Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 49

Full Length Research Paper

DeutJ: An ImageJ plugin for improved automatic masking and segmentation of images from confocal microscopy

Cui Sunny
  • Cui Sunny
  • School of Computer Science, Carnegie Mellon University, United States.
  • Google Scholar

  •  Received: 22 December 2022
  •  Accepted: 25 January 2023
  •  Published: 28 February 2023


Due to advances in microscopic imaging, there are a plethora of biological molecules that can now be tagged and subsequentially imaged from almost any cell, organism, or tissue. However, the ability of software to analyze these images remains to be a challenge. ImageJ is open source software that allows for the processing of these images, but faces challenges when dealing with images that show weak contrast between objects of interest and background. DeutJ is an ImageJ plugin that color corrects and brightness corrects gradients that inhibit segmentation in confocal microscopy images. It can analyze hundreds of images from a given folder and produces binary mask images that are superior to existing ImageJ functions.


Key words: ImageJ, image analysis, cell segmentation, ImageJ plugin.