Imagej threshold to selection how to#
Imagej threshold to selection update#
Imagej threshold to selection full#
Imagej threshold to selection download#

Images and stacks that are impossible to threshold remain unchanged.Ĥ. The “Try all” option retains the 16 bit format to still show the images with methods that might fail to obtain a threshold. This is to keep the data untouched in the remaining slices. However, for stacks where only 1 slice is thresholded, the result is still a 16 bit container with the thresholded phase shown as white. The result of 16 bit images and stacks (when processing all slices) is an 8 bit container showing the result in white to comply with the concept of “binary image” (i.e. 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 threshold to selection 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).

Imagej threshold to selection download#

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 threshold to selection 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 threshold to selection how to#

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