnosis.