Dataset Information

Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy.

ABSTRACT: Despite the remarkable progress that has been made to reduce global malaria mortality by 29% in the past 5 years, malaria is still a serious global health problem. Inadequate diagnostics is one of the major obstacles in fighting the disease. An automated system for malaria diagnosis can help to make malaria screening faster and more reliable. We present an automated system to detect and segment red blood cells (RBCs) and identify infected cells in Wright-Giemsa stained thin blood smears. Specifically, using image analysis and machine learning techniques, we process digital images of thin blood smears to determine the parasitemia in each smear. We use a cell extraction method to segment RBCs, in particular overlapping cells. We show that a combination of RGB color and texture features outperforms other features. We evaluate our method on microscopic blood smear images from human and mouse and show that it outperforms other techniques. For human cells, we measure an absolute error of 1.18% between the true and the automatic parasite counts. For mouse cells, our automatic counts correlate well with expert and flow cytometry counts. This makes our system the first one to work for both human and mouse.

SUBMITTER: Poostchi M

PROVIDER: S-EPMC6290955 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy.

Poostchi Mahdieh M Ersoy Ilker I McMenamin Katie K Gordon Emile E Palaniappan Nila N Pierce Susan S Maude Richard J RJ Bansal Abhisheka A Srinivasan Prakash P Miller Louis L Palaniappan Kannappan K Thoma George G Jaeger Stefan S

Journal of medical imaging (Bellingham, Wash.) 20181001 4

Despite the remarkable progress that has been made to reduce global malaria mortality by 29% in the past 5 years, malaria is still a serious global health problem. Inadequate diagnostics is one of the major obstacles in fighting the disease. An automated system for malaria diagnosis can help to make malaria screening faster and more reliable. We present an automated system to detect and segment red blood cells (RBCs) and identify infected cells in Wright-Giemsa stained thin blood smears. Specifi ...[more]

PMID: 30840746

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Project description:BackgroundManual microscopic examination of Leishman/Giemsa stained thin and thick blood smear is still the "gold standard" for malaria diagnosis. One of the drawbacks of this method is that its accuracy, consistency, and diagnosis speed depend on microscopists' diagnostic and technical skills. It is difficult to get highly skilled microscopists in remote areas of developing countries. To alleviate this problem, in this paper, we propose to investigate state-of-the-art one-stage and two-stage object detection algorithms for automated malaria parasite screening from microscopic image of thick blood slides.ResultsYOLOV3 and YOLOV4 models, which are state-of-the-art object detectors in accuracy and speed, are not optimized for detecting small objects such as malaria parasites in microscopic images. We modify these models by increasing feature scale and adding more detection layers to enhance their capability of detecting small objects without notably decreasing detection speed. We propose one modified YOLOV4 model, called YOLOV4-MOD and two modified models of YOLOV3, which are called YOLOV3-MOD1 and YOLOV3-MOD2. Besides, new anchor box sizes are generated using K-means clustering algorithm to exploit the potential of these models in small object detection. The performance of the modified YOLOV3 and YOLOV4 models were evaluated on a publicly available malaria dataset. These models have achieved state-of-the-art accuracy by exceeding performance of their original versions, Faster R-CNN, and SSD in terms of mean average precision (mAP), recall, precision, F1 score, and average IOU. YOLOV4-MOD has achieved the best detection accuracy among all the other models with a mAP of 96.32%. YOLOV3-MOD2 and YOLOV3-MOD1 have achieved mAP of 96.14% and 95.46%, respectively.ConclusionsThe experimental results of this study demonstrate that performance of modified YOLOV3 and YOLOV4 models are highly promising for detecting malaria parasites from images captured by a smartphone camera over the microscope eyepiece. The proposed system is suitable for deployment in low-resource setting areas.

Project description:Importance:Decades of effort have been devoted to establishing an automated microscopic diagnosis of malaria, but there are challenges in achieving expert-level performance in real-world clinical settings because publicly available annotated data for benchmark and validation are required. Objective:To assess an expert-level malaria detection algorithm using a publicly available benchmark image data set. Design, Setting, and Participants:In this diagnostic study, clinically validated malaria image data sets, the Taiwan Images for Malaria Eradication (TIME), were created by digitizing thin blood smears acquired from patients with malaria selected from the biobank of the Taiwan Centers for Disease Control from January 1, 2003, to December 31, 2018. These smear images were annotated by 4 clinical laboratory scientists who worked in medical centers in Taiwan and trained for malaria microscopic diagnosis at the national reference laboratory of the Taiwan Centers for Disease Control. With TIME, a convolutional neural network-based object detection algorithm was developed for identification of malaria-infected red blood cells. A diagnostic challenge using another independent data set within TIME was performed to compare the algorithm performance against that of human experts as clinical validation. Main Outcomes and Measures:Performance on detecting Plasmodium falciparum-infected blood cells was measured by average precision, and performance on detecting P falciparum infection at the image level was measured using sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). Results:The TIME data sets contained 8145 images of 36 blood smears from patients with suspected malaria (30 P falciparum-positive and 6 P falciparum-negative smears) that had reliable annotations. For clinical validation, the average precision was 0.885 for detecting P falciparum-infected blood cells and 0.838 for ring form. For detecting P falciparum infection on blood smear images, the algorithm had expert-level performance (sensitivity, 0.995; specificity, 0.900; AUC, 0.997 [95% CI, 0.993-0.999]), especially in detecting ring form (sensitivity, 0.968; specificity, 0.960; AUC, 0.995 [95% CI, 0.990-0.998]) compared with experienced microscopists (mean sensitivity, 0.995 [95% CI, 0.993-0.998]; mean specificity, 0.955 [95% CI, 0.885-1.000]). Conclusions and Relevance:The findings suggest that a clinically validated expert-level malaria detection algorithm can be developed by using reliable data sets.

Dataset Information

Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy.

Publications

Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy.

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