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BoneJ specifications


Unique identifier OMICS_13884
Name BoneJ
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 1.4.2
Stability Stable
ImageJ, 3D viewer, JRE
Maintained Yes




No version available


Publication for BoneJ

BoneJ citations


Trabecular architecture in the sciuromorph femoral head: allometry and functional adaptation

PMCID: 5954450
PMID: 29785282
DOI: 10.1186/s40851-018-0093-z

[…] Analysis of CT-scan data was done using the Fiji contribution of ImageJ vers. 1.51k [, ] and the plugin BoneJ vers. 1.4.2 []. An analysis Java script (Additional file ) was composed and applied to all specimens. Prior to the analysis, each femur was oriented within the stack coordinate system using the […]


Alterations in Cell Motility, Proliferation, and Metabolism in Novel Models of Acquired Temozolomide Resistant Glioblastoma

Sci Rep
PMCID: 5940876
PMID: 29740146
DOI: 10.1038/s41598-018-25588-1

[…] FIJI (ImageJ) was used to measure the thickness of F-actin fibers. Grayscale images of phalloidin-stained cells were converted to binary using the Threshold tool (black/white). The BoneJ plugin was then used to measure fiber thickness in pixels. The mean thickness per cell is reported for 28-29 individual cells per cell line. […]


Mechanical adaptation of trabecular bone morphology in the mammalian mandible

Sci Rep
PMCID: 5940912
PMID: 29740057
DOI: 10.1038/s41598-018-25597-0
call_split See protocol

[…] ne teeth.Figure 5Each VOI was exported as a stack of TIFF images and imported into ImageJ v1.48, (National Institute of Health, USA), where a histomorphometric analysis was performed using the plugin BoneJ to measure the parameters of BV/TV, Tb.Th and Tb.Sp.Non-parametric Mann-Whitney analyses demonstrated that there were rarely significant differences in the histomorphometric parameters between t […]


VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function

Biochim Biophys Acta
PMCID: 5906731
PMID: 29409756
DOI: 10.1016/j.bbadis.2018.01.028

[…] th, London, UK. Hematoxylin and eosin (H&E) and picrosirius red stains were imaged on a Zeiss Axioplan2 microscope with a Zeiss AxioCam HRc colour camera. Epidermal thickness was calculated using the BoneJ ImageJ plugin []. The number of cells was counted using the ImageJ Cell Counter plugin and reported per 100 μm of the dermal-epidermal junction. Keratinocyte size was calculated as total epiderm […]


Alcohol exposure decreases osteopontin expression during fracture healing and osteopontin mediated mesenchymal stem cell migration in vitro

PMCID: 5921778
PMID: 29699560
DOI: 10.1186/s13018-018-0800-7

[…] and soft tissue was defined as the remaining tissue within the ROI less than 0.0000619 on the image histogram. These thresholds were applied to each sample, and the volumes were calculated using the BoneJ plugin [] for ImageJ. In addition to the volume, the polar moment of inertia (Ipol) was calculated using the slice geometry function in BoneJ. Ipol values were averaged over the 71 sections as p […]


Transient peak strain matching partially recovers the age impaired mechanoadaptive cortical bone response

Sci Rep
PMCID: 5924380
PMID: 29703931
DOI: 10.1038/s41598-018-25084-6
call_split See protocol

[…] Whole bone analysis was performed using BoneJ (version 1.4.0, an ImageJ plugin). Following segmentation, alignment and fibula removal from the dataset, a minimum threshold was used in “Slice Geometry” (BoneJ). The main characteristics of bo […]


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BoneJ institution(s)
Department of Bioengineering, Imperial College London, South Kensington, London, UK; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut Curie, Section de Recherche, Plate-forme d’Imagerie Cellualire et Tissulaire, CNRS UMR 3348, Centre Universitaire, Orsay, France; OptiNav Inc., Redmond, WA, USA; Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Department of Neurobiology and Genetics, University of Würzberg, Germany; Structure and Motion Laboratory, The Royal Veterinary College, North Mymms, Hatfield, Hertfordshire, UK
BoneJ funding source(s)
This work was partly funded by the UK Biotechnology and Biological Sciences Research Council.

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