Ridge detection

Detects ridge objects in an image from the workspace.

Description

Detects ridge objects in an image from the workspace. A ridge is considered as a line of higher (or lower) intensity pixels in an image. Ridges are output as objects to the workspace with relevant measurements associated with each object (e.g. ridge length). This module uses the "Ridge Detection" plugin, which itself is based on the paper "An Unbiased Detector of Curvilinear Structures" (Steger, C., IEEE Transactions on Pattern Analysis and Machine Intelligence (1998) 20 113–125).

Note: This module detects ridges in 2D, but can be run on multi-dimensional images. For higher dimensionality images than 2D, ridge detection is performed slice-by-slice, with output objects confined to a single slice.

Parameters

Parameter	Description
Input image	Image from the workspace on which ridges will be identified. This can be a multi-dimensional image, although ridges are currently only detected in 2D. In the case of higher-dimensionality images, ridges are detected on a slice-by-slice basis.
Output objects	Output ridge objects, which will be added to the workspace. These objects will have measurements associated with them.
Contour contrast	Controls if we are detecting dark lines on a lighter background or light lines on a darker background.
Lower threshold	Lower response threshold for points on a line to be accepted. This threshold is based on the value of points after the ridge enhancement filtering and is not a reflection of their absolute pixel intensities.
Upper threshold	Upper response threshold for points on a line to be accepted. This threshold is based on the value of points after the ridge enhancement filtering and is not a reflection of their absolute pixel intensities.
Sigma	Sigma of the derivatives to be applied to the input image when detecting ridges. This is related to the width of the lines to be detected and is greater than or equal to "width/(2*sqrt(3))".
Calibrated units	When selected, spatial values are assumed to be specified in calibrated units (as defined by the "Input control" parameter "Spatial unit"). Otherwise, pixel units are assumed.
Extend line	Lines are extended in an attempt to locate more junction points.
Estimate width	When this is selected, the width of each line is estimated and exported as a measurement. This allows the output objects to be exported as "wide" objects, although only if Apply width to output is also selected
Apply width to output	When selected, the output ridge objects will have the width applied (rather than having single pixel width).
Overlap mode	Controls how intersecting lines should be handled. For more information see https://imagej.net/Ridge_Detection.html#Overlap_resolution. "None" Ridges are terminated at line intersections, so two overlapping ridges will likely be identified as at least four separate ridge objects. "Slope" When selected, this will attempt to resolve ridge overlaps such that two overlapping ridges would be identified as two separate objects. Ridges output in this manner can have common, shared paths (i.e. during the overlap region).
Minimum length	Minimum length of a detected line for it to be retained and output. Specified in pixel units, unless "Calibrated units" is selected.
Maximum length	Maximum length of a detected line for it to be retained and output. Specified in pixel units, unless "Calibrated units" is selected.
Join at junctions
Link ends	When selected, ridges with ends in close proximity will be linked into a single object.
Alignment range (px)	If linking contours, but limiting the end misalignment, this is the number of points from each contour end for which the orientation of that end is calculated.
Maximum end separation (px)
Maximum end misalignment (degs)	If linking contours, but limiting the end misalignment, this is the maximum permitted misalignment of each contour end.