when adjust the threshhold well,"apply" icon is clicked.After that, a dialogue box "set background pixels to nan"popuping. If i tick it, the gray clolor of the images to be analyzed is going to became thin, and the fininal value of the mean intensity is less than the one in which the popup box not ticked.
Moreover, the mean density of area outside of selected region in mask by thresholding and using ticking "set background pixels to nan" is much higer than the not ticking one. e.g. 146vs NaN
So, how to understand "set background pixels to NaN" popuping box when using threshold function?
hello again,
NaN means "not a number". If you check this option it converts the intensity values of the background to "nothing" rather than to 0 and keeps the other values, which can be very useful. If you intend to do image analyses more frequently, I can recommend the following document by Peter Bankhead. It is very well written and helps understanding the basics of image analysis.
http://blogs.qub.ac.uk/ccbg/files/2014/05/2014-05_Analyzing_fluorescence_microscopy_images.pdf
Here the according passage in the document:
"9.4.1 Using NaNs
Although not obviously integral to the idea of thresholding, bit-depths and image types are relevant in two main ways. The first appears when you click Apply in the Threshold... dialog box for a 32-bit image. This presents the option Set Background Pixels to NaN, which instead of making a binary image would give give an image in which the foreground pixels retain their original values, while background pixels are Not A Number. This is a special value that can only be stored in floating point images, which ImageJ ignores when making measurements later. It is therefore used to mask out regions."
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