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Integrated Center for In Vivo Microscopy

G. Allan Johnson, Ph.D. (gjohnson@duke.edu)
P41 EB015897
Active

Center Overview

The goal of the Duke Center for in Vivo Microscopy (CIVM) is to develop novel preclinical imaging tools and make these methods widely available to collaborators in the basic sciences for comprehensive insight into major diseases. We develop multimodality protocols that integrate the best of different imaging technologies. CIVM has played a major role in developing and enhancing MR microscopy, as well as developing MR with hyperpolarized gases like 3He and 129Xe, now moving into the clinical arena. Beyond specialized MR systems, our imaging technologies also include micro-CT, micro-SPECT, optical imaging, and a computer infrastructure that integrates our research and services. Amounts of data can be staggering, so we are developing novel approaches that enable users to interact with the large datasets. 

Tags

Hyperpolarized gases, preclinical imaging, Small Animal Imaging

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
Mouse brain segmentation pipeline
Integrated Center for In Vivo Microscopy
NIBIB

Suite of segmentation tools (Avants et al. 2008) for human neuroimaging adapted and streamlined for segmentation of mouse brain images acquired with multispectral MR protocols.

Mac OSX NifTI (.nia), NifTI (.nii,...(more) N/A N/A
3D coronal Reeler mouse brain
Integrated Center for In Vivo Microscopy
NIBIB

Contrast-enhanced MR scans of fixed perfused mouse brains at 9.4 T.

Linux, Mac OSX, Windows MRI 0 - 500MB
3D MR datasets C57BL/6 mouse embryos
Integrated Center for In Vivo Microscopy
NIBIB

Web-accessible atlas of high-resolution normal, transgenic, and mutant mouse models at embryonic and neonatal stages.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 500MB - 2GB
5-dimensional micro-CT of cardiac cycle
Integrated Center for In Vivo Microscopy
NIBIB

A retrospectively-gated dual energy scan with optimized filters and voltages, and a series of computational operations to reconstruct the data results in 5-dimensional volumetric images that distinguish different materials at different points in time.

Linux, Mac OSX, Windows Binary CT 500MB - 2GB
Adult Wistar rat atlas
Integrated Center for In Vivo Microscopy
NIBIB

MR histology atlas aligned with the Paxinos-Watson atlas, based on optical sections, compares histochemical and immuno-marker data.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 0 - 500MB
Alzheimer's disease mouse model
Integrated Center for In Vivo Microscopy
NIBIB

Automated analyses to produce an unbiased longitudinal view of volumetric changes in a transgenic mouse model for Alzheimer's disease (AD) shows that MR microscopy can expand our view of AD, from the earliest amyloid deposits to the most remote volumetric changes.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 0 - 500MB
Developing Wistar rat brain
Integrated Center for In Vivo Microscopy
NIBIB

Developmental neuro-ontology designed specifically to track regional changes in MR biomarkers throughout rat postnatal neurodevelopment.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 500MB - 2GB
Micro-CT for tumor vasculature
Integrated Center for In Vivo Microscopy
NIBIB

Novel post-reconstruction spectral filtration scheme to decompose results into 3D iodine and gold maps to allow simultaneous measurement of extravasated gold and intravascular iodine concentrations. Demonstrates in vivo application to measure fractional blood volume and vascular permeability of active tumor growth over 5 days.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) CT 0 - 500MB
Micro-CT pipeline
Integrated Center for In Vivo Microscopy
NIBIB

Quantitative analysis of 4D cardiac images needs segmentation of cardiac chambers at each time point, which is very time-consuming if done manually. We show a pipeline for registration-based segmentation and functional analysis of 4D cardiac micro-CT mouse data.

Linux, Mac OSX, Windows CT 0 - 500MB
Mouse embryos
Integrated Center for In Vivo Microscopy
NIBIB

A genetic marker and novel MR microscopy techniques demonstrate origins of dorsal mesenchymal protrusion in the dorsal mesocardium, and its substantial contribution to atrioventricular septation.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) Microscopy 0 - 500MB
MR histology data for control and aged rat kidneys
Integrated Center for In Vivo Microscopy
NIBIB

Uses MR histology to determine background pathology in kidneys due to chronic disease, inflammation, or age-related degeneration. Several contrast mechanisms were explored to optimize scanning protocols.

Linux, Mac OSX, Windows MRI MRI 500MB - 2GB
Phenotyping of the mouse heart
Integrated Center for In Vivo Microscopy
NIBIB

4D acquisition with high spatial resolution, high temporal resolution (9.6 ms), and fast acquisition time (16 minutes) allows for rapid measurement of heart function in 3 mouse strains for both left and right ventricular volumes.

Linux, Mac OSX, Windows JPEG (.jpg, .jpeg, .JPG,...(more) MRI 0 - 500MB
Post-natal Wistar rat brain development
Integrated Center for In Vivo Microscopy
NIBIB

MR atlas to analyze regional morphometric changes and variability throughout rat neurodevelopment.

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more) MRI 500MB - 2GB
Waxholm Space comprehensive mouse brain atlas
Integrated Center for In Vivo Microscopy
NIBIB

Normal adult mouse brains acquired at 43-micron isotropic resolution using a streamlined protocol (specimen fixation, staining, image acquisition, reconstruction, and normalization to a common reference space, called Waxholm Space).

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more) MRI 0 - 500MB
Waxholm Space mouse brain atlas (DTI)
Integrated Center for In Vivo Microscopy
NIBIB

Data provides a critical addition to Waxholm Space, our online comprehensive atlas of the mouse brain. Averaged values of DTI indices were computed in 9 white matter structures in each brain.

Linux, Mac OSX, Windows DTI 0 - 500MB