title: Detection and segmentation of virus plaque using HOG and SVM: toward automatic plaque assay.
abstract: Plaque assaying, measurement of the number, diameter, and area of plaques in a Petri dish image, is a standard procedure gauging the concentration of phage in biology. This paper presented a novel and effective method for implementing automatic plaque assaying. The method was mainly comprised of the following steps: In the training stage, after pre-processing the images for noise suppression, an initial training set was readied by sampling positive (with a plaque at the center) and negative (plaque-free) patches from the training images, and extracting the HOG features from each patch. The linear SVM classifier was trained in a self-learnt supervised learning strategy to avoid possible missing detection. Specifically, the training set which contained positive and negative patches sampled manually from training images was used to train the preliminary classifier which exhaustively searched the training images to predict the label for the unlabeled patches. The mislabeled patches were evaluated by experts and relabeled. And all the newly labeled patches and their corresponding HOG features were added to the initial training set to train the final classifier. In the testing stage, a sliding-window technique was first applied to the unseen image for obtaining HOG features, which were inputted into the classifier to predict whether the patch was positive. Second, a locally adaptive Otsu method was performed on the positive patches to segment the plaques. Finally, after removing the outliers, the parameters of the plaques were measured in the segmented plaques. The experimental results demonstrated that the accuracy of the proposed method was similar to the one measured manually by experts, but it took less than 30 seconds.
authors.affiliation: School of Basic Medical Science, Fudan University, Shanghai 200032, China.
authors.forename: Yihao
authors.initials: Y
authors.lastname: Mao
authors.affiliation: School of Basic Medical Science, Fudan University, Shanghai 200032, China Biosafety Level-3 Laboratory, Fudan University, Shanghai 200032, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Liu
authors.affiliation: School of Basic Medical Science, Fudan University, Shanghai 200032, China Biosafety Level-3 Laboratory, Fudan University, Shanghai 200032, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Ye
authors.affiliation: School of Basic Medical Science, Fudan University, Shanghai 200032, China Digital Medical Research Center, Shanghai Key Lab of MICCAI, Shanghai 200032, China.
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Shi
authors.affiliation: School of Basic Medical Science, Fudan University, Shanghai 200032, China Digital Medical Research Center, Shanghai Key Lab of MICCAI, Shanghai 200032, China.
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Song
mesh_terms: D000465:Algorithms; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D010781:Photography / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012815:Signal Processing, Computer-Assisted; D060388:Support Vector Machine; D010948:Viral Plaque Assay; D014780:Viruses / Q000302:isolation & purification*
keywords: HOG; Plaque assay; SVM; local adaptive image segmentation