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BoneJ specifications

Information


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
Requirements
ImageJ, 3D viewer, JRE
Maintained Yes

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Publication for BoneJ

BoneJ in pipeline

2016
PMCID: 5087619
PMID: 27578784
DOI: 10.1242/dev.134098

[…] with chimera from ucsf (). raw data movies of gaudílxbbw were rendered with vaa3d (). quantification of clone size was conducted by thresholding for nuclei and measuring clone volume with the bonej command ‘particle analyser’ (). this clone size was divided by a standard size of cell nuclei found in the data (4.4 µm³) and rounded down to next full number. subsequently, clones consisting […]


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BoneJ in publications

 (97)
PMCID: 5940876
PMID: 29740146
DOI: 10.1038/s41598-018-25588-1

[…] being at 0 hr., 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., 8mgba-wt and 8mgba-tmzres cells were seeded […]

PMCID: 5940912
PMID: 29740057
DOI: 10.1038/s41598-018-25597-0

[…] teeth.figure 5, each 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 […]

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

[…] tip, held at 90° to the well surface. an evos xl core widefield light microscope (life technologies) was used to image the scratch at 0, 16 and 24 h. the area of the scratch was quantified using the bonej imagej plugin []., primary murine keratinocytes or fibroblasts at 1 × 105 cells/ml were seeded into tissue cultured treated dishes, fixed after 1 h and stained with alexa-labelled wheat germ […]

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 […]

PMCID: 5924380
PMID: 29703931
DOI: 10.1038/s41598-018-25084-6

[…] for analysis of proximal tibia metaphyseal trabecular bone; 5% of total bone length from this point (towards diaphysis) was utilised for trabecular analysis., 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 […]


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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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