James C. Gee

Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows

The paper introduces LAMNr flows for multimodal data analysis, enabling shared latent subspaces and cross-view imputation, with applications in biological imaging.

The ANTsX Ecosystem for Mapping the Mouse Brain

The paper demonstrates the use of ANTsX for precise spatial mapping of the mouse brain using standardized coordinate systems and presents novel workflows for longitudinal trajectory analysis and automated morphological measurements.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

Thoracic Aortic Three-Dimensional Geometry

The paper develops a deep learning method to quantify 3D aortic geometry in large biobanks, expanding available phenotypes for studying aortic degeneration.

Effect of Stroma-directed Drugs in Combination with Chemotherapy Against Pancreatic Cancer- a Preclinical Study

This study compares chemotherapy with and without stroma-directed drugs in a mouse model of pancreatic cancer, finding enhanced tumor growth inhibition and changes in tumor microenvironment.

Developmental Mouse Brain Common Coordinate Framework

The paper develops a 3D developmental common coordinate framework (DevCCF) for mouse brains across multiple developmental stages to enable data integration and analysis of brain development.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

HiDiver: A Suite of Methods to Merge Magnetic Resonance Histology, Light Sheet Microscopy, and Complete Brain Delineations

HiDiver integrates multimodal brain imaging data to enable 3D quantitative analysis of brain structure and function in mice.

Multimodal Magnetic Resonance Histology and Light Sheet Imaging for Quantitative Neurogenetics of the Mouse

The paper develops a combined MRI and light sheet imaging approach to generate high-resolution brain phenotypes for neurogenetic studies in mice.

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

Cellular Anatomy of the Mouse Primary Motor Cortex

The paper provides a detailed cellular-resolution map of the mouse primary motor cortex, defining cell types and their connectivity.

Joint ex vivo MRI and histology detect iron-rich cortical gliosis in Tau and TDP-43 proteinopathies

This study uses joint ex vivo MRI and histology to identify distinct iron-rich gliosis patterns in FTLD-Tau and FTLD-TDP, distinguishing them from other neurodegenerative conditions.

The influence of axial length upon the retinal ganglion cell layer of the human eye

The paper examines how axial length affects retinal ganglion cell layer thickness and volume, finding a positive relationship between axial length and GCL tissue volume.

Interpretable Multimodality Embedding of Cerebral Cortex Using Attention Graph Network for Identifying Bipolar Disorder

This paper develops an Edge-weighted Graph Attention Network to classify Bipolar Disorder from healthy controls using structural and functional brain data, achieving improved accuracy and F1-score.