G. Allan Johnson

A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans

The paper develops a hierarchical atlas for gray-matter parcellation across multiple species, validated through cross-species comparisons and connectivity analysis.

High-resolution MRI Guided Whole Mouse Brain Cell Type Atlas using Deep Learning

This paper develops a deep learning framework combining high-resolution MRI and spatial transcriptomics to create a whole-brain mouse cell type atlas at 10 micrometer resolution.

Directed connectomes across species reveal conserved and divergent pathways of neural signaling

The paper constructs directed connectomes across species using viral tracing and diffusion MRI to identify conserved and divergent neural pathways.

Global dissection of the impact of Alzheimer's disease on brain architecture and behavior: High resolution MRH resolves robust regional effects

This study quantifies the impact of Alzheimer's disease mutations on brain regions in mice, revealing bidirectional volume changes and sex-specific effects.

Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability

This study identifies ASD-like transcriptomic changes in oligodendrocytes and microglia of C58/J mice amygdala, dependent on sex and sociability, using bulk RNA-Seq and snRNA-Seq.

An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain

The paper creates a multimodal 3D mouse brain atlas using MR histology and light sheet microscopy, improving spatial resolution and enabling stereotaxic labeling of brain images.

A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology

This paper introduces a workflow combining light sheet microscopy and magnetic resonance histology to accurately count neurons and assess neuronal density in mouse brains, showing improved accuracy and broad applicability.

Restoring morphology of light sheet microscopy data based on magnetic resonance histology

This paper presents a method to register light sheet microscopy data with magnetic resonance histology to restore in-skull morphology, achieving accurate registration with low displacement error.

Measuring nonapoptotic caspase activity with a transgenic reporter in mice

The paper develops a transgenic mouse model with a fluorescent caspase activity reporter to quantify nonapoptotic caspase activity in rodent brains and demonstrates its use in studying neurophysiological and stress-related effects.

Resolution and b value dependent Structural Connectome in ex vivo Mouse Brain

This study investigates how resolution and b value affect structural connectome in ex vivo mouse brains, finding that higher angular resolution and b value improve tractography and connectome stability.

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.

GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans

This study shows GLIS1 regulates trabecular meshwork function and intraocular pressure, with a human variant linked to glaucoma.

A time-course study of actively stained mouse brains: DTI parameter and connectomic stability over one year

This study examines DTI parameters and connectomic stability in fixed mouse brains over one year, finding that most metrics stabilize within two weeks of fixation.

Heritability of the Mouse Brain Connectome

This study examines the heritability of mouse brain connectomes using high-resolution MRI and finds high heritability in brain volumes and diffusion metrics.

3D Exploration of the Brainstem in 50-micron Resolution MRI

This study creates a detailed 3D map of the human brainstem using high-resolution MRI and validates it against histological atlases.

Mapping the human subcortical auditory system using histology, post mortem MRI and in vivo MRI at 7T

The paper maps the human subcortical auditory system using histology, post mortem MRI, and in vivo 7T MRI, creating atlases and connectivity maps with high-resolution data.