Duke Center for In-Vivo Microscopy (CIVM) High Resolution MRI Images | Biomedical Informatics Research Network (BIRN)

Filed under: Datasets

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Duke Center for In-Vivo Microscopy (CIVM) contains high resolution MR brain images of normal and human-disease-model mice, including multiple MRI modalities and structural segmentation.

All datasets for each study are available for review and download from CIVMSpace, the Duke Center for In-Vivo Microscopy’s Web portal.

System Requirements

CIVMSpace is designed to work on the Microsoft Windows and Mac OS X platforms. Supported browsers on Windows are Internet Explorer versions 6.0 and above, and Mozilla Firefox versions 1.0 and above. On the Mac, Safari versions 1.3 and above and Mozilla Firefox versions 1.0 and above are supported.

VoxStation requires a working Java installation. It has been tested with Java 1.4, 1.5 and 1.6 on Windows, and Java 1.4 and 1.5 on Mac OS X.

Common Specimen

A collection of 8 brains imaged with two protocols: a T1 and a T2 weighted protocol with 43x43x90 microns resolution.

The project efforts are focused on the development and application of correlated imaging approaches (confocal and electron microscopy, microscopic MRI) to Parkinson’s Disease (PD) – applied first to recently generated transgenic animal models of PD (alpha-synuclein). These MRI scans will allow the examination and comparison volumes of brain structures quantitatively, as well as qualitative changes in tissue content, in both the a-SYN transgenic and age-matched control animals.

DAT-KO

A collection of Male DAT-KO (n = 4) and WT mice (n = 4) between 4 and 8 months of age were used in this study. Images were acquired with 3 dimensional rf refocused spin warp encoding on 3 D (256 × 256 × 512) image arrays covering an 11 × 11 × 22 mm field of view yielding isotropic voxels of 43 × 43 × 43 μm (8 × 10−5 mm3) T1 weighted images were acquired with TR = 100 ms, TE = 5 ms, NEX = 4. Perfusion with contrast agent reduces the mean T1 to <200 ms allowing acquisition of a T2 weighted image with a much shorter TR (200 ms) and TE (15 ms) than might be used with unstained (formalin fixed) tissues. NEX was reduced to 2.

Reference

Neuroimage. 2005 May 15;26(1):83-90. Magnetic resonance imaging at microscopic resolution reveals subtle morphological changes in a mouse model of dopaminergic hyperfunction. Cyr M, Caron MG, Johnson GA, Laakso A. Department of Cell Biology, Center for Models of Human Disease, Duke University Medical Center, Durham, NC 27710, USA.

Unstained mouse brains

A collection of 6 brains imaged with a multispectral protocol (5 constrast). The three-dimensional (3D) MR datasets acquired at 90-microm isotropic resolution. 21 labeles structures and the whole brain were identified in those brains.

Reference

Neuroimage. 2005 Aug 15;27(2):425-35. Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. Ali AA, Dale AM, Badea A, Johnson GA. Center for In Vivo Microscopy, Box 3302, Duke University Medical Center, Durham, NC 27710, USA. anjum.ali at duke dot edu

Stained Mouse Brain

A collection of 6 stained brains imaged witin the skull using two protocols: a T1 weighted protocol and a T2 image (MEFIC enhanced 3D CPMG). Automated segmentations of the brains in 33 structures are provided, as well as as an atlas brain.

References

Sharief et al. in press. Badea A, Ali-Sharief AA, Johnson GA. Morphometric analysis of the C57BL/6J mouse brain. Neuroimage. 2007 Sep 1;37(3):683-93. Epub 2007 Jun 7.

Johnson GA, Ali-Sharief A, Badea A, Brandenburg J, Cofer G, Fubara B, Gewalt S, Hedlund LW, Upchurch L. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.
Neuroimage. 2007 Aug 1;37(1):82-9. Epub 2007 May 18.

Reeler mouse model

A collection of 12 high resolution three-dimensional (3D) MR data acquired at 21.5-micron isotropic resolution.

Reference

Neuroimage. 2007 Feb 15;34(4):1363-74. Epub 2006 Dec 20. Neuroanatomical phenotypes in the reeler mouse. Badea A, Nicholls PJ, Johnson GA, Wetsel WC. Center for In Vivo Microscopy, Box 3302, Duke University Medical Center, Durham, NC 27710, USA.

Genetic reference population

A collection of 24 brains : C57BL/6, DBA2 and 10 BXD strains selected for large hippocampal volume variations. The images are high resolution three-dimensional (3D) MR data acquired at 21.5-micron isotropic resolution (T1) and matched 43-micron resolution MEFIC processed scans (T2). The results of automated segmentation into 33 structures are also provided.

The panel of isogenic BXD strains of mice provides a superb resource to study the genetic basis of differences in brain structure and function. In previous work several research groups have discovered significant heritable differences in the size of the hippocampus, striatum, cerebellum, thalamus, olfactory bulb, neocortex, and amygdala. In many cases this variation has been linked to gene loci. However, it has not yet been practical to systematically quantify genetic covariance across multiple brain regions using a single “coherent” set of animals. In this study we addressed this problem by exploiting high-resolution MR microscopy and automated segmentation. We segmented 33 brain regions in a subset of BXD strains with maximal differences in hippocampal weight. We describe between strain differences in the volumes of these 33 brain structures. These differences in volume range for example from 20.42 mm³ to 30.42 mm³, with a coefficient of variation of 12.99% for hippocampus, from 14.51 mm³ to 24.66 mm³, with a coefficient of variation of 12.58% for striatum, and from 43.95 mm³ to 62.69 mm³, with a coefficient of variation of 8.68% for cerebellum. Data on the volume variability across these BXD strains are accessible online at www.genenetwork.org.

alpha-synuclein Parkinson disease model

A collection of 10 high resolution three-dimensional (3D) MR data acquired at 21.5-micron isotropic resolution (T1) and 10 matched 43-micron resolution MEFIC processed scans (T2).

Correlated Imaging Approaches and Multi-scale Databases for Research in Parkinson’s Disease. The goal of this project is to examine the brains of a transgenic mouse model of Parkinsonism using rodent MRI imaging. Specimens will include age matched non-transgenic controls. All efforts will be made to have a sufficient number of animals per group (with equal numbers of male and female animals). This study is designed to clarify the results of an earlier pilot study (UCSD-CIVM) in which a low number of subjects precluded our ability to ascertain the presence of gross volumetric and regional signal intensity differences in alpha-synuclein transgenic animals in comparison with non-transgenic control animals. The changes in structural volumes should coincide with areas known to be predisposed to either neuronal cell death or reactive gliosis. Regional changes in signal intensity may be associated with protein aggregations, neuronal cell death, or reactive gliosis. The MRI scans can then be reconciled with large scale images of protein distributions in similar animals. We hypothesize that there are such differences in the transgenic animals and that this new MRI study (with higher group N’s and higher scanning resolutions) will provide us with the necessary information to determine which scenario is most likely.

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Duke Center for In-Vivo Microscopy (CIVM) contains high resolution MR brain images of normal and human-disease-model mice, including multiple MRI modalities and structural segmentation. All datasets for each study are available for review and download from CIVMSpace, the Duke Center for In-Vivo Microscopy’s Web portal. System Requirements CIVMSpace is designed to work on the Microsoft Windows and Mac OS X platforms. Supported browsers on Windows are Internet Explorer versions 6.0 and above, and Mozilla Firefox versions 1.0 and above. On the Mac, Safari versions 1.3 and above and Mozilla Firefox versions 1.0 and above are supported. VoxStation requires a working Java installation. It has been tested with Java 1.4, 1.5 and 1.6 on Windows, and Java 1.4 and 1.5 on Mac OS X. Common Specimen A collection of 8 brains imaged with two protocols: a T1 and a T2 weighted protocol with 43x43x90 microns resolution. The project efforts are focused on the development and application of correlated imaging approaches (confocal and electron microscopy, microscopic MRI) to Parkinson’s Disease (PD) – applied first to recently generated transgenic animal models of PD (alpha-synuclein). These MRI scans will allow the examination and comparison volumes of brain structures quantitatively, as well as qualitative changes in tissue content, in both the a-SYN transgenic and age-matched control animals. DAT-KO A collection of Male DAT-KO (n = 4) and WT mice (n = 4) between 4 and 8 months of age were used in this study. Images were acquired with 3 dimensional rf refocused spin warp encoding on 3 D (256 × 256 × 512) image arrays covering an 11 × 11 × 22 mm field of view yielding isotropic voxels of 43 × 43 × 43 μm (8 × 10−5 mm3) T1 weighted images were acquired with TR = 100 ms, TE = 5 ms, NEX = 4. Perfusion with contrast agent reduces the mean T1 to <200 ms allowing acquisition of a T2 weighted image with a much shorter TR (200 ms) and TE (15 ms) than might be used with unstained (formalin fixed) tissues. NEX was reduced to 2. Reference Neuroimage. 2005 May 15;26(1):83-90. Magnetic resonance imaging at microscopic resolution reveals subtle morphological changes in a mouse model of dopaminergic hyperfunction. Cyr M, Caron MG, Johnson GA, Laakso A. Department of Cell Biology, Center for Models of Human Disease, Duke University Medical Center, Durham, NC 27710, USA. Unstained mouse brains A collection of 6 brains imaged with a multispectral protocol (5 constrast). The three-dimensional (3D) MR datasets acquired at 90-microm isotropic resolution. 21 labeles structures and the whole brain were identified in those brains. Reference Neuroimage. 2005 Aug 15;27(2):425-35. Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. Ali AA, Dale AM, Badea A, Johnson GA. Center for In Vivo Microscopy, Box 3302, Duke University Medical Center, Durham, NC 27710, USA. anjum.ali at duke dot edu Stained Mouse Brain A collection of 6 stained brains imaged witin the skull using two protocols: a T1 weighted protocol and a T2 image (MEFIC enhanced 3D CPMG). Automated segmentations of the brains in 33 structures are provided, as well as as an atlas brain. References Sharief et al. in press. Badea A, Ali-Sharief AA, Johnson GA. Morphometric analysis of the C57BL/6J mouse brain. Neuroimage. 2007 Sep 1;37(3):683-93. Epub 2007 Jun 7. Johnson GA, Ali-Sharief A, Badea A, Brandenburg J, Cofer G, Fubara B, Gewalt S, Hedlund LW, Upchurch L. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage. 2007 Aug 1;37(1):82-9. Epub 2007 May 18. Reeler mouse model A collection of 12 high resolution three-dimensional (3D) MR data acquired at 21.5-micron isotropic resolution. Reference Neuroimage. 2007 Feb 15;34(4):1363-74. Epub 2006 Dec 20. Neuroanatomical phenotypes in the reeler mouse. Badea A, Nicholls PJ, Johnson GA, Wetsel WC. Center for In Vivo Microscopy, Box 3302, Duke University Medical Center, Durham, NC 27710, USA. Genetic reference population A collection of 24 brains : C57BL/6, DBA2 and 10 BXD strains selected for large hippocampal volume variations. The images are high resolution three-dimensional (3D) MR data acquired at 21.5-micron isotropic resolution (T1) and matched 43-micron resolution MEFIC processed scans (T2). The results of automated segmentation into 33 structures are also provided. The panel of isogenic BXD strains of mice provides a superb resource to study the genetic basis of differences in brain structure and function. In previous work several research groups have discovered significant heritable differences in the size of the hippocampus, striatum, cerebellum, thalamus, olfactory bulb, neocortex, and amygdala. In many cases this variation has been linked to gene loci. However, it has not yet been practical to systematically quantify genetic covariance across multiple brain regions using a single “coherent” set of animals. In this study we addressed this problem by exploiting high-resolution MR microscopy and automated segmentation. We segmented 33 brain regions in a subset of BXD strains with maximal differences in hippocampal weight. We describe between strain differences in the volumes of these 33 brain structures. These differences in volume range for example from 20.42 mm³ to 30.42 mm³, with a coefficient of variation of 12.99% for hippocampus, from 14.51 mm³ to 24.66 mm³, with a coefficient of variation of 12.58% for striatum, and from 43.95 mm³ to 62.69 mm³, with a coefficient of variation of 8.68% for cerebellum. Data on the volume variability across these BXD strains are accessible online at www.genenetwork.org. alpha-synuclein Parkinson disease model A collection of 10 high resolution three-dimensional (3D) MR data acquired at 21.5-micron isotropic resolution (T1) and 10 matched 43-micron resolution MEFIC processed scans (T2). Correlated Imaging Approaches and Multi-scale Databases for Research in Parkinson’s Disease. The goal of this project is to examine the brains of a transgenic mouse model of Parkinsonism using rodent MRI imaging. Specimens will include age matched non-transgenic controls. All efforts will be made to have a sufficient number of animals per group (with equal numbers of male and female animals). This study is designed to clarify the results of an earlier pilot study (UCSD-CIVM) in which a low number of subjects precluded our ability to ascertain the presence of gross volumetric and regional signal intensity differences in alpha-synuclein transgenic animals in comparison with non-transgenic control animals. The changes in structural volumes should coincide with areas known to be predisposed to either neuronal cell death or reactive gliosis. Regional changes in signal intensity may be associated with protein aggregations, neuronal cell death, or reactive gliosis. The MRI scans can then be reconciled with large scale images of protein distributions in similar animals. We hypothesize that there are such differences in the transgenic animals and that this new MRI study (with higher group N’s and higher scanning resolutions) will provide us with the necessary information to determine which scenario is most likely. 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