BoneJ2 - refactoring established research software

Domander, Richard; Felder, Alessandro; Doube, Michael

doi:10.12688/wellcomeopenres.16619.2

Cited by 65 publications

(57 citation statements)

References 15 publications

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“…Importantly, one of us (M.D.) previously developed an ImageJ plugin (BoneJ) with modules designed for analysis of bone geometry ( Domander et al, 2021 ). ImageJ’s ability to load and segment XMT data was the starting point we required.…”

Section: Resultsmentioning

confidence: 99%

A New Pipeline to Automatically Segment and Semi-Automatically Measure Bone Length on 3D Models Obtained by Computed Tomography

Diaz

H’ng

et al. 2021

Front. Cell Dev. Biol.

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The characterization of developmental phenotypes often relies on the accurate linear measurement of structures that are small and require laborious preparation. This is tedious and prone to errors, especially when repeated for the multiple replicates that are required for statistical analysis, or when multiple distinct structures have to be analyzed. To address this issue, we have developed a pipeline for characterization of long-bone length using X-ray microtomography (XMT) scans. The pipeline involves semi-automated algorithms for automatic thresholding and fast interactive isolation and 3D-model generation of the main limb bones, using either the open-source ImageJ plugin BoneJ or the commercial Mimics Innovation Suite package. The tests showed the appropriate combination of scanning conditions and analysis parameters yields fast and comparable length results, highly correlated with the measurements obtained via ex vivo skeletal preparations. Moreover, since XMT is not destructive, the samples can be used afterward for histology or other applications. Our new pipelines will help developmental biologists and evolutionary researchers to achieve fast, reproducible and non-destructive length measurement of bone samples from multiple animal species.

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Section: Resultsmentioning

confidence: 99%

A New Pipeline to Automatically Segment and Semi-Automatically Measure Bone Length on 3D Models Obtained by Computed Tomography

Diaz

H’ng

et al. 2021

Front. Cell Dev. Biol.

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“…Collagen cluster thickness was quantified by using “BoneJ” macro in ImageJ. In brief, BoneJ macro fits spheres along the collagen fibers after a threshold is applied to the image and calculates the thickness as the average largest circle that can fit within the fibers 57 , 58 . A thermal map for fibronectin was created by pseudo coloring the fluorescent confocal images with thermal lookup table (LUT) in ImageJ (Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

Hypoxia induces stress fiber formation in adipocytes in the early stage of obesity

Anvari

Bellas

2021

Sci Rep

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In obese adipose tissue (AT), hypertrophic expansion of adipocytes is not matched by new vessel formation, leading to AT hypoxia. As a result, hypoxia inducible factor-1⍺ (HIF-1⍺) accumulates in adipocytes inducing a transcriptional program that upregulates profibrotic genes and biosynthetic enzymes such as lysyl oxidase (LOX) synthesis. This excess synthesis and crosslinking of extracellular matrix (ECM) components cause AT fibrosis. Although fibrosis is a hallmark of obese AT, the role of fibroblasts, cells known to regulate fibrosis in other fibrosis-prone tissues, is not well studied. Here we have developed an in vitro model of AT to study adipocyte-fibroblast crosstalk in a hypoxic environment. Further, this in vitro model was used to investigate the effect of hypoxia on adipocyte mechanical properties via ras homolog gene family member A (RhoA)/Rho-associated coiled-coil kinases (ROCK) signaling pathways. We confirmed that hypoxia creates a diseased phenotype by inhibiting adipocyte maturation and inducing actin stress fiber formation facilitated by myocardin-related transcription factor A (MRTF-A/MKL1) nuclear translocation. This work presents new potential therapeutic targets for obesity by improving adipocyte maturation and limiting mechanical stress in obese AT.

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“…SegmentGeometry follows BoneJ in implementing second moment of area calculations around the major and minor principal axes, and a user-determined neutral axis ( Doube et al. 2009 , 2010; Domander et al. 2021 ).…”

Section: Segmentgeometrymentioning

confidence: 99%

“…The BoneJ plug-in for FIJI ( Doube et al. 2010 ; Domander et al. 2021 ) is the most commonly used, but more recently, morphomap was developed to perform many of the same functions in an R environment ( Profico et al.…”

Section: Introductionmentioning

confidence: 99%

SegmentGeometry: A Tool for Measuring Second Moment of Area in 3D Slicer

Huie

Summers

Kawano

2022

Integrative Organismal Biology

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Second moment of area is a measure of how well the cross-section of a beam will resist bending because of its shape. Many have used second moment of area to investigate the mechanical adaptations of biological structures from stingray jaws to animal limb bones. In this context it is important to acknowledge the assumptions of beam theory, in which second moment of area plays a key role, if reasonable results are desired. For example, to minimize shear the structure should be at least ten times longer than it is wide and deflection should be minimal. Analyzing the internal geometry of biological structures has never been easier or more accessible given the wide, and growing availability of micro-CT scans. Here, we offer a guide on the care that needs to be taken when interpreting second moment of area, and present open-access, open-source software that can process hundreds if not thousands of structures in a short time frame. SegmentGeometry, an extension for the open-source imaging platform 3D Slicer, iterates slice-by-slice through 3D structures calculating second moment of area and other cross-sectional properties. We analyzed two case studies to demonstrate the power of this tool and to highlight interpretations that can be gleaned from second moment of area. Second moment of area is just one part of the Euler-Bernoulli beam theory and considering the full equation would greatly increase the number and diversity of questions that can be answered.

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BoneJ2 - refactoring established research software

Cited by 65 publications

References 15 publications

A New Pipeline to Automatically Segment and Semi-Automatically Measure Bone Length on 3D Models Obtained by Computed Tomography

A New Pipeline to Automatically Segment and Semi-Automatically Measure Bone Length on 3D Models Obtained by Computed Tomography

Hypoxia induces stress fiber formation in adipocytes in the early stage of obesity

SegmentGeometry: A Tool for Measuring Second Moment of Area in 3D Slicer

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