Interphase fluorescence in situ hybridization signal detection by computing intensity variance along the optical axis

Zheng Li, Bin Zheng, Liqiang Ren, Hong Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations


Fluorescence in situ Hybridization technology is a commonly used tool to detect chromosome aberrations, which are often pathologically significant. Since manual FISH analysis is a tedious and time-consuming procedure, reliable and robust automated image acquisition and analysis are in demand. Under high magnification objective lenses such as 60x and 100x, the depth of field will often be too small and the FISH probes may not always lie in the same focal plane. A statistical variance based automated FISH analysis method is developed in order to address this problem. On a stack of slices at consecutive image planes with a step size d, the statistical variance alone the z-axis is calculated to form a 2-D matrix. Since pixels shift dramatically to high intensity at FISH probe location, the probes will manifest high peak values in the matrix. A computer-aided detection scheme based on top-hat transform is applied to the matrix to detect FISH probe signals. This study demonstrates a simple and robust method for FISH probe detection as well as a way of 2- D representation of 3-D data.

Original languageEnglish (US)
Title of host publicationBiophotonics and Immune Responses IX
ISBN (Print)9780819498571
StatePublished - 2014
Externally publishedYes
EventBiophotonics and Immune Responses IX - San Francisco, CA, United States
Duration: Feb 3 2014Feb 3 2014

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


ConferenceBiophotonics and Immune Responses IX
Country/TerritoryUnited States
CitySan Francisco, CA


  • Extended depth of field
  • Fluorescence in situ hybridization
  • Fluorescence microscopy

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Biomaterials
  • Radiology Nuclear Medicine and imaging


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