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. 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. 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.
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