A novel approach for computing 3D mice distal femur properties using high-resolution micro-computed tomography scanning

Mehadji, Brahim; Ahmed, Yoseph; Berteau, Jean-Philippe

doi:10.1016/j.micron.2019.02.011

Cited by 7 publications

(5 citation statements)

References 29 publications

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“…Micro‐computed tomography (µCT) has been widely used to characterize 3D morphology at the micron level, including CC (Kerckhofs et al, 2012 ; Mehadji et al, 2019 ). In contrast to histology and SEM, only minimal sample processing is required in µCT.…”

Section: Introductionmentioning

confidence: 99%

Automated analysis of rabbit knee calcified cartilage morphology using micro‐computed tomography and deep learning

et al. 2021

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Section: Introductionmentioning

confidence: 99%

Automated analysis of rabbit knee calcified cartilage morphology using micro‐computed tomography and deep learning

et al. 2021

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“…There are a wide range of software solutions that can analyze XMT data in the form of digital imaging communications in medicine (DICOM) files to segment a variety of high-contrast tissues like lungs ( Weissheimer et al, 2012 ; Reynisson et al, 2015 ), liver ( Okada et al, 2008 ; Huhdanpaa et al, 2011 ) and bone ( Rios et al, 2014 ; Mehadji et al, 2019 ; Taghizadeh et al, 2019 ). After some pilot testing of both open-source and commercial solutions, we settled on the Mimics Innovation Suite (Materialize, Leuven, Belgium) as the one that most readily suited our needs.…”

Section: Introductionmentioning

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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“…There are a wide range of software solutions that can analyse XMT data in the form of digital imaging communications in medicine (DICOM) files to segment a variety of high-contrast tissues like lungs (Reynisson et al, 2015;Weissheimer et al, 2012), liver (Huhdanpaa et al, 2011;Okada et al, 2008) and bone (Mehadji et al, 2019;Rios et al, 2014;Taghizadeh et al, 2019). After some pilot testing of both opensource and commercial solutions, we settled on the Mimics Innovation Suite (Materialise, Leuven, Belgium) as the one that most readily suited our needs.…”

Section: Introductionmentioning

confidence: 99%

A new pipeline to automatically segment and semi-automatically measure bone length on 3D models obtained by Computed Tomography

Diaz

Fung

et al. 2020

Preprint

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statement: Beltran Diaz et al. present a semi-automated pipeline for fast and versatile characterization of bone length from micro-CT images of mouse developmental samples. Abstract: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 analysed. To address this issue, we have developed a pipeline for characterization of long-bone length using micro-CT scans. It involves a semi-automated algorithm that uses the Mimics Innovation Suite package (Materialise) for automatic thresholding and fast interactive isolation and 3D-model generation of the main limb bones. All the image-processing steps are included in a user-friendly Python script. We show that the appropriate combination of scanning and in silico analysis conditions yields fast and reproducible length results, highly correlated with the measurements obtained via ex vivo skeletal preparations. Moreover, since micro-CT is not destructive, the samples can be used afterwards for histology or other applications. Our new pipeline will help developmental biologists and evolution researchers to achieve fast, reproducible and non-destructive length measurement of bone samples from multiple animal species.

show abstract

A novel approach for computing 3D mice distal femur properties using high-resolution micro-computed tomography scanning

Cited by 7 publications

References 29 publications

Automated analysis of rabbit knee calcified cartilage morphology using micro‐computed tomography and deep learning

Automated analysis of rabbit knee calcified cartilage morphology using micro‐computed tomography and deep learning

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

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