Algorithms for Cytoplasm Segmentation of Fluorescence Labelled Cells

Automatic cell segmentation has various applications in cytometry, and while the nucleus is often very distinct and easy to identify, the cytoplasm provides a lot more challenge. A new combination of image analysis algorithms for segmentation of cells imaged by fluorescence microscopy is presented. The algorithm consists of an image pre‐processing step, a general segmentation and merging step followed by a segmentation quality measurement. The quality measurement consists of a statistical analysis of a number of shape descriptive features. Objects that have features that differ to that of correctly segmented single cells can be further processed by a splitting step. By statistical analysis we therefore get a feedback system for separation of clustered cells. After the segmentation is completed, the quality of the final segmentation is evaluated. By training the algorithm on a representative set of training images, the algorithm is made fully automatic for subsequent images created under similar conditions. Automatic cytoplasm segmentation was tested on CHO‐cells stained with calcein. The fully automatic method showed between 89% and 97% correct segmentation as compared to manual segmentation.

• Publication year

  2002

• Venue

  Analytical Cellular Pathology

• Publication date

  2002-01-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1155/2002/821782PMID 12446959PMCID 4618826
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2001cited by this paper
• Perimeter and Area Estimates for Digitized Objects

  2001influential reference
• Better decisions through science.

  2000cited by this paper
• Handbook of medical imaging

  2000cited by this paper
• Automatic Cell Segmentation in Cyto- and Histometry Using Dominant Contour Feature Points

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• Length estimators for digitized contours

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  1986cited by this paper
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• Numerical Methods for Scientists and Engineers

  1962cited by this paper

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