Local auto-threshold
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
- Input image (default = "") Image to apply threshold to.
- Apply to input image (default = "true") 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 (default = "") Name of the output image created during the thresholding process. This image will be added to the workspace.
- Threshold mode (default = "Slice-by-slice") 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) (default = "Bernsen") 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) (default = "Bernsen") 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 (default = "1.0") 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 (default = "false") 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 (default = "0.0") Lowest absolute threshold value that can be applied.
- Local radius (default = "1.0") Radius of region to be used when calculating local intensity thresholds. Units controlled by "Spatial units mode" control.
- Spatial units mode (default = "Pixel/slice") 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") (default = "false") 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 (default = "Black (0) background") Controls whether objects are considered to be white (255 intensity) on a black (0 intensity) background, or black on a white background.