title: An automated method for cell detection in zebrafish.
abstract: Quantification of cells is a critical step towards the assessment of cell fate in neurological disease or developmental models. Here, we present a novel cell detection method for the automatic quantification of zebrafish neuronal cells, including primary motor neurons, Rohon-Beard neurons, and retinal cells. Our method consists of four steps. First, a diffused gradient vector field is produced. Subsequently, the orientations and magnitude information of diffused gradients are accumulated, and a response image is computed. In the third step, we perform non-maximum suppression on the response image and identify the detection candidates. In the fourth and final step the detected objects are grouped into clusters based on their color information. Using five different datasets depicting zebrafish cells, we show that our method consistently displays high sensitivity and specificity of over 95%. Our results demonstrate the general applicability of this method to different data samples, including nuclear staining, immunohistochemistry, and cell death detection.
authors.affiliation: The Center for Biomedical Informatics, The Methodist Hospital Research Institute, Houston, TX, USA.
authors.forename: Tianming
authors.initials: T
authors.lastname: Liu
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.forename: Jingxin
authors.initials: J
authors.lastname: Nie
authors.forename: Ashley
authors.initials: A
authors.lastname: Tarokh
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Zhou
authors.forename: Lei
authors.initials: L
authors.lastname: Guo
authors.forename: Jarema
authors.initials: J
authors.lastname: Malicki
authors.forename: Weiming
authors.initials: W
authors.lastname: Xia
authors.forename: Stephen T C
authors.initials: ST
authors.lastname: Wong
mesh_terms: D000465:Algorithms; D000818:Animals; D001331:Automation / Q000379:methods / Q000592:standards; D002452:Cell Count / Q000379:methods; D016923:Cell Death / Q000502:physiology; D002490:Central Nervous System / Q000166:cytology* / Q000502:physiology; D003198:Computer Simulation / Q000592:standards* / Q000639:trends; D005455:Fluorescent Antibody Technique / Q000379:methods; D019044:Image Cytometry / Q000295:instrumentation / Q000379:methods*; D007150:Immunohistochemistry / Q000379:methods; D008856:Microscopy, Fluorescence / Q000379:methods; D023421:Models, Animal; D009474:Neurons / Q000166:cytology* / Q000502:physiology; D012160:Retina / Q000166:cytology / Q000502:physiology; D012984:Software / Q000592:standards / Q000639:trends; D012985:Software Design; D013194:Staining and Labeling / Q000379:methods; D015027:Zebrafish / Q000033:anatomy & histology* / Q000502:physiology