Authors: Rose Nakasi, Jeremy Francis Tusubira, Aminah Zawedde, Ali Mansourian, Ernest Mwebaze Description: Malaria is a public health problem which affects developing countries world-wide. Inadequate skilled lab technicians in remote areas of developing countries result in untimely diagnosis of malaria parasites making it hard for effective control of the disease in highly endemic areas. The development of remote systems that can provide fast, accurate and timely diagnosis is thus a necessary innovation. With availability of internet, mobile phones and computers, rapid dissemination and timely reporting of medical image analytics is possible. This study aimed at developing and implementing an automated web-based Malaria diagnostic system for thick blood smear images under light microscopy to identify parasites. We implement an image processing algorithm based on a pre-trained model of Faster Convolutional Neural Network (Faster R-CNN) and then integrate it with web-based technology to allow easy and convenient online identification of parasites by medical practitioners. Experiments carried out on the online system with test images showed that the system could identify pathogens with a mean average precision of 0.9306. The system holds the potential to improve the efficiency and accuracy in malaria diagnosis, especially in remote areas of developing countries that lack adequate skilled labor.