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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.

The generation of small-caliber vascular grafts remains a significant challenge within the field of tissue engineering. In pursuit of this objective, fibrin has emerged as a promising scaffold material. However, its lack of biomechanical strength has limited its utility in the construction of tissue engineered vascular grafts. We have previously reported about the implementation of centrifugal casting molding to generate compacted fibrin tubes with a highly increased biomechanical strength. In this study, we conducted a structural analysis of compacted fibrin tubes using the open-source software Fiji/BoneJ. The primary aim was to validate the hypothesis that the compaction of fibrin leads to a more complex structure characterized by increased crosslinking of fibrin fibers. Structural analysis revealed a strong correlation between fibrin's structure and its biomechanical strength. Moreover, we enhanced fibrin compaction in a subsequent dehydration process, leading to a significant increase of biomechanical strength. Thus, the presented method in combination with an adequate imaging, e.g., micro-CT, has substantial potential as a powerful tool for quality assurance in the development of fibrin-based vascular grafts. To validate this concept, acellular highly compacted fibrin tubes were implanted as substitutes of a segment of the carotid artery in a sheep model (n = 4). After 6 months explanted segments exhibited distinct remodeling, transitioning into newly formed arteries. [Display omitted] • Rotational molding leads to a significant compaction of fibrin. • Compaction of fibrin results in a significantly more complex and crosslinked fibrin structure. • Further dehydration improves fibrin's structure and biomechanical strength. [ABSTRACT FROM AUTHOR]

Bone histomorphometry allows quantitative evaluation of bone micro-architecture, bone formation, and bone remodeling by providing an insight to cellular changes. Histomorphometry plays an important role in monitoring changes in bone properties because of systemic skeletal diseases like osteoporosis and osteomalacia. Besides, quantitative evaluation plays an important role in fracture healing studies to explore the effect of biomaterial or drug treatment. However, until today, to our knowledge, bone histomorphometry remain time-consuming and expensive. This incited us to set up an open-source freely available semi-automated solution to measure parameters like trabecular area, osteoid area, trabecular thickness, and osteoclast activity. Here in this study, the authors present the adaptation of Trainable Weka Segmentation plugin of ImageJ to allow fast evaluation of bone parameters (trabecular area, osteoid area) to diagnose bone related diseases. Also, ImageJ toolbox and plugins (BoneJ) were adapted to measure osteoclast activity, trabecular thickness, and trabecular separation. The optimized two different scripts are based on ImageJ, by providing simple user-interface and easy accessibility for biologists and clinicians. The scripts developed for bone histomorphometry can be optimized globally for other histological samples. The showed scripts will benefit the scientific community in histological evaluation.

Bone histomorphometry allows quantitative evaluation of bone micro-architecture, bone formation, and bone remodeling by providing an insight to cellular changes. Histomorphometry plays an important role in monitoring changes in bone properties because of systemic skeletal diseases like osteoporosis and osteomalacia. Besides, quantitative evaluation plays an important role in fracture healing studies to explore the effect of biomaterial or drug treatment. However, until today, to our knowledge, bone histomorphometry remain time-consuming and expensive. This incited us to set up an open-source freely available semi-automated solution to measure parameters like trabecular area, osteoid area, trabecular thickness, and osteoclast activity. Here in this study, the authors present the adaptation of Trainable Weka Segmentation plugin of ImageJ to allow fast evaluation of bone parameters (trabecular area, osteoid area) to diagnose bone related diseases. Also, ImageJ toolbox and plugins (BoneJ) were adapted to measure osteoclast activity, trabecular thickness, and trabecular separation. The optimized two different scripts are based on ImageJ, by providing simple user-interface and easy accessibility for biologists and clinicians. The scripts developed for bone histomorphometry can be optimized globally for other histological samples. The showed scripts will benefit the scientific community in histological evaluation. [ABSTRACT FROM AUTHOR]

Peripheral quantitative computed tomography (pQCT) imaging has been used to quantify muscle area and density as well as intermuscular adipose tissue (IMAT) and subcutaneous adipose tissue (SAT) area in the lower and upper limb. Numerous protocols have been reported to derive these soft-tissue outcomes, but their precision has not been assessed in community-dwelling postmenopausal women. The objective of this study was to compare the precision of previously reported analysis protocols for quantifying muscle area and density, as well as IMAT and SAT area in postmenopausal women. Six image analysis protocols using two available software suites (Stratec XCT, BoneJ) were identified from the pQCT literature. Analysis protocols were applied to a sample of 35 older female adults (mean age 73.7; SD 7.2 years), randomly selected from a population based-cohort and scanned twice within an average of 9.7 (SD 3.6) days. Relative precision was calculated as absolute values and as a percentage of the sample mean (root mean square coefficient of variation; CV% RMS ). Soft-tissue outcomes across protocols were compared on their log-transformed coefficients of variation using multilevel linear models and Tukey contrasts. For most protocols, CV% RMS for muscle area, density, and SAT area ranged between 2.1 and 3.7%, 0.7 and 1.9%, and 2.4 and 6.4%, respectively. Precision for IMAT area varied considerably, from 3 to 42%. Consideration of these study results will aid in the selection of appropriate image analysis protocols for pQCT-derived soft-tissue outcomes in postmenopausal women. [ABSTRACT FROM AUTHOR]

Research software is often developed with expedience as a core development objective because experimental results, but not the software, are specified and resourced as a project output. While such code can help find answers to specific research questions, it may lack longevity and flexibility to make it reusable. We reimplemented BoneJ, our software for skeletal biology image analysis, to address design limitations that put it at risk of becoming unusable. We improved the quality of BoneJ code by following contemporary best programming practices. These include separation of concerns, dependency management, thorough testing, continuous integration and deployment, source code management, code reviews, issue and task ticketing, and user and developer documentation. The resulting BoneJ2 represents a generational shift in development technology and integrates with the ImageJ2 plugin ecosystem., Competing Interests: No competing interests were disclosed., (Copyright: © 2021 Domander R et al.)