Modules

Global auto-threshold

Binarise an image in the workspace such that the output only has pixel values of 0 and 255.

Description

Binarise an image in the workspace such that the output only has pixel values of 0 and 255. Uses the built-in ImageJ global auto-thresholding algorithms.

Note: Currently only works on 8-bit images. Images with other bit depths will be automatically converted to 8-bit based on the "Fill target range (normalise)" scaling method from the "Image type converter" module.

Parameters

Parameter Description
Input image Image to apply threshold to.
Output mode Controls if the threshold is applied to the input image or only calculated and stored as a measurement:
  • "Calculate and apply" Calculate the threshold and apply it to the input image. Whether the binarised image updates the input image or is saved as a separate image to the workspace is controlled by the "Apply to input image" parameter. In this mode the calculated threshold is still stored as a measurement of the input image.
  • "Calculate only" Calculate the threshold, but do not apply it to the input image. The calculated threshold is only stored as a measurement of the input image.
Apply to input image Select if the threshold should be applied directly to the input image, or if it should be applied to a duplicate, then stored as a different image in the workspace.
Output image Name of the output image created during the thresholding process. This image will be added to the workspace.
Algorithm Global thresholding algorithm to use. Choices are: Huang, Intermodes, IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen.
Threshold multiplier Prior to application of automatically-calculated thresholds the threshold value is multiplied by this value. This allows the threshold to be systematically increased or decreased. For example, a "Threshold multiplier" of 0.9 applied to an automatically-calculated threshold of 200 will see the image thresholded at the level 180.
Use lower threshold limit Limit the lowest threshold that can be applied to the image. This is used to prevent unintentional segmentation of an image containing only background (i.e. no features present).
Lower threshold limit Lowest absolute threshold value that can be applied.
Binary logic Controls whether objects are considered to be white (255 intensity) on a black (0 intensity) background, or black on a white background.
Measure on objects
Input objects