Article Text

other Versions

A public-domain image processing tool for automated quantification of fluorescence in situ hybridization signals
  1. Juho Konsti (juho.konsti{at}
  1. University of Helsinki, Finland
    1. Johan Lundin (johan.lundin{at}
    1. University of Helsinki, Finland
      1. Mervi Jumppanen (mervi.jumppanen{at}
      1. University of Tampere, Finland
        1. Mikael Lundin (mikael.lundin{at}
        1. University of Helsinki, Finland
          1. Arttu Viitanen (arttu.viitanen{at}
          1. University of Tampere, Finland
            1. Jorma Isola (jorma.isola{at}
            1. University of Tampere, Finland


              Aims: To develop and evaluate an automated method for quantification of HER2 fluorescence in situ hybridization (FISH) signals.

              Methods: Using a popular, open source image manipulation tool, ImageJ, a macro for FISH signal assessment was created. A comparison against traditional manual counting was performed in breast cancer specimens from 42 patients. The tumor specimens were hybridized with probes for HER2 and chromosome 17 centromere (CEP17) and selected areas digitized for image processing. Hybridization signals were calculated both manually and automatically with the ImageJ custom macro.

              Results: The correlation coefficient between the automatic and manual HER2/CEP17 ratios was 0.98. The corresponding percent-agreement was 90% and the kappa value 0.82.

              Conclusions: This study shows that it is possible to automate the determination of HER2 amplification by the use of open-source software with results comparable to manual counting. The automated counting decreases the time needed for sample analysis and provides possibilities to enhance inter- and intralaboratory reproducibility of results. The FISH quantification tool (FishJ), is available for download as an ImageJ macro or alternatively, it can be utilized through a web interface ( with an option of uploading FISH images for hybridization signal counting. Combined with digitization of FISH samples, the FishJ macro enables gene copy number to be assessed and re-evaluated on any area of a digitized specimen.

              • Genes, erbB-2
              • Image Processing, Computer-Assisted
              • In Situ Hybridization, Fluorescence

              Statistics from

              Request permissions

              If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.