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Brain pathologies often manifest as partial or complete loss of tissue. The goal of many neuroimaging studies is to capture the location and amount of tissue changes with respect to a clinical variable of interest, such as disease progression. Morphometric analysis approaches capture local differences in the distribution of tissue or other quantities of interest in relation to a clinical variable. We propose to augment morphometric analysis with an additional feature extraction step based on unbalanced optimal transport. The optimal transport feature extraction step increases statistical power for pathologies that cause spatially dispersed tissue loss, minimizes sensitivity to shifts due to spatial misalignment or differences in brain topology, and separates changes due to volume differences from changes due to tissue location. We demonstrate the proposed optimal transport feature extraction step in the context of a volumetric morphometric analysis of the OASIS-1 study for Alzheimer's disease. The results demonstrate that the proposed approach can identify tissue changes and differences that are not otherwise measurable. [Display omitted] • Novel brain image morphometry approach for exploratory population analysis. • Increased statistical power for diffuse tissue loss. • Differentiate between anatomical shape changes and tissue loss. • Flexible approach that can be integrated in various morphometry methods. [ABSTRACT FROM AUTHOR]

Correlative microscopy is a sophisticated approach that combines the capabilities of typically separate, but powerful microscopy platforms: often including, but not limited, to conventional light, confocal and super-resolution microscopy, atomic force microscopy, transmission and scanning electron microscopy, magnetic resonance imaging and micro/nano CT (computed tomography). When targeting rare or specific events within large populations or tissues, correlative microscopy is increasingly being recognized as the method of choice. Furthermore, this multi-modal assimilation of technologies provides complementary and often unique information, such as internal and external spatial, structural, biochemical and biophysical details from the same targeted sample. The development of a continuous stream of cutting-edge applications, probes, preparation methodologies, hardware and software developments will enable realization of the full potential of correlative microscopy. [ABSTRACT FROM AUTHOR]

Abstract: This research develops an algorithm which provides excellent localization of Lamb wave dispersion curves while eliminating spurious components. This result is achieved by combining a differential reassignment procedure with non-linear anisotropic diffusion. This study examines the reassignment and diffusion components individually, before developing a combined algorithm. This combined algorithm is then applied to experimentally measured Lamb waves to develop an image of the dispersion curves of a plate with excellent clarity and definition. These dispersion curves are then used to increase the accuracy of a previously developed procedure to locate a notch. [Copyright &y& Elsevier]

Background: Non-human primates are commonly used in neuroimaging research for which general anaesthesia or sedation is typically required for data acquisition. In this analysis, the cumulative effects of exposure to ketamine, Telazol® (tiletamine and zolazepam), and the inhaled anaesthetic isoflurane on early brain development were evaluated in two independent cohorts of typically developing rhesus macaques.Methods: Diffusion MRI scans were analysed from 43 rhesus macaques (20 females and 23 males) at either 12 or 18 months of age from two separate primate colonies.Results: Significant, widespread reductions in fractional anisotropy with corresponding increased axial, mean, and radial diffusivity were observed across the brain as a result of repeated anaesthesia exposures. These effects were dose dependent and remained after accounting for age and sex at time of exposure in a generalised linear model. Decreases of up to 40% in fractional anisotropy were detected in some brain regions.Conclusions: Multiple exposures to commonly used anaesthetics were associated with marked changes in white matter microstructure. This study is amongst the first to examine clinically relevant anaesthesia exposures on the developing primate brain. It will be important to examine if, or to what degree, the maturing brain can recover from these white matter changes. [ABSTRACT FROM AUTHOR]

This paper presents a method for automatic color and intensity normalization of digitized histology slides stained with two different agents. In comparison to previous approaches, prior information on the stain vectors is used in the plane estimation process, resulting in improved stability of the estimates. Due to the prevalence of hematoxylin and eosin staining for histology slides, the proposed method has significant practical utility. In particular, it can be used as a first step to standardize appearance across slides and is effective at countering effects due to differing stain amounts and protocols and counteracting slide fading. The approach is validated against non-prior plane-fitting using synthetic experiments and 13 real datasets. Results of application of the method to adjustment of faded slides are given, and the effectiveness of the method in aiding statistical classification is shown. [ABSTRACT FROM AUTHOR]

• We propose a DADP framework for longitudinal knee MR image analysis. • A DL pipeline is proposed to extract 2D cartilage thickness maps from 3D images. • A DFMEM is proposed for dynamic abnormality detection and progression. • Statistical inferences are introduced for both association and subgroup analysis. • Statistical disease mapping is conducted at both population and subgroup level. [Display omitted] Osteoarthritis (OA) is the most common disabling joint disease. Magnetic resonance (MR) imaging has been commonly used to assess knee joint degeneration due to its distinct advantage in detecting morphologic cartilage changes. Although several statistical methods over conventional radiography have been developed to perform quantitative cartilage analyses, little work has been done capturing the development and progression of cartilage lesions (or abnormal regions) and how they naturally progress. There are two major challenges, including (i) the lack of building spatial-temporal correspondences and correlations in cartilage thickness and (ii) the spatio-temporal heterogeneity in abnormal regions. The goal of this work is to propose a dynamic abnormality detection and progression (DADP) framework for quantitative cartilage analysis, while addressing the two challenges. First, spatial correspondences are established on flattened 2D cartilage thickness maps extracted from 3D knee MR images both across time within each subject and across all subjects. Second, a dynamic functional mixed effects model (DFMEM) is proposed to quantify abnormality progression across time points and subjects, while accounting for the spatio-temporal heterogeneity. We systematically evaluate our DADP using simulations and real data from the Osteoarthritis Initiative (OAI). Our results show that DADP not only effectively detects subject-specific dynamic abnormal regions, but also provides population-level statistical disease mapping and subgroup analysis. [ABSTRACT FROM AUTHOR]

Abstract: Chorea-acanthocytosis (ChAc) is an uncommon autosomal recessive disorder due to mutations of the VPS13A gene, which encodes for the membrane protein chorein. ChAc presents with progressive limb and orobuccal chorea, but there is often a marked dysexecutive syndrome. ChAc may first present with neuropsychiatric disturbance such as obsessive–compulsive disorder (OCD), suggesting a particular role for disruption to striatal structures involved in non-motor frontostriatal loops, such as the head of the caudate nucleus. Two previous studies have suggested a marked reduction in volume in the caudate nucleus and putamen, but did not examine morphometric change. We investigated morphometric change in 13 patients with genetically or biochemically confirmed ChAc and 26 age- and gender-matched controls. Subjects underwent magnetic resonance imaging and manual segmentation of the caudate nucleus and putamen, and shape analysis using a non-parametric spherical harmonic technique. Both structures showed significant and marked reductions in volume compared with controls, with reduction greatest in the caudate nucleus. Both structures showed significant shape differences, particularly in the head of the caudate nucleus. No significant correlation was shown between duration of illness and striatal volume or shape, suggesting that much structural change may have already taken place at the time of symptom onset. Our results suggest that striatal neuron loss may occur early in the disease process, and follows a dorsal–ventral gradient that may correlate with early neuropsychiatric and cognitive presentations of the disease. [Copyright &y& Elsevier]

Abstract: Frontostriatal circuit mediated cognitive dysfunction has been implicated in frontotemporal lobar degeneration (FTLD) and may differ across subtypes of FTLD. We manually segmented the neostriatum (caudate nucleus and putamen) in FTLD subtypes: behavioral variant frontotemporal dementia, FTD, n =12; semantic dementia, SD, n =13; and progressive non-fluent aphasia, PNFA, n =9); in comparison with controls (n =27). Diagnoses were based on international consensus criteria. Manual bilateral segmentation of the caudate nucleus and putamen was conducted blind to diagnosis by a single analyst, on MRI scans using a standardized protocol. Intracranial volume was calculated via a stereological point counting technique and was used for normalizing the shape analysis. Segmented binaries were analyzed using the Spherical Harmonic (SPHARM) Shape Analysis tools (University of North Carolina) to perform comparisons between FTLD subtypes and controls for global shape difference, local significance maps and mean magnitude maps of shape displacement. Shape analysis revealed that there was significant shape difference between FTLD subtypes and controls, consistent with the predicted frontostriatal dysfunction and of significant magnitude, as measured by displacement maps. These differences were not significant for SD compared to controls; lesser for PNFA compared to controls; whilst FTD showed a more specific pattern in regions relaying fronto- and corticostriatal circuits. Shape analysis shows regional specificity of atrophy, manifest as shape deflation, with a differential between FTLD subtypes, compared to controls. [ABSTRACT FROM AUTHOR]

Abstract: This paper proposes the use of the surface-based Laplace–Beltrami and the volumetric Laplace eigenvalues and eigenfunctions as shape descriptors for the comparison and analysis of shapes. These spectral measures are isometry invariant and therefore allow for shape comparisons with minimal shape pre-processing. In particular, no registration, mapping, or remeshing is necessary. The discriminatory power of the 2D surface and 3D solid methods is demonstrated on a population of female caudate nuclei (a subcortical gray matter structure of the brain, involved in memory function, emotion processing, and learning) of normal control subjects and of subjects with schizotypal personality disorder. The behavior and properties of the Laplace–Beltrami eigenvalues and eigenfunctions are discussed extensively for both the Dirichlet and Neumann boundary condition showing advantages of the Neumann vs. the Dirichlet spectra in 3D. Furthermore, topological analyses employing the Morse–Smale complex (on the surfaces) and the Reeb graph (in the solids) are performed on selected eigenfunctions, yielding shape descriptors, that are capable of localizing geometric properties and detecting shape differences by indirectly registering topological features such as critical points, level sets and integral lines of the gradient field across subjects. The use of these topological features of the Laplace–Beltrami eigenfunctions in 2D and 3D for statistical shape analysis is novel. [Copyright &y& Elsevier]