CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

Source Code for Biology and Medicine

Arvid Lundervold²  Hans-Hermann Gerdes¹  Dominik Michael Frei¹  Tanja Kögel¹  Erlend Hodneland¹ 

[1] Department of Biomedicine, University of Bergen, Bergen, Norway;Department of Radiology, Haukeland University Hospital, Bergen, Norway

关键词: Surface staining;    Nucleus staining;    High-throughput;    CellSegm;    Cell segmentation;    Automated analysis;   

Others  :  805211
DOI  :  10.1186/1751-0473-8-16

 received in 2012-11-27, accepted in 2013-07-30,  发布年份 2013

【 摘 要 】

The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CELLSEGM, the software presented in this work, is a MATLAB based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CELLSEGM has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CELLSEGM. The command-line interface of CELLSEGM facilitates scripting of the separate tools, all implemented in MATLAB, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CELLSEGM enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

【 授权许可】

   
2013 Hodneland et al.; licensee BioMed Central Ltd.

【 图 表 】

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