Technical specifications

This is the main page of the technical specification for BoneJ2 - a collection of plugins for Fiji/ImageJ2. Most of the project's code reimplement functionality from BoneJ1. However the code has been heavily refactored to improve quality among other things. A lot of it has been moved away from the BoneJ packages to other components such as net.imagej.ops and org.scijava.

Plug-ins in BoneJ2

This list details the status of the legacy plug-ins in the new BoneJ2. Compare with list at bonej.org. Missing entries have not been implemented yet. Entries link to individual technical documentation.

Analyse skeleton

Anisotropy

Connectivity

Density distribution

• All pQCT related tools have been moved to Fiji/PQCT. They have their own update site, and can be installed without BoneJ.

Dilate

• Dilate command already present in ImageJ2, no implementation needed

Element fraction

• Re-implemented from Volume Fraction

Erode

• Erode command already present in ImageJ2, no implementation needed

Fit ellipsoid

Fractal dimension

Help

• Won't implement. Modern ImageJ has a search bar that finds help from wiki.imagej.net and forum.imagej.net. Documentation will move there.

Interpolate ROIs

• Won't implement. Not relevant any more.

Inter-trabecular angles

• Replaces Triple point angles. Isn't limited to just triple points, but user adjustable n--m -points.

Kontron IMG

• The BoneJ1 plugin that offered support for the Kontron IMG files has been reimplemented as a part of SCIFIO
• Works in ImageJ "out-of-the-box" when SCIFIO is enabled
• Supports arbitrarily large images
• Can open images by dragging and dropping
• Location io.scif.formats

Neck shaft angle

• Won't implement. Not relevant anymore.

Scanco ISQ

• The BoneJ1 plugin that offered support for the Scanco ISQ files has been reimplemented as a part of SCIFIO
• Works in ImageJ "out-of-the-box" when SCIFIO is enabled
• Supports arbitrarily large images
• Can open images by dragging and dropping
• Location io.scif.formats

Shared table

• A results table shared by the (modern) BoneJ plug-ins.

Skeletonise

Stratec pQCT

• The BoneJ1 plugin that offered support for the Stratec pQCT files has been reimplemented as a part of SCIFIO
• Works in ImageJ "out-of-the-box" when SCIFIO is enabled
• Supports arbitrarily large images
• Can open images by dragging and dropping
• When using legacy UI, doesn't work with ij-1.50e.jar or older. Tested successfully with ij-1.51g.jar.
• Location io.scif.formats
• Without SCIFIO, use Read Stratec File from Fiji/PQCT

Structural model index

• Won't implement. Will be replaced by modern Ellipsoid factor.

Surface area

• Re-implemented from Isosurface

Surface fraction

• Re-implemented from Volume Fraction

Thickness