Fuzzy Object Skeletonization: Theory, Algorithms, and Applications

MSO-GP: 3-D segmentation of large and complex conjoined tree structures

Robust segmentation of large and complex conjoined tree structures in 3-D is a major challenge in computer vision. This is particularly true in computational biology, where we often encounter large data structures in size, but few in number, which poses a hard problem for learning algorithms. We show that merging multiscale opening with geodesic path propagation, can shed new light on this classic machine vision challenge, while circumventing the learning issue by developing an unsupervised visual geometry approach (digital topology/morphometry). The novelty of the proposed MSO-GP method comes from the geodesic path propagation being guided by a skeletonization of the conjoined structure that helps to achieve robust segmentation results in a particularly challenging task in this area, that of artery-vein separation from non-contrast pulmonary computed tomography angiograms. This is an important first step in measuring vascular geometry to then diagnose pulmonary diseases and to develop image-based phenotypes. We first present proof-of-concept results on synthetic data, and then verify the performance on pig lung and human lung data with less segmentation time and user intervention needs than those of the competing methods.

Quantitative approaches in multimodal fundus imaging: State of the art and future perspectives

When it first appeared, multimodal fundus imaging revolutionized the diagnostic workup and provided extremely useful new insights into the pathogenesis of fundus diseases. The recent addition of quantitative approaches has further expanded the amount of information that can be obtained. In spite of the growing interest in advanced quantitative metrics, the scientific community has not reached a stable consensus on repeatable, standardized quantitative techniques to process and analyze the images. Furthermore, imaging artifacts may considerably affect the processing and interpretation of quantitative data, potentially affecting their reliability. The aim of this survey is to provide a comprehensive summary of the main multimodal imaging techniques, covering their limitations as well as their strengths. We also offer a thorough analysis of current quantitative imaging metrics, looking into their technical features, limitations, and interpretation. In addition, we describe the main imaging artifacts and their potential impact on imaging quality and reliability. The prospect of increasing reliance on artificial intelligence-based analyses suggests there is a need to develop more sophisticated quantitative metrics and to improve imaging technologies, incorporating clear, standardized, post-processing procedures. These measures are becoming urgent if these analyses are to cross the threshold from a research context to real-life clinical practice.

A Simple and Stable Centeredness Measure for 3D Curve Skeleton Extraction

Existing methods for extracting 3D curve skeletons mostly suffer from the difficulty of finding the center points of 3D shapes and tedious manual adjustments of the thresholds for pruning spurious branches due to the influence of shape boundary perturbations. In this article, we present a method based on medial surfaces of 3D shapes for the convenient and fast extraction of high-quality curve skeletons. Our main contribution is a simple and stable centeredness measure. It is based on simulating fire propagation via the scheme of inside-out evolution from the interior to the boundary, differentiating it from existing methods that use the scheme of outside-in evolution from the boundary to the interior. Thus, our measure is much more localized, and it can be implemented with a high degree of parallelism. In addition, we propose measures to effectively suppress the influence of details to obtain a stable measurement, and employ minimum set covers to optimize the center points to generate compact skeletons, which enables spurious branches to be effectively excluded without the tedious work of manually adjusting thresholds. Our experiments show the superiority of our method over existing methods, including its convenient generation of clean, compact and centered curve skeletons while running much faster than state-of-the-art methods.

ArGSLab: a tool for analyzing experimental or simulated particle networks

Microscopy and particle-based simulations are both powerful techniques to study aggregated particulate matter such as colloidal gels. The data provided by these techniques often contains information on a wide array of length scales, but structural analysis methods typically focus on the local particle arrangement, even though the data also contains information about the particle network on the mesoscopic length scale. In this paper, we present a MATLAB software package for quantifying mesoscopic network structures in colloidal samples. ArGSLab (Arrested and Gelated Structures Laboratory) extracts a network backbone from the input data, which is in turn transformed into a set of nodes and links for graph theory-based analysis. The routines can process both image stacks from microscopy as well as explicit coordinate data, and thus allows quantitative comparison between simulations and experiments. ArGSLab furthermore enables the accurate analysis of microscopy data where, e.g., an extended point spread function prohibits the resolution of individual particles. We demonstrate the resulting output for example datasets from both microscopy and simulation of colloidal gels, in order to showcase the capability of ArGSLab to quantitatively analyze data from various sources. The freely available software package can be used either with a provided graphical user interface or directly as a MATLAB script.

Effects of fluoride intake on cortical and trabecular bone microstructure at early adulthood using multi-row detector computed tomography (MDCT)

PURPOSE

The aim of this study was to examine the effects of period-specific and cumulative fluoride (F) intake on bone at the levels of cortical and trabecular bone microstructural outcomes at early adulthood using emerging multi-row detector computed tomography (MDCT)-based novel techniques.

METHODS

Ultra-high resolution MDCT distal tibia scans were collected at age 19 visits under the Iowa Bone Development Study (IBDS), and cortical and trabecular bone microstructural outcomes were computed at the distal tibia using previously validated methods. CT scans of a tissue characterization phantom were used to calibrate CT numbers (Hounsfield units) into bone mineral density (mg/cc). Period-specific and cumulative F intakes from birth up to the age of 19 years were assessed for IBDS participants through questionnaire, and their relationships with MDCT-derived bone microstructural outcomes were examined using bivariable and multivariable analyses, adjusting for height, weight, maturity offset (years since age of peak height velocity (PHV)), physical activity (questionnaire for adolescents (PAQ-A)), healthy eating index version 2010 (HEI-2010) scores, and calcium and protein intakes.

RESULTS

MDCT distal tibia scans were acquired for 324 participants from among the total of 329 participants at age 19 visits. No motion artifacts were observed in any MDCT scans, and all images were successfully processed to measure cortical and trabecular bone microstructural outcomes. At early adulthood, males were observed to have stronger trabecular bone microstructural features, as well as thicker cortical bone (p < 0.01), as compared to age-similar females; however, females were found to have less cortical bone porosity as compared to males. Among participants with available F intake estimates (75 to 91% of the 324 with MDCT scans, depending on the period-specific F intake measure), no statistically significant associations were detected between any period-specific or cumulative F intake and bone microstructural outcomes of the tibia at the p < 0.01 level. Only for females, statistically suggestive associations (p < 0.05) were found between recent F intake (from 14 to 19 years) and trabecular mean plate width and trabecular thickness at the tibia. Those associations became somewhat weaker, but still statistically suggestive, for trabecular thickness in fully adjusted analysis with height, weight, PHV, calcium and protein intake, and HEI-2010 and PAQ-A scores as covariates.

CONCLUSION

The findings show that the effects of lifelong or period-specific F intake from combined sources for adolescents typical to the United States Midwest region are not strongly associated with bone microstructural outcomes at age 19 years. These findings are generally consistent with previously reported results of IBDS analyses, which further confirms that effects of lifelong or period-specific F intake on skeletons in early adulthood are absent or weak, even at the levels of cortical and trabecular bone microstructural details.

Quantitative CT-Based Methods for Bone Microstructural Measures and Their Relationships With Vertebral Fractures in a Pilot Study on Smokers

Osteoporosis causes fragile bone, and bone microstructural quality is a critical determinant of bone strength and fracture risk. This study pursues technical validation of novel CT-based methods for assessment of peripheral bone microstructure together with a human pilot study examining relationships between bone microstructure and vertebral fractures in smokers. To examine the accuracy and reproducibility of the methods, repeat ultra-high-resolution (UHR) CT and micro-CT scans of cadaveric ankle specimens were acquired. Thirty smokers from the University of Iowa COPDGene cohort were recruited at their 5-year follow-up visits. Chest CT scans, collected under the parent study, were used to assess vertebral fractures. UHR CT scans of distal tibia were acquired for this pilot study to obtain peripheral cortical and trabecular bone (Cb and Tb) measures. UHR CT-derived Tb measures, including volumetric bone mineral density (BMD), network area, transverse trabecular density, and mean plate width, showed high correlation (r > 0.901) with their micro-CT-derived values over small regions of interest (ROIs). Both Cb and Tb measures showed high reproducibility-intra-class correlation (ICC) was greater than 0.99 for all Tb measures except erosion index and greater than 0.97 for all Cb measures. Female sex was associated with lower transverse Tb density (p < 0.1), higher Tb spacing (p < 0.05), and lower cortical thickness (p < 0.001). Participants with vertebral fractures had significantly degenerated values (p < 0.05) for all Tb measures except thickness. There were no statistically significant differences for Cb measures between non-fracture and fracture groups. Vertebral fracture-group differences of Tb measures remained significant after adjustment with chronic obstructive pulmonary disease (COPD) status. Although current smokers at baseline had more fractures-81.8% versus 63.2% for former smokers-the difference was not statistically significant. This pilot cross-sectional human study demonstrates CT-based peripheral bone microstructural differences among smokers with and without vertebral fractures. © 2021 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

A comparative study of trabecular bone micro-structural measurements using different CT modalities

Osteoporosis, characterized by reduced bone mineral density and micro-architectural degeneration, significantly enhances fracture-risk. There are several viable methods for trabecular bone micro-imaging, which widely vary in terms of technology, reconstruction principle, spatial resolution, and acquisition time. We have performed an excised cadaveric bone specimen study to evaluate different computed tomography (CT)-imaging modalities for trabecular bone micro-structural analysis. Excised cadaveric bone specimens from the distal radius were scanned using micro-CT and fourin vivoCT imaging modalities: high-resolution peripheral quantitative computed tomography (HR-pQCT), dental cone beam CT (CBCT), whole-body multi-row detector CT (MDCT), and extremity CBCT. A new algorithm was developed to optimize soft thresholding parameters for individualin vivoCT modalities for computing quantitative bone volume fraction maps. Finally, agreement of trabecular bone micro-structural measures, derived from differentin vivoCT imaging, with reference measures from micro-CT imaging was examined. Observed values of most trabecular measures, including trabecular bone volume, network area, transverse and plate-rod micro-structure, thickness, and spacing, forin vivoCT modalities were higher than their micro-CT-based reference values. In general, HR-pQCT-based trabecular bone measures were closer to their reference values as compared to otherin vivoCT modalities. Despite large differences in observed values of measures among modalities, high linear correlation (rε [0.94 0.99]) was found between micro-CT andin vivoCT-derived measures of trabecular bone volume, transverse and plate micro-structural volume, and network area. All HR-pQCT-derived trabecular measures, except the erosion index, showed high correlation (rε [0.91 0.99]). The plate-width measure showed a higher correlation (rε [0.72 0.91]) amongin vivoand micro-CT modalities than its counterpart binary plate-rod characterization-based measure erosion index (rε [0.65 0.81]). Although a strong correlation was observed between micro-structural measures fromin vivoand micro-CT imaging, large shifts in their values forin vivomodalities warrant proper scanner calibration prior to adopting in multi-site and longitudinal studies.

Deep Learning Based High-Resolution Reconstruction of Trabecular Bone Microstructures from Low-Resolution CT Scans using GAN-CIRCLE

Osteoporosis is a common age-related disease characterized by reduced bone density and increased fracture-risk. Microstructural quality of trabecular bone (Tb), commonly found at axial skeletal sites and at the end of long bones, is an important determinant of bone-strength and fracture-risk. High-resolution emerging CT scanners enable in vivo measurement of Tb microstructures at peripheral sites. However, resolution-dependence of microstructural measures and wide resolution-discrepancies among various CT scanners together with rapid upgrades in technology warrant data harmonization in CT-based cross-sectional and longitudinal bone studies. This paper presents a deep learning-based method for high-resolution reconstruction of Tb microstructures from low-resolution CT scans using GAN-CIRCLE. A network was developed and evaluated using post-registered ankle CT scans of nineteen volunteers on both low- and high-resolution CT scanners. 9,000 matching pairs of low- and high-resolution patches of size 64×64 were randomly harvested from ten volunteers for training and validation. Another 5,000 matching pairs of patches from nine other volunteers were used for evaluation. Quantitative comparison shows that predicted high-resolution scans have significantly improved structural similarity index (p < 0.01) with true high-resolution scans as compared to the same metric for low-resolution data. Different Tb microstructural measures such as thickness, spacing, and network area density are also computed from low- and predicted high-resolution images, and compared with the values derived from true high-resolution scans. Thickness and network area measures from predicted images showed higher agreement with true high-resolution CT (CCC = [0.95, 0.91]) derived values than the same measures from low-resolution images (CCC = [0.72, 0.88]).

Efeito do Diabetes Mellitus tipo I na organização espacial das trabéculas ósseas: análise por meio do processo de esqueletonização

Introdução: Diabetes mellitus é uma doença metabólica que afeta vários órgãos-alvo, incluindo os ossos. OBJETIVO: Avaliar pelo método de esqueletonização o efeito do Diabetes mellitus tipo I (DM1) na microarquitetura de osso esponjoso. Material e Métodos: Quatorze ratos Wistar foram divididos em: Saudável (S, n=7) e Diabético (D, n=7). O DM1 foi induzido por meio de injeção endovenosa de estreptozotocina no grupo D, sendo a confirmação da condição realizada por checagem do nível glicêmico. Os animais foram sacrificados após 35 dias da indução no grupo D, juntamente com os do grupo S. As epífises femorais foram seccionadas, removidas, desmineralizadas e incluídas em parafina. Dois cortes (5 µm) foram obtidos, corados em Hematoxilina e Eosina, e analisados ao Microscópio de Luz. Foi realizada a delimitação interativa das trabéculas ósseas, seguido pelo processo de binarização utilizando threshold global, feita por dois operadores distintos.  Depois, foi realizado o processo de esqueletonização para acesso às características das trabéculas e da rede de interconexão entre elas. Os parâmetros avaliados foram: Área óssea em micrômetros quadrados (B.Ar), Índice de Modelo estrutural (SMI), Dimensão Fractal (FD), Número de trabéculas (Tb.N), Número de ramos (B.N), Número total de junções (Junc.N), Média de pontos terminais (End.p), Média de extensão de cada ramo (R.Le) e Número de junções triplas (Triple.points.N). Resultados: Houve diferença significante apenas no parâmetro SMI para os diferentes operadores (p<0,0001), sendo o mesmo retirado da análise entre diabetes vs saudável. Houve diferença significante na quantidade óssea, sendo maior no grupo S (0,46±0,09) comparado ao grupo D (0,41±0,07) (p=0,0082). Os demais parâmetros não mostraram diferença significante. Conclusão: Conclui-se que a área óssea no grupo saudável é maior em comparação ao DM1. Dentro das limitações deste estudo, parece que a distribuição espacial das trabéculas e suas características de interconexão não são alteradas no diabetes.

Quantitative imaging of peripheral trabecular bone microarchitecture using MDCT

PURPOSE

Osteoporosis associated with reduced bone mineral density (BMD) and microarchitectural changes puts patients at an elevated risk of fracture. Modern multidetector row CT (MDCT) technology, producing high spatial resolution at increasingly lower dose radiation, is emerging as a viable modality for trabecular bone (Tb) imaging. Wide variation in CT scanners raises concerns of data uniformity in multisite and longitudinal studies. A comprehensive cadaveric study was performed to evaluate MDCT-derived Tb microarchitectural measures. A human pilot study was performed comparing continuity of Tb measures estimated from two MDCT scanners with significantly different image resolution features.

METHOD

Micro-CT imaging of cadaveric ankle specimens (n=25) was used to examine the validity of MDCT-derived Tb microarchitectural measures. Repeat scan reproducibility of MDCT-based Tb measures and their ability to predict mechanical properties were examined. To assess multiscanner data continuity of Tb measures, the distal tibias of 20 volunteers (age:26.2±4.5Y,10F) were scanned using the Siemens SOMATOM Definition Flash and the higher resolution Siemens SOMATOM Force scanners with an average 45-day time gap between scans. The correlation of Tb measures derived from the two scanners over 30% and 60% peel regions at the 4% to 8% of distal tibia was analyzed.

RESULTS

MDCT-based Tb measures characterizing bone network area density, plate-rod microarchitecture, and transverse trabeculae showed good correlations (r∈0.85,0.92) with the gold standard micro-CT-derived values of matching Tb measures. However, other MDCT-derived Tb measures characterizing trabecular thickness and separation, erosion index, and structure model index produced weak correlation (r<0.8) with their micro-CT-derived values. Most MDCT Tb measures were found repeatable (ICC∈0.94,0.98). The Tb plate-width measure showed a strong correlation (r = 0.89) with experimental yield stress, while the transverse trabecular measure produced the highest correlation (r = 0.81) with Young's modulus. The data continuity experiment showed that, despite significant differences in image resolution between two scanners (10% MTF along xy-plane and z-direction - Flash: 16.2 and 17.9 lp/cm; Force: 24.8 and 21.0 lp/cm), most Tb measures had high Pearson correlations (r > 0.95) between values estimated from the two scanners. Relatively lower correlation coefficients were observed for the bone network area density (r = 0.91) and Tb separation (r = 0.93) measures.

CONCLUSION

Most MDCT-derived Tb microarchitectural measures are reproducible and their values derived from two scanners strongly correlate with each other as well as with bone strength. This study has highlighted those MDCT-derived measures which show the greatest promise for characterization of bone network area density, plate-rod and transverse trabecular distributions with a good correlation (r ≥ 0.85) compared with their micro-CT-derived values. At the same time, other measures representing trabecular thickness and separation, erosion index, and structure model index produced weak correlations (r < 0.8) with their micro-CT-derived values, failing to accurately portray the projected trabecular microarchitectural features. Strong correlations of Tb measures estimated from two scanners suggest that image data from different scanners can be used successfully in multisite and longitudinal studies with linear calibration required for some measures. In summary, modern MDCT scanners are suitable for effective quantitative imaging of peripheral Tb microarchitecture if care is taken to focus on appropriate quantitative metrics.