Multimodal mapping of cell types and projections in the central nucleus of the amygdala.

The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-seq) to classify molecularly defined cell types in the CEA and identified marker genes to map the location of these neuronal types using expansion-assisted iterative fluorescence in situ hybridization (EASI-FISH).

EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains.

Fast predictive simple geodesic regression.

Deformable image registration and regression are important tasks in medical image analysis. However, they are computationally expensive, especially when analyzing large-scale datasets that contain thousands of images. Hence, cluster computing is typically used, making the approaches dependent on such computational infrastructure.

Joint Intensity Fusion Image Synthesis Applied to Multiple Sclerosis Lesion Segmentation.

We propose a new approach to Multiple Sclerosis lesion segmentation that utilizes synthesized images. A new method of image synthesis is considered: joint intensity fusion (JIF). JIF synthesizes an image from a library of deformably registered and intensity normalized atlases.

THE IMPACT OF MATCHING FUNCTIONAL ON ATROPHY MEASUREMENT FROM GEODESIC SHOOTING IN DIFFEOMORPHISMS.

Longitudinal registration has been used to map brain atrophy and tissue loss patterns over time, in both healthy and demented subjects. However, we have not seen a thorough application of the geodesic shooting in diffeomorphisms framework for this task. The registration model is complex and several choices must be made that may significantly impact the quality of results.

ADAPTIVE GRADIENT DESCENT OPTIMIZATION OF INITIAL MOMENTA FOR GEODESIC SHOOTING IN DIFFEOMORPHISMS.

Diffeomorphic image registration algorithms are widely used in medical imaging, and require optimization of a high-dimensional nonlinear objective function. The function being optimized has many characteristics that are relevant for optimization but are typically not well understood. Due to that complexity, most authors have used a simple gradient descent, but it is not often discussed how step sizes are chosen or if line searches are used.

A Riemannian Framework for Intrinsic Comparison of Closed Genus-Zero Shapes.

We present a framework for intrinsic comparison of surface metric structures and curvatures. This work parallels the work of Kurtek et al. on parameterization-invariant comparison of genus zero shapes.

Simultaneous Longitudinal Registration with Group-Wise Similarity Prior.

Here we present an algorithm for the simultaneous registration of N longitudinal image pairs such that information acquired by each pair is used to constrain the registration of each other pair. More specifically, in the geodesic shooting setting for Large Deformation Diffeomorphic Metric Mappings (LDDMM) an average of the initial momenta characterizing the N transformations is maintained throughout and updates to individual momenta are constrained to be similar to this average. In this way, the N registrations are coupled and explore the space of diffeomorphisms as a group, the variance of which is constrained to be small.

A Transformation Similarity Constraint for Groupwise Nonlinear Registration in Longitudinal Neuro Imaging Studies.

Patients with Alzheimer's disease and other brain disorders often show a similar spatial distribution of volume change throughout the brain over time, but this information is not yet used in registration algorithms to refine the quantification of change. Here, we develop a mathematical basis to incorporate that prior information into a longitudinal structural neuroimaging study. We modify the canonical minimization problem for non-linear registration to include a term that couples a collection of registrations together to enforce group similarity.