Project description:The gold-standard of preclinical micro-computed tomography (μCT) data processing is still manual delineation of complete organs or regions by specialists. However, this method is time-consuming, error-prone, has limited reproducibility, and therefore is not suitable for large-scale data analysis. Unfortunately, robust and accurate automated whole body segmentation algorithms are still missing. In this publication, we introduce a database containing 225 murine 3D whole body μCT scans along with manual organ segmentation of most important organs including heart, liver, lung, trachea, spleen, kidneys, stomach, intestine, bladder, thigh muscle, bone, as well as subcutaneous tumors. The database includes native and contrast-enhanced, regarding spleen and liver, μCT data. All scans along with organ segmentation are freely accessible at the online repository Figshare. We encourage researchers to reuse the provided data to evaluate and improve methods and algorithms for accurate automated organ segmentation which may reduce manual segmentation effort, increase reproducibility, and even reduce the number of required laboratory animals by reducing a source of variability and having access to a reliable reference group.
Project description:The oviduct plays a crucial role in the reproductive process, serving as the stage for fertilization and the early stages of embryonic development. When the environment of this organ has been mimicked, it has been shown to enhance in vitro embryo epigenetic reprogramming and to improve the yield of the system. This study explores the anatomical intricacies of two oviduct regions, the uterotubal junction (UTJ) and the ampullary-isthmic junction (AIJ) by using micro-computed tomography (MicroCT). In this study, we have characterized and 3D-reconstructed the oviduct structure, by measuring height and width of the oviduct's folds, along with the assessments of fractal dimension, lacunarity and shape factor. Results indicate distinct structural features in UTJ and AIJ, with UTJ displaying small, uniformly distributed folds and high lacunarity, while AIJ shows larger folds with lower lacunarity. Fractal dimension analysis reveals values for UTJ within 1.189-1.1779, while AIJ values range from 1.559-1.770, indicating differences in structural complexity between these regions. Additionally, blind sacs or crypts are observed, akin to those found in various species, suggesting potential roles in sperm sequestration or reservoir formation. These morphological differences align with functional variations and are essential for developing an accurate 3D model. In conclusion, this research provides information about the oviduct anatomy, leveraging MicroCT technology for detailed 3D reconstructions, which can significantly contribute to the understanding of geometric-morphological characteristics influencing functional traits, providing a foundation for a biomimetic oviduct-on-a-chip.
Project description:ObjectiveHistopathological grading of osteochondral (OC) tissue is widely used in osteoarthritis (OA) research, and it is relatively common in post-surgery in vitro diagnostics. However, relying on thin tissue section, this approach includes a number of limitations, such as: (1) destructiveness, (2) sample processing artefacts, (3) 2D section does not represent spatial 3D structure and composition of the tissue, and (4) the final outcome is subjective. To overcome these limitations, we recently developed a contrast-enhanced μCT (CEμCT) imaging technique to visualize the collagenous extracellular matrix (ECM) of articular cartilage (AC). In the present study, we demonstrate that histopathological scoring of OC tissue from CEμCT is feasible. Moreover, we establish a new, semi-quantitative OA μCT grading system for OC tissue.ResultsPathological features were clearly visualized in AC and subchondral bone (SB) with μCT and verified with histology, as demonstrated with image atlases. Comparison of histopathological grades (OARSI or severity (0-3)) across the characterization approaches, CEμCT and histology, excellent (0.92, 95% CI = [0.84, 0.96], n = 30) or fair (0.50, 95% CI = [0.16, 0.74], n = 27) intra-class correlations (ICC), respectively. A new μCT grading system was successfully established which achieved an excellent cross-method (μCT vs histology) reader-to-reader intra-class correlation (0.78, 95% CI = [0.58, 0.89], n = 27).ConclusionsWe demonstrated that histopathological information relevant to OA can reliably be obtained from CEμCT images. This new grading system could be used as a reference for 3D imaging and analysis techniques intended for volumetric evaluation of OA pathology in research and clinical applications.
Project description:Geometric morphometrics (GMM) is an advanced morphometric method enabling quantitative analysis of shape and size variations in biological structures. Through high-resolution imaging and mathematical algorithms, GMM provides valuable insights into taxonomy, ecology, and evolution, making it increasingly relevant in plant science. This review synthesizes the existing literature and explores methodological details, research questions, and future directions, establishing a strong foundation for further study in plant biology. Following PRISMA 2020 guidelines, a rigorous literature search finally identified 83 studies for review. The review organized data on plant species, organs studied, GMM objectives, and methodological aspects, such as imaging and landmark positioning. Leaf and flower structures emerged as the most frequently analyzed organs, primarily in studies of shape variations. This review assesses the use of GMM in plant sciences, identifying knowledge gaps and inconsistencies, and suggesting areas for future research. By highlighting unaddressed topics and emerging trends, the review aims to guide researchers towards methodological challenges and innovations necessary for advancing the field.
Project description:The use of animal models of arthritis is a key component in the evaluation of therapeutic strategies against the human disease rheumatoid arthritis (RA). Here we present quantitative measurements of bone degradation characterised by the cortical bone profile using glucose-6-phosphate isomerase (G6PI) induced arthritis. We applied micro-computed tomography (μCT) during three arthritis experiments and one control experiment to image the metatarsals of the hind paws and to investigate the effect of experimental arthritis on their cortical bone profile. For measurements of the cortical profile we automatically identified slices that are orthogonal to individual metatarsals, thereby making the measurements independent of animal placement in the scanner. We measured the average cortical thickness index (CTI) of the metatarsals, as well as the thickness changes along the metatarsal. In this study we introduced the cortical thickness gradient (CTG) as a new measure and we investigated how arthritis affects this measure. We found that in general both CTI and CTG are able to quantify arthritic progression, whilst CTG was found to be the more sensitive measure.
Project description:Historically, micro-computed tomography (μCT) has been considered unsuitable for histologic analysis of unstained formalin-fixed, paraffin-embedded soft tissue biopsy specimens because of a lack of image contrast between the tissue and the paraffin. However, we recently demonstrated that μCT can successfully resolve microstructural detail in routinely prepared tissue specimens. Herein, we illustrate how μCT imaging of standard formalin-fixed, paraffin-embedded biopsy specimens can be seamlessly integrated into conventional histology workflows, enabling nondestructive three-dimensional (3D) X-ray histology, the use and benefits of which we showcase for the exemplar of human lung biopsy specimens. This technology advancement was achieved through manufacturing a first-of-kind μCT scanner for X-ray histology and developing optimized imaging protocols, which do not require any additional sample preparation. 3D X-ray histology allows for nondestructive 3D imaging of tissue microstructure, resolving structural connectivity and heterogeneity of complex tissue networks, such as the vascular network or the respiratory tract. We also demonstrate that 3D X-ray histology can yield consistent and reproducible image quality, enabling quantitative assessment of a tissue's 3D microstructures, which is inaccessible to conventional two-dimensional histology. Being nondestructive, the technique does not interfere with histology workflows, permitting subsequent tissue characterization by means of conventional light microscopy-based histology, immunohistochemistry, and immunofluorescence. 3D X-ray histology can be readily applied to a plethora of archival materials, yielding unprecedented opportunities in diagnosis and research of disease.
Project description:Psittacosaurus is one of the most abundant and speciose genera in the Dinosauria, with fifteen named species. The genus is geographically and temporally widespread with large sample sizes of several of the nominal species allowing detailed analysis of intra- and interspecific variation. We present a reanalysis of three separate, coeval species within the Psittacosauridae; P. lujiatunensis, P. major, and Hongshanosaurus houi from the Lujiatun beds of the Yixian Formation, northeastern China, using three-dimensional geometric morphometrics on a sample set of thirty skulls in combination with a reevaluation of the proposed character states for each species. Using these complementary methods, we show that individual and taphonomic variation are the joint causes of a large range of variation among the skulls when they are plotted in a morphospace. Our results demonstrate that there is only one species of Psittacosaurus within the Lujiatun beds and that the three nominal species represent different taphomorphotypes of P. lujiatunensis. The wide range of geometric morphometric variation in a single species of Psittacosaurus implies that the range of variation found in other dinosaurian groups may also be related to taphonomic distortion rather than interspecific variation. As the morphospace is driven primarily by variation resulting from taphonomic distortion, this study demonstrates that the geometric morphometric approach can only be used with great caution to delineate interspecific variation in Psittacosaurus and likely other dinosaur groups without a complementary evaluation of character states. This study presents the first application of 3D geometric morphometrics to the dinosaurian morphospace and the first attempt to quantify taphonomic variation in dinosaur skulls.
Project description:Appendage regeneration occurs within the opaque exoskeleton in arthropods, making it challenging to visualize the regenerative processes dynamically. In this protocol, we present a strategy to scan and capture the high-resolution details of microstructural tissues at certain regeneration points through micro-computed tomography (micro-CT). We describe steps for tissue preparation, fixation, critical point drying, micro-CT scanning, and 3D visualization. This approach promises significant utility in the field of regeneration, particularly in studies involving arthropods such as insects and crustaceans. For complete details on the use and execution of this protocol, please refer to Ren et al.1.
Project description:Vascular exploration of small animals requires imaging hardware with a very high spatial resolution, capable of differentiating large as well as small vessels, in both in vivo and ex vivo studies. Micro Computed Tomography (micro-CT) has emerged in recent years as the preferred modality for this purpose, providing high resolution 3D volumetric data suitable for analysis, quantification, validation, and visualization of results. The usefulness of micro-CT, however, can be adversely affected by a range of factors including physical animal preparation, numerical quantification, visualization of results, and quantification software with limited possibilities. Exacerbating these inherent difficulties is the lack of a unified standard for micro-CT imaging. Most micro-CT today is aimed at particular applications and the software tools needed for quantification, developed mainly by imaging hardware manufacturers, lack the level of detail needed to address more specific aims. This review highlights the capabilities of micro-CT for vascular exploration, describes the current state of imaging protocols, and offers guidelines and suggestions aimed at making micro-CT more accurate, replicable, and robust.