Width Profile Tools

Tools to estimate the width-profile of an object given as a binary mask image.

Calculate the width profile of the object

• as local thickness
• as voronoi distance between two parts of the contour-line
• perpendicular to the axis of inertia
• at regular distances using rays perpendicular to a centerline segment

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The source code in github can be found here. Example images can be downloaded from the toolset.

Getting started

You must have the MorphoLibJ-plugin [1] installed.

To install the tool save the file width_profile_tools.ijm into the folder macros/toolsets of your FIJI installation. Start FIJI and select the width_profile_tools-toolset from the >>-button.

Press the install/update-button (cloud with an arrow) to install the tools and restart FIJI after the installation finished.

• the first button opens this help-page.
• the t-button calculates the width profile using the local thickness plugins
• the v-button calculates the width profile using the voronoi-distance between two parts of the outline of the object
• the i-button calculates the width profile from line-segments perpendicular to the axis of inertia of the object
• the c-button calculates the width profile from line-segments perpendicular to the centerline of the object
• the utilities-menu contains utilities to
  • select the centerline
  • smooth a mask image
  • create a line-roi from a mask image containing a one pixel wide line
  • re-measure the local-thickness after having suppressed widths from the thickness-image
• the install/update-button installs the tools or updates them to a different version.
• the images-menu allows to download an example dataset and to open the images from the dataset.

Width profile using local thickness

The local thickness at a point p in a structure is defined in [2] as the diameter of the largest sphere with that contains the point p and that fits entirely into the structure. In the 2D-case we use a circle instead of the sphere.

To calculate the local thickness, create a binary mask and press the t-button.

Literature

[1] Legland, D., Arganda-Carreras, I., & Andrey, P. (2016). MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics, btw413. doi:10.1093/bioinformatics/btw413

[2] Hildebrand, T., and Rüegsegger, P. (1997). A new method for the model‐independent assessment of thickness in three‐dimensional images. Journal of Microscopy 185, 67–75. 10.1046/j.1365-2818.1997.1340694.x.