Modules

Local 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 and 2D local 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.
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.
Threshold mode Local thresholding algorithm mode to use.
  • "Slice-by-slice" Local thresholds are applied to a multidimensional image stack one 2D image at a time. Images are processed independently.
  • "3D" Local threshold algorithms are calculated in 3D and applied to all slices of an image in a single run. This is more computationally expensive.
Algorithm (slice-by-slice) Algorithms available for calculating local threshold on a slice-by-slice basis. These are described at https://imagej.net/Auto_Local_Threshold. Algorithms available: Bernsen, Contrast, Mean, Median, MidGrey, Niblack, Otsu, Phansalkar, Sauvola
Algorithm (3D) Algorithms available for calculating local threshold on 3D stack in a single run (all slices processed together). These are 3D modifications of the algorithms described at https://imagej.net/Auto_Local_Threshold. Algorithms available: Bernsen, Contrast, Mean, Median, Phansalkar
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.
Local radius Radius of region to be used when calculating local intensity thresholds. Units controlled by "Spatial units mode" control.
Spatial units mode Controls whether spatial values are assumed to be specified in calibrated units (as defined by the "Input control" parameter "Spatial unit") or pixel units.
Use full Z-range ("Global Z") When performing 3D local thresholding, this takes all z-values at a location into account. If disabled, pixels will be sampled in z according to the "Local radius" setting.
Binary logic Controls whether objects are considered to be white (255 intensity) on a black (0 intensity) background, or black on a white background.