Utility Plugins

Erode 3D and Dilate 3D

These plugins by Benjamin Schmid are included in BoneJ because we found they were a very useful along with Purify when filtering topological noise prior to running Connectivity. See the official documentation for full details. They are found under Plugins>Process.

Delete Slice Range

This small utility quickly removes a range of slices from a stack, so that cropping in the Z direction is practical. It is found under Plugins > Stacks.

Check Voxel Depth

Check whether ImageJ has calibrated the slice spacing correctly. Some DICOM images contain slice thickness data in the header information, but thickness is not necessarily the same as the physical distance between consecutive slices' positions. It is found under Plugins > Stacks.

Stratec pQCT

This file reader by Timo Rantalainen was provided to open Stratec pQCT images for analysis with the Density Distribution plugin. It is found under File>Import>Stratec pQCT. If you use it, please cite the paper:

Rantalainen T, Nikander R, Heinonen A, Daly RM, Sievanen H. An open source approach for regional cortical bone mineral density analysis. J. Musculoskelet. Neuronal Interact. 2011 Sep;11(3):243-8.

Scanco ISQ

This file reader by Karl-Heinz Kunzelmann allows opens the ISQ file format generated by Scanco X-ray microtomography scanners. Is is found under File > Import. Drag-n-drop support is handled natively by Fiji and in ImageJ after installing Handle Extra File Types.

Interpolate ROIs

A common segmentation approach is to draw ROIs on every slice in a stack, which put together define a 3D ROI. Interpolate ROIs (Plugins > Stacks > Interpolate ROIs) uses the signed integer transform to interpolate between ROIs. Useage is as follows:

  1. Draw an ROI on your stack
  2. Add it to the ROI manager with [t]
  3. Advance a few slices (depends on the detail in the image)
  4. Repeat steps 1-3
  5. Run Interpolate ROIs to get ROIs added to the ROI Manager for every slice

Please note that Interpolate ROIs uses only the ROI shape and not the underlying image information to generate the interpolated series.

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