Automatic White Blood Cell Detection and Segmentation in ...
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RESEARCH POSTER PRESENTATION DESIGN © 2015 www.PosterPresentations.com Automatic analysis of microscopic images of blood smears with parasite-infected red blood cells can assist field workers in screening and monitoring malarial infection. Millions of blood slides are manually screened for parasites every year, which is a time consuming and error- prone process. We have developed a smartphone-based software to perform this task using machine learning and image analysis methods for counting infected red blood cells automatically. The software runs on a standard Android smartphone attached to a microscope by a low- cost adapter. The smartphone’s built-in camera views images of thin blood smear slides through the eyepiece of the microscope. Our method first detects and segments red blood cells in these images. However, the presence of white blood cells (WBCs) adversely affects the accuracy of red blood cell detection and segmentation since WBCs are often mistaken for red blood cells by current automatic cell detection methods. Therefore, a pre-processing step for WBC elimination is necessary, which requires WBC detection and segmentation methods. Segmentation of WBCs is a complex process due to the morphological diversity of WBCs and staining differences. We introduce an algorithm that successfully detects white blood cells in microscopic images of thin blood smears following a range filtering approach that accurately estimates the boundary of each cell using a level-set algorithm. Our method is capable of detecting different types of white blood cells with different shades of staining. We test our algorithm on more than 1300 thin blood smear images exhibiting about 1350 WBCs, which are manually annotated by a professional slide reader. For cell detection, we achieve 96.4% precision, 98.4% recall, and 97.4% F1-score. For cell segmentation, we assess the performance by a pixel-wise comparison of the manual segmentations with our machine segmentations, which has resulted in an overlap of 82% based on the Jaccard similarity index. These results are promising outcomes for automatic WBC analysis, which lead to higher accuracy in the counting of red blood cells and a concomitant improvement in screening performance. We evaluate the two processing steps of our algorithm, cell detection and cell segmentation, separately: WBC Detection Step WBC Segmentation Step Illustrated, the output segmentation mask and ground truth mask are compared for three sample images. The green pixels represent the pixels falsely included in the segmented area (false positives) and the pink pixels show those falsely excluded from the segmented area (false negatives). Also known as “Leukocytes” Nucleated cells in the blood that protect the body against infectious disease Five main types: Segmentation challenges in blood smear images: More than 1300 slide images containing about 1350 WBCs were acquired at Chittagong Medical College Hospital in Bangladesh Annotated manually by an experienced professional slide reader using the Firefly annotation tool (firefly.cs.missouri.edu) WHITE BLOOD CELLS DATASET & ANNOTATION The proposed algorithm includes three main steps Pre-processing To extract regions of interest (ROI) and perform illumination correction and color enhancement White Blood Cell Detection To specify the location of any white blood cell present in an image using a range filtered version of the image White Blood Cell Segmentation To segment the detected cells employing an accurate level-set algorithm METHOD RESULTS CONCLUSIONS We introduced an algorithm that successfully detects white blood cells in microscopic images of thin blood smears following a range filtering approach. This method is capable of detecting different types of white blood cells with different shades of staining. The proposed algorithm accurately estimates the boundary of each cell, using a level-set algorithm. The results demonstrate that our algorithm provides promising segmentation outcomes. In future work, we will add this algorithm to our current smartphone application for malaria cell counting. REFFERENCES [1] http:// www.uwosh.edu/med_tech/what-is-elementary- hematology/white-blood-cells [2] M. Poostchi, I. Ersoy, A. Bansal, K. Palaniappan, S. Antani, S. Jaeger, G. Thoma, “Image Analysis of Blood Slides for Automatic Malaria Diagnosis”, NIH-IEEE Strategic Conference on Healthcare Innovations and Point-of-Care Technologies for Precision Medicine (HI-POCT), 2015. [3] Z. Liang, A. Powell, I Ersoy, M. Poostchi, K. Silamut, K. Palaniappan, P. Guo, Md. Hossain, S. Antani, R. J. Maude, J. X. Huang, S. Jaeger, G. Thoma, “CNN-Based Image Analysis for Malaria Diagnosis”, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016. [4] S. Jaeger, K. Silamut, H. Yu, M. Poostchi, I. Ersoy, A. Powell, Z. Liang, M. Hossain, S. Antani, K. Palaniappan, R. Maude, G. Thoma, “Reducing the Diagnostic Burden of Malaria Using Microscopy Image Analysis and Machine Learning in the Field”. Annual Meeting of the American Society of Tropical Medicine & Hygiene (ASTMH), Atlanta, USA, 2016. ACKNOWLEDGMENT This research is supported by the Intramural Research Program of NIH, NLM, and Lister Hill National Center for Biomedical Communications. Mahidol-Oxford Tropical Medicine Research Unit is funded by the Wellcome Trust of Great Britain. Neutrophils Eosinophils Basophils Lymphocytes Monocytes Smartphone Adapter Blood Slide Automatic White Blood Cell Detection and Segmentation in Microscopy Images of Thin Blood Smears Golnaz Moallem 1 , Mahdieh Poostchi 2 , Hang Yu 2 , Nila Palaniappan 3 , Kamolrat Silamut 4 , Richard J. Maude 4 , Md Amir Hossain 5 , Stefan Jaeger 2 , Sameer Antani 2 , George Thoma 2 1 Department of Electrical and Computer Engineering, Texas Tech University, United States 2 Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine, United States 3 University of Missouri, Kansas City, United States 4 Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand 5 Chittagong Medical College Hospital, Chittagong, Bangladesh Microscope PRE-PROCESSING WBC SEGMENTATION WBC DETECTION IMAGE RESULT Measure Value Precision 96.37 Recall 98.37 F1 Score 97.36 Measure Value Jaccard Index 82.28 Dice Index 78.33 INTRODUCTION Initial mask from detection step Estimated boundary after segmentation The outcome of the proposed method for sample images from our dataset is demonstrated below. RESULTS (cont.) Shape diversities Size variation Low boundary contrast Cell staining differences Uneven illumination Cell texture complexity
Transcript of Automatic White Blood Cell Detection and Segmentation in ...
RESEARCH POSTER PRESENTATION DESIGN © 2015
www.PosterPresentations.com
Automatic analysis of microscopic images of blood smears withparasite-infected red blood cells can assist field workers in screeningand monitoring malarial infection. Millions of blood slides are manuallyscreened for parasites every year, which is a time consuming and error-prone process. We have developed a smartphone-based software toperform this task using machine learning and image analysis methodsfor counting infected red blood cells automatically. The software runson a standard Android smartphone attached to a microscope by a low-cost adapter. The smartphone’s built-in camera views images of thinblood smear slides through the eyepiece of the microscope. Our methodfirst detects and segments red blood cells in these images. However, thepresence of white blood cells (WBCs) adversely affects the accuracy ofred blood cell detection and segmentation since WBCs are oftenmistaken for red blood cells by current automatic cell detectionmethods. Therefore, a pre-processing step for WBC elimination isnecessary, which requires WBC detection and segmentation methods.Segmentation of WBCs is a complex process due to the morphologicaldiversity of WBCs and staining differences. We introduce an algorithmthat successfully detects white blood cells in microscopic images of thinblood smears following a range filtering approach that accuratelyestimates the boundary of each cell using a level-set algorithm. Ourmethod is capable of detecting different types of white blood cells withdifferent shades of staining. We test our algorithm on more than 1300thin blood smear images exhibiting about 1350 WBCs, which aremanually annotated by a professional slide reader. For cell detection, weachieve 96.4% precision, 98.4% recall, and 97.4% F1-score. For cellsegmentation, we assess the performance by a pixel-wise comparison ofthe manual segmentations with our machine segmentations, which hasresulted in an overlap of 82% based on the Jaccard similarity index.These results are promising outcomes for automatic WBC analysis,which lead to higher accuracy in the counting of red blood cells and aconcomitant improvement in screening performance.
We evaluate the two processing steps of our algorithm, celldetection and cell segmentation, separately:
WBC Detection Step
WBC Segmentation Step
Illustrated, the output segmentation mask and ground truthmask are compared for three sample images. The green pixelsrepresent the pixels falsely included in the segmented area(false positives) and the pink pixels show those falsely excludedfrom the segmented area (false negatives).
Also known as “Leukocytes” Nucleated cells in the blood that protect the body against
infectious disease Five main types:
Segmentation challenges in blood smear images:
More than 1300 slide images containing about 1350 WBCswere acquired at Chittagong Medical College Hospital inBangladesh
Annotated manually by an experienced professional slide readerusing the Firefly annotation tool (firefly.cs.missouri.edu)
WHITE BLOOD CELLS
DATASET & ANNOTATIONThe proposed algorithm includes three main steps Pre-processing
To extract regions of interest (ROI) and performillumination correction and color enhancement
White Blood Cell Detection To specify the location of any white blood cell
present in an image using a range filtered version ofthe image
White Blood Cell Segmentation To segment the detected cells employing an accurate
level-set algorithm
METHOD
RESULTS CONCLUSIONSWe introduced an algorithm that successfully detects white bloodcells in microscopic images of thin blood smears following a rangefiltering approach. This method is capable of detecting differenttypes of white blood cells with different shades of staining. Theproposed algorithm accurately estimates the boundary of each cell,using a level-set algorithm. The results demonstrate that ouralgorithm provides promising segmentation outcomes. In futurework, we will add this algorithm to our current smartphoneapplication for malaria cell counting.
REFFERENCES[1] http://www.uwosh.edu/med_tech/what-is-elementary-hematology/white-blood-cells[2] M. Poostchi, I. Ersoy, A. Bansal, K. Palaniappan, S. Antani, S. Jaeger,G. Thoma, “Image Analysis of Blood Slides for Automatic MalariaDiagnosis”, NIH-IEEE Strategic Conference on Healthcare Innovationsand Point-of-Care Technologies for Precision Medicine (HI-POCT), 2015.[3] Z. Liang, A. Powell, I Ersoy, M. Poostchi, K. Silamut, K. Palaniappan,P. Guo, Md. Hossain, S. Antani, R. J. Maude, J. X. Huang, S. Jaeger, G.Thoma, “CNN-Based Image Analysis for Malaria Diagnosis”, IEEEInternational Conference on Bioinformatics and Biomedicine (BIBM),2016.[4] S. Jaeger, K. Silamut, H. Yu, M. Poostchi, I. Ersoy, A. Powell, Z.
Liang, M. Hossain, S. Antani, K. Palaniappan, R. Maude, G.Thoma, “Reducing the Diagnostic Burden of Malaria Using MicroscopyImage Analysis and Machine Learning in the Field”. Annual Meeting ofthe American Society of Tropical Medicine & Hygiene (ASTMH), Atlanta,USA, 2016.
ACKNOWLEDGMENTThis research is supported by the Intramural Research Program ofNIH, NLM, and Lister Hill National Center for BiomedicalCommunications. Mahidol-Oxford Tropical Medicine ResearchUnit is funded by the Wellcome Trust of Great Britain.
Neutrophils Eosinophils Basophils Lymphocytes Monocytes
Smartphone
Adapter
Blood Slide
Automatic White Blood Cell Detection and Segmentation in Microscopy Images of Thin Blood SmearsGolnaz Moallem1, Mahdieh Poostchi2, Hang Yu2, Nila Palaniappan3, Kamolrat Silamut4, Richard J. Maude4, Md Amir Hossain5, Stefan Jaeger2, Sameer Antani2, George Thoma2
1 Department of Electrical and Computer Engineering, Texas Tech University, United States2 Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine, United States
3 University of Missouri, Kansas City, United States 4 Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
5 Chittagong Medical College Hospital, Chittagong, Bangladesh
Microscope
PRE-PROCESSING
WBC SEGMENTATION
WBC DETECTION
IMAGE
RESULT
Measure ValuePrecision 96.37
Recall 98.37F1 Score 97.36
Measure ValueJaccard Index 82.28
Dice Index 78.33
INTRODUCTION
Initial mask from detection
step
Estimated boundary
after segmentation
The outcome of the proposed method for sample images fromour dataset is demonstrated below.
RESULTS (cont.)
Shape diversities Size variation Low boundary contrast
Cell staining differences Uneven illumination Cell texture complexity
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