The user can chooseīetween mesh-based (Hildebrand & Rüegsegger method, preferred) and voxel-based (SkyScan) structure dilation. Structure Model Index Calculates the structure model index (SMI), a measure of how rod- or plate-like trabeculae are. Skeletonise 3D Find the skeleton of a structure using a topology-maintaining medial axis thinning algorithm implemented by Ignacio Arganda Carreras. Purify Prepares an image for connectivity analysis. Isosurface Creates and optionally displays a 3D surface mesh and measures the surface area, to calculate bone surface (BS). Fractal Count Uses the box counting method to calculate fractal dimension. Ellipsoid Factor Fits ellipsoids within the structure's geometry and computes a local Ellipsoid Factor classification basd on ellipsoid aspect ratios. Connectivity Calculates the Euler characteristic of an image, and works out the connectivity density (Conn.D), which can be interpreted as trabecular number per mm 3. Anisotropy Use the mean intercept length (MIL) method to determine degree of anisotropy. Based on Ignacio Arganda Carreras' AnalyzeSkeleton_. To run ImageJ 3D Viewer, which will prompt you to install Java's 3D libraries if you don't already have them.īoneJ1 was downloaded 50,932 times between March 2010 and May 2020, and its final version was 1.4.3 (8 August 2018).įor Trabeculae Analyse Skeleton Classify, count and measure skeleton branches and junctions. Installation is the same as for BoneJ drag the link to the. There is one important dependency - Benjamin Schmid's 3D Viewer. In your ImageJ/plugins directory and refresh ImageJ's plugins with Help->Refresh Menus. To install BoneJ, make sure you have a recent version of ImageJ and drag this link to BoneJ_.jar onto ImageJ, or save it Legacy versions of BoneJ 1.x and its documentation will remain available here for reproducibility purposes The green OA author manuscript is available here.Īll users are encouraged to switch to BoneJ2, available from the ImageJ2 updater. > BoneJ) and ImageJ (Help > About ImageJ) because these represent defined states of the programs, which can be looked up and examined thanks to Git tagging. Remember to list the version numbers of BoneJ (Help > About Plugins. (2010) BoneJ: free and extensible bone image analysis in ImageJ. If you use BoneJ in your work, please cite:ĭoube M, Kłosowski MM, Arganda-Carreras I, Cordeliéres F, Dougherty RP, Jackson J, Schmid B, Hutchinson JR, Shefelbine SJ. So, in the spirit of public openness, BoneJ is available to all our funders.
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