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

2020 ◽  
Author(s):  
Santiago Beltran Diaz ◽  
Xinli Qu ◽  
Sarah Fung ◽  
Michael de Veer ◽  
Olga Panagiotopoulou ◽  
...  
Keyword(s):  
Ex Vivo ◽  
3D Models ◽  
Linear Measurement ◽  
Long Bone ◽  
Micro Ct ◽  
Bone Length ◽  
Automated Algorithm ◽  
Highly Correlated ◽  
User Friendly

AbstractThe 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.Summary statementBeltran Diaz et al. present a semi-automated pipeline for fast and versatile characterization of bone length from micro-CT images of mouse developmental samples.

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

2021 ◽  
Vol 9 ◽  
Author(s):  
Santiago Beltran Diaz ◽  
Chee Ho H’ng ◽  
Xinli Qu ◽  
Michael Doube ◽  
John Tan Nguyen ◽  
...  
Keyword(s):  
Ex Vivo ◽  
3D Models ◽  
Linear Measurement ◽  
Long Bone ◽  
Bone Length ◽  
Highly Correlated ◽  
Automated Algorithms ◽  
Non Destructive ◽  
Imagej Plugin

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.

scholarly journals Ex vivo characterization of articular cartilage and bone lesions in a rabbit ACL transection model of osteoarthritis using MRI and micro-CT

2004 ◽  
Vol 12 (12) ◽  
pp. 986-996 ◽  
Author(s):  
Danika L. Batiste ◽  
Alexandra Kirkley ◽  
Sheila Laverty ◽  
Lisa M.F. Thain ◽  
Alison R. Spouge ◽  
...  
Keyword(s):  
Articular Cartilage ◽  
Ex Vivo ◽  
Bone Lesions ◽  
Micro Ct ◽  
Acl Transection

scholarly journals Ten Years of Micro-CT in Dentistry and Maxillofacial Surgery: A Literature Overview

2020 ◽  
Vol 10 (12) ◽  
pp. 4328 ◽  
Author(s):  
Ilaria Campioni ◽  
Raffaella Pecci ◽  
Rossella Bedini
Keyword(s):  
Bone Structure ◽  
Ex Vivo ◽  
Maxillofacial Surgery ◽  
Three Dimensional ◽  
3D Models ◽  
Micro Ct ◽  
Micro Computed Tomography ◽  
Scientific Publications ◽  
Ct Analysis

Micro-computed tomography (micro-CT) is a consolidated imaging technology allowing non-destructive three-dimensional (3D) qualitative and quantitative analysis by the observation of microstructures with high resolution. This paper aims at delivering a structured overview of literature about studies performed using micro-CT in dentistry and maxillofacial surgery (MFS) by analyzing the entire set of articles to portray the state of the art of the last ten years of scientific publications on the topic. It draws the scenario focusing on biomaterials, in vitro and in/ex vivo applications, bone structure analysis, and tissue engineering. It confirms the relevance of the micro-CT analysis for traditional research applications and mainly in dentistry with respect to MFS. Possible developments are discussed in relation to the use of the micro-CT combined with other, traditional, and not, techniques and technologies, as the elaboration of 3D models based on micro-CT images and emerging numerical methods. Micro-CT results contribute effectively with whose ones obtained from other techniques in an integrated multimethod approach and for multidisciplinary studies, opening new possibilities and potential opportunities for the next decades of developments.

Efficacy of single-source rapid kV-switching dual-energy CT for characterization of non-uric acid renal stones: a prospective ex vivo study using anthropomorphic phantom

2019 ◽  
Vol 45 (4) ◽  
pp. 1092-1099
Author(s):  
Roberto Cannella ◽  
Mohammed Shahait ◽  
Alessandro Furlan ◽  
Feng Zhang ◽  
Joel D. Bigley ◽  
...  
Keyword(s):  
Uric Acid ◽  
Ex Vivo ◽  
Renal Stones ◽  
Dual Energy ◽  
Dual Energy Ct ◽  
Single Source ◽  
Anthropomorphic Phantom ◽  
Ex Vivo Study

scholarly journals Morpho-molecular ex vivo detection and grading of non-muscle-invasive bladder cancer using forward imaging probe based multimodal optical coherence tomography and Raman spectroscopy

The Analyst ◽  
2020 ◽  
Vol 145 (4) ◽  
pp. 1445-1456 ◽  
Author(s):  
Fabian Placzek ◽  
Eliana Cordero Bautista ◽  
Simon Kretschmer ◽  
Lara M. Wurster ◽  
Florian Knorr ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Optical Coherence Tomography ◽  
Imaging System ◽  
Ex Vivo ◽  
Large Field ◽  
Optical Coherence ◽  
Fiber Optic Probe ◽  
Optic Probe ◽  
Muscle Invasive

Characterization of bladder biopsies, using a combined fiber optic probe-based optical coherence tomography and Raman spectroscopy imaging system that allows a large field-of-view imaging and detection and grading of cancerous bladder lesions.

scholarly journals Consequences of SUR2[A478V] Mutation in Skeletal Muscle of Murine Model of Cantu Syndrome

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1791
Author(s):  
Rosa Scala ◽  
Fatima Maqoud ◽  
Nicola Zizzo ◽  
Giuseppe Passantino ◽  
Antonietta Mele ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Katp Channel ◽  
Ex Vivo ◽  
Channel Modulation ◽  
Flexor Digitorum Brevis ◽  
Inflammatory Edema ◽  
Flexor Digitorum ◽  
Channel Currents

(1) Background: Cantu syndrome (CS) arises from gain-of-function (GOF) mutations in the ABCC9 and KCNJ8 genes, which encode ATP-sensitive K+ (KATP) channel subunits SUR2 and Kir6.1, respectively. Most CS patients have mutations in SUR2, the major component of skeletal muscle KATP, but the consequences of SUR2 GOF in skeletal muscle are unknown. (2) Methods: We performed in vivo and ex vivo characterization of skeletal muscle in heterozygous SUR2[A478V] (SUR2wt/AV) and homozygous SUR2[A478V] (SUR2AV/AV) CS mice. (3) Results: In SUR2wt/AV and SUR2AV/AV mice, forelimb strength and diaphragm amplitude movement were reduced; muscle echodensity was enhanced. KATP channel currents recorded in Flexor digitorum brevis fibers showed reduced MgATP-sensitivity in SUR2wt/AV, dramatically so in SUR2AV/AV mice; IC50 for MgATP inhibition of KATP currents were 1.9 ± 0.5 × 10−5 M in SUR2wt/AV and 8.6 ± 0.4 × 10−6 M in WT mice and was not measurable in SUR2AV/AV. A slight rightward shift of sensitivity to inhibition by glibenclamide was detected in SUR2AV/AV mice. Histopathological and qPCR analysis revealed atrophy of soleus and tibialis anterior muscles and up-regulation of atrogin-1 and MuRF1 mRNA in CS mice. (4) Conclusions: SUR2[A478V] “knock-in” mutation in mice impairs KATP channel modulation by MgATP, markedly so in SUR2AV/AV, with atrophy and non-inflammatory edema in different skeletal muscle phenotypes.

scholarly journals Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1338
Author(s):  
Morgan E. Meissner ◽  
Emily J. Julik ◽  
Jonathan P. Badalamenti ◽  
William G. Arndt ◽  
Lauren J. Mills ◽  
...  
Keyword(s):  
Error Rates ◽  
Maximum Depth ◽  
Sequencing Data ◽  
Background Error ◽  
High Background ◽  
Immunodeficiency Virus ◽  
User Friendly ◽  
Viral Mutagenesis ◽  
Hiv 1

Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

scholarly journals Design of a force-measuring setup for colorectal compression anastomosis and first ex-vivo results

2021 ◽  
Author(s):  
Jana Steger ◽  
Isabella Patzke ◽  
Maximilian Berlet ◽  
Stefanie Ficht ◽  
Markus Eblenkamp ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Tissue Fixation ◽  
Force Transmission ◽  
Tissue Thickness ◽  
Colon Tissue ◽  
Device Development ◽  
Compression Anastomosis ◽  
Technical Requirements ◽  
Significant Difference

Abstract Purpose The introduction of novel endoscopic instruments is essential to reduce trauma in visceral surgery. However, endoscopic device development is hampered by challenges in respecting the dimensional restrictions, due to the narrow access route, and by achieving adequate force transmission. As the overall goal of our research is the development of a patient adaptable, endoscopic anastomosis manipulator, biomechanical and size-related characterization of gastrointestinal organs are needed to determine technical requirements and thresholds to define functional design and load-compatible dimensioning of devices. Methods We built an experimental setup to measure colon tissue compression piercing forces. We tested 54 parameter sets, including variations of three tissue fixation configurations, three piercing body configurations (four, eight, twelve spikes) and insertion trajectories of constant velocities (5 mms−1, 10 mms−1,15 mms−1) and constant accelerations (5 mms−2, 10 mms−2, 15 mms−2) each in 5 samples. Furthermore, anatomical parameters (lumen diameter, tissue thickness) were recorded. Results There was no statistically significant difference in insertion forces neither between the trajectory groups, nor for variation of tissue fixation configurations. However, we observed a statistically significant increase in insertion forces for increasing number of spikes. The maximum mean peak forces for four, eight and twelve spikes were 6.4 ± 1.5 N, 13.6 ± 1.4 N and 21.7 ± 5.8 N, respectively. The 5th percentile of specimen lumen diameters and pierced tissue thickness were 24.1 mm and 2.8 mm, and the 95th percentiles 40.1 mm and 4.8 mm, respectively. Conclusion The setup enabled reliable biomechanical characterization of colon material, on the base of which design specifications for an endoscopic anastomosis device were derived. The axial implant closure unit must enable axial force transmission of at least 28 N (22 ± 6 N). Implant and applicator diameters must cover a range between 24 and 40 mm, and the implant gap, compressing anastomosed tissue, between 2 and 5 mm.

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