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Article
White matter development and language abilities during infancy in autism spectrum disorder
White matter (WM) fiber tract differences are present in autism spectrum disorder (ASD) and could be important markers of behavior. One of the earliest phenotypic differences in ASD are language atypicalities....
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Chapter and Conference Paper
Microscopy Image Segmentation via Point and Shape Regularized Data Synthesis
Current deep learning-based approaches for the segmentation of microscopy images heavily rely on large amount of training data with dense annotation, which is highly costly and laborious in practice. Compared ...
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Chapter and Conference Paper
SlicerSALT: From Medical Images to Quantitative Insights of Anatomy
Three-dimensional (3D) shape lies at the core of understanding the physical objects that surround us. In the biomedical field, shape analysis has been shown to be powerful in quantifying how anatomy changes wi...
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Chapter and Conference Paper
Hierarchical Geodesic Polynomial Model for Multilevel Analysis of Longitudinal Shape
Longitudinal analysis is a core aspect of many medical applications for understanding the relationship between an anatomical subject’s function and its trajectory of shape change over time. Whereas mixed-effec...
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Chapter and Conference Paper
2D/3D Quasi-Intramodal Registration of Quantitative Magnetic Resonance Images
Quantitative Magnetic Resonance Imaging (qMRI) is backed by extensive validation in research literature but has seen limited use in clinical practice because of long acquisition times, lack of standardization ...
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Chapter and Conference Paper
ContraReg: Contrastive Learning of Multi-modality Unsupervised Deformable Image Registration
Establishing voxelwise semantic correspondence across distinct imaging modalities is a foundational yet formidable computer vision task. Current multi-modality registration techniques maximize hand-crafted int...
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Chapter and Conference Paper
Q-space Conditioned Translation Networks for Directional Synthesis of Diffusion Weighted Images from Multi-modal Structural MRI
Current deep learning approaches for diffusion MRI modeling circumvent the need for densely-sampled diffusion-weighted images (DWIs) by directly predicting microstructural indices from sparsely-sampled DWIs. H...
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Chapter and Conference Paper
Equivariant Spherical Deconvolution: Learning Sparse Orientation Distribution Functions from Spherical Data
We present a rotation-equivariant self-supervised learning framework for the sparse deconvolution of non-negative scalar fields on the unit sphere. Spherical signals with multiple peaks naturally arise in Dif...
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Chapter and Conference Paper
Hierarchical Geodesic Modeling on the Diffusion Orientation Distribution Function for Longitudinal DW-MRI Analysis
The analysis of anatomy that undergoes rapid changes, such as neuroimaging of the early develo** brain, greatly benefits from spatio-temporal statistical analysis methods to represent population variations b...
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Chapter and Conference Paper
A Framework to Construct a Longitudinal DW-MRI Infant Atlas Based on Mixed Effects Modeling of dODF Coefficients
Building of atlases plays a crucial role in the analysis of brain images. In scenarios where early growth, aging or disease trajectories are of key importance, longitudinal become necessary as references, mo...
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Chapter and Conference Paper
Trajectories from Distribution-Valued Functional Curves: A Unified Wasserstein Framework
Temporal changes in medical images are often evaluated along a parametrized function that represents a structure of interest (e.g. white matter tracts). By attributing samples along these functions with distri...
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Chapter and Conference Paper
Multi-modal Perceptual Adversarial Learning for Longitudinal Prediction of Infant MR Images
Longitudinal magnetic resonance imaging (MRI) is essential in neuroimaging studies of early brain development. However, incomplete data is an inevitable problem in longitudinal studies because of participant a...
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Chapter and Conference Paper
Self-supervised Denoising via Diffeomorphic Template Estimation: Application to Optical Coherence Tomography
Optical Coherence Tomography (OCT) is pervasive in both the research and clinical practice of Ophthalmology. However, OCT images are strongly corrupted by noise, limiting their interpretation. Current OCT deno...
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Chapter and Conference Paper
Robust Non-negative Tensor Factorization, Diffeomorphic Motion Correction, and Functional Statistics to Understand Fixation in Fluorescence Microscopy
Fixation is essential for preserving cellular morphology in biomedical research. However, it may also affect spectra captured in multispectral fluorescence microscopy, impacting molecular interpretations. To i...
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Chapter and Conference Paper
Hierarchical Multi-geodesic Model for Longitudinal Analysis of Temporal Trajectories of Anatomical Shape and Covariates
Longitudinal regression analysis for clinical imaging studies is essential to investigate unknown relationships between subject-wise changes over time and subject-specific characteristics, represented by covar...
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Chapter and Conference Paper
Spatiotemporal Modeling for Image Time Series with Appearance Change: Application to Early Brain Development
There has been considerable research effort into image registration and regression, which address the problem of determining correspondence primarily through estimating models of structural change. There has ...
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Article
User-Guided Segmentation of Multi-modality Medical Imaging Datasets with ITK-SNAP
ITK-SNAP is an interactive software tool for manual and semi-automatic segmentation of 3D medical images. This paper summarizes major new features added to ITK-SNAP over the last decade. The main focus of the ...
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Chapter and Conference Paper
4D Continuous Medial Representation Trajectory Estimation for Longitudinal Shape Analysis
Morphological change of anatomy over time has been of great interest for tracking disease progression, aging, and growth. Shape regression methods have shown great success to model the shape changes over time ...
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Chapter and Conference Paper
SlicerSALT: Shape AnaLysis Toolbox
SlicerSALT is an open-source platform for disseminating state-of-the-art methods for performing statistical shape analysis. These methods are developed as 3D Slicer extensions to take advantage of its powerful...
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Chapter and Conference Paper
Analysis of Morphological Changes of Lamina Cribrosa Under Acute Intraocular Pressure Change
Glaucoma is the second leading cause of blindness worldwide. Despite active research efforts driven by the importance of diagnosis and treatment of the optic degenerative neuropathy, the relationship between s...
