CShaperApp:Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo  

作　　者：Jianfeng Cao Lihan Hu Guoye Guan Zelin Li Zhongying Zhao Chao Tang Hong Yan 

机构地区：[1]Department of Electrical Engineering,City University of Hong Kong,Hong Kong,China [2]Centre for Intelligent Multidimensional Data Analysis Limited,Hong Kong,China [3]College of Computer and Information,Hohai University,Nanjing,China [4]Center for Quantitative Biology,Peking University,Beijing,China [5]Department of Biology,Hong Kong Baptist University,Hong Kong,China [6]State Key Laboratory of Environmental and Biological Analysis,Hong Kong Baptist University,Hong Kong,China [7]Peking-Tsinghua Center for Life Sciences,Peking University,Beijing,China [8]School of Physics,Peking University,Beijing,China

出　　处：《Quantitative Biology》2024年第3期329-334,共6页定量生物学（英文版）

基　　金：National Natural Science Foundation of China,Grant/Award Numbers:12090053,32088101;Hong Kong Innovation and Technology Fund,Grant/Award Numbers:GHP/176/21SZ,InnoHK Project CIMDA;Hong Kong Research Grants Council,Grant/Award Numbers:11204821,HKBU12101323,HKBU12101520,HKBU12101522,N_HKBU201/18。

摘　　要：Caenorhabditis elegans has been widely used as a model organism in developmental biology due to its invariant development.In this study,we developed a desktop software CShaperApp to segment fluorescence-labeled images of cell membranes and analyze cellular morphologies interactively during C.elegans embryogenesis.Based on the previously proposed framework CShaper,CShaperApp empowers biologists to automatically and efficiently extract quantitative cellular morphological data with either an existing deep learning model or a fine-tuned one adapted to their in-house dataset.Experimental results show that it takes about 30 min to process a three-dimensional time-lapse(4D)dataset,which consists of 150 image stacks at a~1.5-min interval and covers C.elegans embryogenesis from the 4-cell to 350-cell stages.The robustness of CShaperApp is also validated with the datasets from different laboratories.Furthermore,modularized implementation increases the flexibility in multi-task applications and promotes its flexibility for future enhancements.As cell morphology over development has emerged as a focus of interest in developmental biology,CShaperApp is anticipated to pave the way for those studies by accelerating the high-throughput generation of systems-level quantitative data collection.The software can be freely downloaded from the website of Github(cao13jf/CShaperApp)and is executable on Windows,macOS,and Linux operating systems.

关 键 词：C.elegans embryogenesis cellular morphology cellular segmentation deep learning desktop software 

分 类 号：Q95-33[生物学—动物学]