Frequently Asked Questions
  • How should I cite ImageJ?
  • How can I report a bug?
  • How does "Auto" thresholding work?
  • How can I get text to look better?

    The ImageJ Documenation Wiki has more ImageJ FAQs.

    How should I cite ImageJ in a scientific paper?
    Here are two possible ways to reference ImageJ:
    1. Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda,
      Maryland, USA, http://rsb.info.nih.gov/ij/, 1997-2007.

    2. Abramoff, M.D., Magelhaes, P.J., Ram, S.J. "Image Processing with ImageJ".
      Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.
    How can I report a bug?
    Send bug reports to wsr at nih.gov. Include the following information:
    • ImageJ version
    • OS version
    • Java version (shown in Help/About ImageJ)
    • Memory assigned to ImageJ (Edit/Options/Memory) and memory available
    • Any error messages
    • Steps needed to reproduce the problem
    Before sending a bug report, upgrade to the latest version of ImageJ and try to reproduce the bug on more than one machine.

    How does "Auto" thresholding work?
    The automatic thresholding function used by Image/Adjust/Threshold, Process/Binary/Make Binary and Process/Binary/Convert to Mask divides the image into objects and background. It does this by taking a test threshold and computing the average of the pixels at or below the threshold and pixels above. It then computes the average of those two, increments the threshold, and repeats the process. Incrementing stops when the threshold is larger than the composite average. That is,
    threshold = (average background + average objects)/2
    The code in ImageJ that implements this function is the getAutoThreshold() method in the ImageProcessor class.

    The online Image Processing Fundamentals tutorial discusses thresholding techniques. ImageJ uses the Isodata algorithm.

    How can I get text to look better?
    On Windows XP, you can get better looking text in menus, dialogs, text windows and the status bar by activating Clear Type, a form of sub-pixel antialiasing:
    • Right click on a blank area of the desktop and choose "Properties"
    • Click on the "Appearance" tab
    • Click "Effects"
    • Check "Use the following method to smooth edges of screen fonts"
    • Select "Clear Type" in the drop down menu
    You can also improve the appearance of tool icons by enabling "Antialiased Tool Icons" in Edit/Options/Misc.

         [ImageJ Window]

    • | Documentation | Home |