If the local contrast is below the contrast threshold the neighbourhood is considered to consist only of one class and the pixel is set to object or background depending on the value of the midgrey. Double clicking on the tool icon will display the Color Picker. Edit Clear, Clear Outside and Cut x use the background color. Edit Draw d and Edit Fill f use the foreground color. If the local contrast (max-min) is above or equal to the contrast threshold, the threshold is set at the local midgrey value (the mean of the minimum and maximum grey values in the local window). In the icon, the ‘eye dropper’ is drawn in the current foreground color while the frame around it is drawn in the current background color. The method uses a user-provided contrast threshold. Any number different than 0 will change the default value. Note that this implementation uses circular windows instead of rectangular in the original. Implements Bernsen’s thresholding method. A popup window will appear (when stacks have more than 25 slices) to confirm whether the procedure should display the stack montages. When processing stacks with many slices, the montages can become very large (several times the original stack size) and one risks running out of ram. This produces a montage with results from all the methods, so one can explore how the different algorithms perform on an image or stack. Which method segments your data best? You can attempt to answer this question using the Try all option. It you are processing a stack, one additional option is available: Stack can be used to process all the slices. Those are detailed below for each method. Special parameters 1 and 2 sets specific values for each method. 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). The radius sets the radius of the local domain over which the threshold will be computed. Method selects the algorithm to be applied (detailed below). After this a new command should appear in Image › Adjust › Auto Local 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. The segmented phase is always shown as white (255).įor global thresholding rather than local, see the Auto Threshold plugin. By ‘local’ here is meant that the threshold is computed for each pixel according to the image characteristings within a window of radius r (in pixel units) around it. This plugin binarises 8-bit images using various local thresholding methods. 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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