Note that for speeding up, the histogram is bracketed to include only the range of bins that contain data (and avoid processing empty histogram bins at both extremes).ģ. Therefore, there might be differences in the results obtained on 16-bit images when using the applet and the true 16-bit results obtained with this plugin. Note that the ImageJ thresholder applet also processes 16-bit images, but in reality ImageJ first computes a histogram with 256 bins.
#IMAGEJ THRESHOLDING FULL#
Since the Auto Threshold plugin processes the full greyscale space, it can be slow when dealing with 16-bit images. From version 1.12 the plugin supports thresholding of 16-bit images. In essence, the Auto Threshold plugin, with the correct settings, can reproduce the results of the applet, but not the way round.Ģ. This means that applying the two commands to the same image can produce apparently different results. While the Auto Threshold plugin can use or ignore the extremes of the image histogram (Ignore black, Ignore white) the applet cannot: the ‘default’ method ignores the histogram extremes but the others methods do not. This plugin is accessed through the Image › Auto Threshold menu entry, however the thresholding methods were also partially implemented in ImageJ’s thresholder applet accessible through the Image › Adjust › Threshold… menu entry. Selecting this option also selects the Stack option above automatically.ġ. Use stack histogram first computes the histogram of the whole stack, then computes the threshold based on that histogram and finally binarises all the slices with that single value. If this option is left unchecked, only the current slice will be processed.
It you are processing a stack, two additional options are available: Stack can be used to process all the slices (the threshold of each slice will be computed separately). Set Threshold instead of Threshold (single images) sets the thresholding LUT, without changing the pixel data. White object on black background sets to white the pixels with values above the threshold value (otherwise, it sets to white the values less or equal to the threshold). This may be useful if the digitised image has under- or over- exposed pixels. The Ignore black and Ignore white options set the image histogram bins for and greylevels to 0 respectively. Method selects the algorithm to be applied (detailed below). After this a new command should appear in Image › Adjust › Auto Threshold.įiji: this plugin is part of the Fiji distribution, there is no need to download it.
#IMAGEJ THRESHOLDING UPDATE#
Download Auto_Threshold-X.Y.Z.jar and copy it into the ImageJ/plugins folder and either restart ImageJ or run the Help › Update Menus command. The segmented phase is always shown as white (255).įor local thresholding rather than global, see the Auto Local Threshold plugin. This plugin binarises 8 and 16-bit images using various global (histogram-derived) thresholding methods.
#IMAGEJ THRESHOLDING HOW TO#
If you’d like to help, check out the how to help guide! The content of this page has not been vetted since shifting away from MediaWiki.
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