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Software used to threshold 16 bits tiff images

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  • Software used to threshold 16 bits tiff images

    Dear all friends

    I am trying to threshold my microCT image sequences to make them a binary image sequence.

    As what I am dealing with is a 16 bits tiff image stack, so I have done the calibration through Matlab. Next stage for me is to decide a threshold value of the greyscale density and then convert them into binary images sequence.

    So, my idea is to have a trial on any image processing software available. Like what we are doing with the histogram. You choose a greyscale value and then all the pixels that is above the threshold value will be highlighted, this will be done over a couple of images by visualization and finally you make sure the threshold value you choose would be able to cover all most all the bone parts available in the images.

    So, is there any software that you guy would recommend, it has to have the ability to deal with images of 16 bits, so the grayscale would be in the range of 0-65524, not 0-255. I tried the ImageJ , it indeed is able to view 16 bits greyscale images but it seems no way to threshold it by visualization. Does anybody have any idea


    Yuan Chen
    PhD student
    University of Sheffield

  • #2
    Re: Software used to threshold 16 bits tiff images

    Hi Yuan,

    Nice work to get the calibration done through Matlab. I think that ImageJ can handle your thresholding step in a pretty straightforward manner: just use the menus to go to Image -> Adjust -> Threshold, and a GUI should pop up that shows you the intensity histogram, along with slider bars to set the range that you want to use. You can do this for a specific slice, or as a stack histogram (the latter seems preferable and also easier).

    If you would prefer to set the threshold automatically rather than manually, the left pull-down menu in the GUI provides a number of options, including the Otsu thresholding method that seems highly referenced.

    If you run into other roadblocks in the process, you might want to go to the ImageJ website ( and search for "threshold", "histogram", or other relevant terms. ImageJ can seem daunting, but the nice thing is that there's a large, helpful community of users (a whole lot like Biomech-L) among whom someone has often encountered a similar problem.

    Hope this helps. Good luck!



    • #3
      Re: Software used to threshold 16 bits tiff images

      hi! if you are looking for a tiff image processing software that can deal with 16bits images and grayscale color. then i have something for you. by the way,great work.