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These links provide access to many types of data acquired for published and yet unpublished CIVM studies.

Instructions for accessing our data: Click on one of the links below. A new browser window or tab will open where you will be prompted to login to CIVMVoxPort. If you do not have login credentials, follow the instructions to register for access. After you login, come back to this page and re-click on a link below to go directly to the desired page.

Data downloaded from this site is for academic use only. If you use this data in a publication please send us a request
for copyright permission and appropriate acknowledgements. Licenses can be granted for commercial use.
Contact the Center for permission.

If data you need is not listed here, please fill out a Data-sharing Project Form (MS Word or pdf). Send form back to us, so we can locate the data you need. Manuscripts are listed by most recent publication date.

Links to data
Types of data
A high-performance computing voxel-based analysis pipeline for the rodent brain with a formal validation framework An automated VBA processing pipeline running on a high-performance computing cluster - MR datasets
Robert J Anderson, et al.,A high-performance computing voxel-based analysis pipeline for the rodent brain with a formal validation framework
CT / MR histology of rat brains Method to register 3D CT images of intact rat brains implanted with metal electrode bundles to an MR histology atlas - CT and MR datasets
- Brain masks
- Registration scripts
JS Borg, et al., Localization of metal electrodes in the intact rat brain using registration of 3-D micro-computed tomography images to a magnetic resonance histology atlas, eNeuro 2(4): pii: e0017, 2015. PMCID: PMC4550316
Comprehensive, probabilistic tractography connectome of mouse brain Improvements in small-animal diffusion tractography by combining ex-vivo MRI with exogenous contrast agents, advanced diffusion acquisition and reconstruction techniques, and probabilistic fiber tracking - tractography 2D color overlays
- movie tutorial of tractography vs. ABA injectome data in 3D
- raw images; estimated fiber data; probabilistic tractography
- connectivity matrix graph
- analysis / processing code

E Calabrese, et al., A diffusion MRI tractography connectome of the mouse brain and comparison with neuronal tracer data, Cerebral Cortex 25(11): 4628-4637, 2015. PMCID: PMC4715247. open access
Microscopic-resolution atlas of rhesus macaque brain - 10 postmortem specimens Previous MR DTI rhesus brain atlases limited by low contast / low spatial resolution. This atlas extends prior analyses by including high-resolution multi-contrast image data - structural MRI and DTI images
- detailed 3D segmentation of 241 anatomic structures,
- diffusion tractography,
- estimates of cortical thickness
- maps of anatomic variability
E Calabrese, et al., A diffusion tensor MRI atlas of the postmortem rhesus macaque brain, Neuroimage 117: 408-416, 2015 PMCID: PMC4512905
Brain mapping diffusion tractography - macaque brain Temporal tradeoff effects between spatial resolution and diffusion sampling on tractography in rhesus macaque brain - complete diffusion datasets
- coronal, axial, sagittal views of tractography from 6 diffusion schemes
E Calabrese, et al., Investigating tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: Time well spent? Human Brain Mapping 35(11):5667-85, 2014. PMCID: PMC4206697
Quantifying blast-induced traumatic brain injury - rat model Voxelwise analysis of diffusion tensor imaging to quantify white matter injury in a rat model of repetitive primary blast exposure - YouTube movies
- 4D diffusion-weighted images; GRE image volumes; tensor volumes
E Calabrese, et al., Diffusion tensor imaging reveals white matter injury in rat model of repetitive blast-induced traumatic brain injury, J Neurotrauma, 2014; 31(10):938-50, 2014. PMCID: PMC4012630
Quantitative parametric maps for markers of toxic insults - rat brain MR histology shows DTI detection of changes in rat brains exposed to trimethyltin (8 mg/Kg and 12 mg/Kg) - conventional MR at 7T
- diffusion-weighted, fractional anisotropy, and color fractional anisotropy images
- movies
GA Johnson, et al., Quantitative mapping of trimethyltin in the rat brain using MR histology, Neurotoxicology, 11;42C:12-23 2014. PMCID: PMC4053477

Ontology-based segmentation scheme

Developmental neuro-ontology tracks regional changes in MR biomarkers through Wistar rat postnatal neurodevelopment

- Neuroscience Lexicon wiki (segmentation - 26 brain structures)
- postnatal days 0, 80
- average isotropic diffusion-weighted and GRE images
- color / grayscale label volumes

E Calabrese, GA Johnson, C Watson, An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI, Neuroimage 67:375-384, 2013. PMCID: PMC3551262

MR histology atlas of postnatal Wistar rat brain development

MR histology atlas to analyze regional morphometric changes / variability through rat neurodevelopment - average GRE images
- average of 5 specimens per time point
- 9 postnatal time points
- label volumes for each time point with 27 anatomic delineations
E Calabrese, et al., A quantitative MR histology atlas of postnatal rat brain development with regional estimates of growth and variability, Neuroimage 71:196-206, 2013. PMCID: PMC3639493
Diffusion tensor MR histology atlas of developing Wistar rat brain MR histology rat atlas to analyze regional changes in diffusion tensor parameters through postnatal neurodevelopment - data tables of diffusion tensor parameters vs. postnatal age
- average mean, radial, and axial diffusivity
- fractional anisotropy maps (9 postnatal time points)
E Calabrese, GA Johnson, Diffusion tensor MR histology reveals microstructural changes in the developing rat brain, Neuroimage 79:329-39, 2013. PMCID: PMC3690820
Adult Wistar rat brain MR histology atlas MR histology atlas aligned with Paxinos-Watson atlas, based on optical sections, compares histochemical and immuno-marker data

- 50-micron isotropic (phase map, b0, diffusion-weighted image, apparent diffusion coefficient, axial and radial diffusivity, fractional anisotropy (FA), color FA)

GA Johnson, E Calabrese, A Badea, G Paxinos, C Watson, A multidimensional MR histology atlas of the Wistar rat brain, Neuroimage 62(3): 1848-1856, 2012. PMCID: PMC3408821

Mouse brain segmentation pipeline Segmentation tools for human neuroimaging adapted / streamlined for mouse brain segmentation using multispectral MR protocols.

- link to software
- demo of pipeline by segmenting 2 test mouse strains (BXD29, APP/TTA)
- actively stained C57BL/6 mouse specimens

A Badea, et al.. Quantitative mouse brain phenotyping based on single and multispectral MR protocols, Neuroimage 63: 1633-1645, 2012. PMCID: PMC3604698

Waxholm Space comprehensive mouse brain atlas

Normal adult mouse brain atlas using streamlined protocol (specimen fixation, staining, image acquisition, reconstruction, normalization to Waxholm Space) - 8 DTI datasets
- T1-, T2*-, T2-weighted MR volumes (Duke)
  - Nissl-stained optical histology (Drexel)
- label volume of 37 structures
- symmetrical versions of 5 volumes (BrainInfo / NeuroMaps)
GA Johnson, et al., Waxholm Space: An image-based reference for coordinating mouse brain research, Neuroimage, 53(2): 365-372, 2010. PMCID: PMC2930145

Waxholm Space mouse brain atlas (diffusion tensor imaging)

Critical addition to Waxholm Space online mouse brain atlas. Averaged values of DTI indices in 9 white matter structures. - T1, T2* contrast
- RGB color map
- mean maps (radial diffusivity [RD]; fractional anisotropy [FA]; angular deviation of primary eigenvector)
- coefficient variation maps (AD, FA)
- probabilistic white matter map
Y Jiang, GA Johnson, Microscopic diffusion tensor atlas of the mouse brain, Neuroimage 56(3): 1235-1243, 2011. PMCID: PMC3085633
Alzheimer's disease (AD) mouse model Automated MR analyses for longitudinal view of volumetric changes in transgenic mouse model of AD from earliest amyloid deposits to remote volumetric changes Tif stacks of mouse brain datasets
A Badea, GA Johnson, JL Jankowsky, Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease, Neuroimage 50(2): 416-427, 2010. PMCID: PMC2823970

Reeler mouse brains - neuroanatomical phenotypes

Contrast-enhanced 9.4 T MR scans of perfusion-fixed mouse brains - WT Reln; heterozygous Reln mutant (Relnrl/+)
- homozygous Reln mutant (Relnrl/rl)
- WT / homozygous Reln mutant
- Movie: hippocampus and ventricles (WT; homozygous Reln mutant)
A Badea, et al., Neuroanatomical phenotypes in the Reeler mouse, Neuroimage 34(4): 1363-1374, 2007. PMCID: PMC1945208
Morphologic phenotyping of mouse brain with MR histology Online, searchable database of 3 standardized MR histology protocols for 3D images of fixed, stained mouse brains. Linked via BIRN infrastructure. - male / female adult C57BL/6J mouse brains
- 4 strains, 6 neurologic knockout models
- T1 (21- / 43 microns) and T2-weighted (43-micron) registered and labeled image data
GA Johnson, A Ali-Sharief, A Badea, et al., High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology, Neuroimage 37(1): 82-89, 2007. PMCID: PMC1994723
3D MR images of a whole mouse and mid-abdomen MR microscopy active staining protocol for 3D imaging of C57BL/6J mouse

Interactive sectioning of male C57BL/6J mouse at increments in 3 planes
- whole mouse navigator
- mid-abdomen navigator

GA Johnson, et al., Morphologic phenotyping by MR microscopy: the visible mouse, Radiology 222(3): 789-793, 2002. Supplement - use updated link in 1st column here to access navigators
Phenotyping of the mouse heart 4D acquisition with high spatial and temporal resolution and fast acquisition time allows rapid measurement of heart function in 3 mouse strains for left/right ventricular volumes

6 of each mouse type
- C57BL/6J wild
- DBA/2J wild
- DBA/2J CSQ+ heart failure mice

E Bucholz, et al., Cardiovascular phenotyping of the mouse heart using a 4D radial acquisition and liposomal Gd-DTPA-BMA, Magn Reson Med 63(4):979-987, 2010. PMCID: PMC2852272
4D MR atlas of C57BL/6 embryos and neonatal mice
Online atlas of high-resolution normal, transgenic, and mutant mouse models at embryonic and neonatal stages

- isotropic 19.5-micron resolution
acquired in 3 hrs
- embryonic days 10.5-19.5; postnatal days 0-32
- labeled normal / abnormal hearts
- labeled C57BL/6 whole body embryos
- H&E sections of embryos matching MR images

AE Petiet, et al., High-resolution MR histology of the embryonic and neonatal mouse: a 4D atlas and morphologic database, Proc Natl Acad Sci U S A. 105(34):12331-12336, 2008. PMCID: PMC2527911
Methods to evaluate renal function - mouse kidney Quantitative susceptibility mapping (QSM) resolves / confirms blooming effect source to be large positive susceptibility of concentrated Gd. Ultra-short echno time (UTE) with QSM can complement traditional magnitude UTE and offer tool to study renal pathophysiology. - point-spread function analysis
- magnitude/phase of phantom tubes, varied Gd concentration
- example datasets (3D/4D magnitude; 3D/4D QSM)
L Xie et al. Dynamic contrast-enhanced with ultrashort echo time MRI for evaluating renal function, Am J Physiol - Renal Physiol 310(2): F174-182, 2016. PMCID: PMC4719043
STI to detect kidney tubules Susceptibility tensor imaging (STI) tracks tubules throughout the kidney, and diffusion tensor imaging for inner medulla - supporting figures
- susceptibility tensor images
- comparison confocal image
- segmented kidney structures
L Xie, et al., Susceptibility tensor imaging of the kidney and its microstructural underpinnings, Magn Reson Med 73 (3):1270-81, 2015. PMCID: PMC4183741
PKD cyst development and rapamycin treatment with DCE MRI Dynamic contrast-enhanced (DCE) MRI capture crucial stages of cyst development and rapamycin treatment used to see if disease progression can be halted Controls and treated mice (3 and 17-weeks)
- anatomical and segmented mages
- time-to-peak maps
- tables and figures
L Xie, et al., 4D MRI of polycystic kidneys from rapamycin-treated Glis3-deficient mice, NMR Biomed 28(5):546-54 2015. PMCID: PMC4400264
Method shows functional developmental changes in mouse kidney structure 125-micron isotropic resolution 3D images show enhanced contrast / clearance over 17 weeks of development - figures show image contrasts to segment 4 kidney regions
- 4D (D3 + time) dataset
L Xie, et al., 4D MRI of rental function in the developing mouse, NMR Biomed 2014; 27(9):1094-102. PMCID: PMC4134394
Quantitative susceptibility mapping (QSM) of mouse kidneys QSM offers new MR contrast mechanism to detect pathology caused by small focal inflammation and fibrosis

- 3D datasets (T1-, T2*-weighted MR histology)
- manuscript figures
- segmentation process
- H&E histology

L Xie, et al., Quantitative susceptibility mapping of kidney inflammation and fibrosis in Type 1 Angiotensin Receptor-deficient mice, NMR Biomed 26(12): 1853-1863, 2013. PMCID: PMC3956055
MR histology data for control and aged rat kidneys MR histology for background pathology in kidneys. Contrast mechanisms optimize scanning protocols. 31-micron isotropic resolution, male Sprague-Dawley rats (8 and 52 weeks)
- T1-weighted; T2*-weighted GRE; SE sequences
L Xie, et al., MR histology of age-related nephropathy in the Sprague Dawley rat, Toxicol Path 40(5):764-778, 2012. PMCID: PMC3515870
Micro-CT for tumor vasculature Novel post-reconstruction spectral filtration scheme; 3D iodine and gold maps measure fractional blood volume /vascular permeability of active tumor growth over 5 days

Mouse model of soft-tissue sarcoma
- 80 kVp, 40 kVp data
- filtered datasets of tumor vasculature using iodine and gold nanoparticles
- figures, movies

DP Clark, et al., In vivo characterization of tumor vasculature using iodine and gold nanoparticles and dual energy micro-CT, Phys Med Biol 58(6):1683-1704, 2013. PMCID: PMC3746324
Micro-CT pipeline for registration-based segmentation / analysis of 4D cardiac data Pipeline for registration-based segmentation and functional analysis of 4D cardiac micro-CT mouse data for quantitative analysis of cardiac images Movies and figures for
- label propagation and manual segmentation (long and short axis)

- 4D animation of complete label propagation
D Clark, et al., Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization, Phys Med Biol 57(19): 6125-45, 2012. PMCID: PMC 3615410
5-dimensional micro-CT of cardiac cycle Retrospectively-gated dual energy CT to reconstruct data in 5D volumetric images distinguishes different materials at different time points - images
- movie (axial view of 5D volume of cardiac cycle)
SM Johnston, GA Johnson, CT Badea, Temporal and spectral imaging with micro-CT. Med Phys 39(8): 4943-4968, 2012. PMCID: PMC3416878
4D microSPECT vs. microCT to assess cardiac function In vivo mouse study compares 4D microSPECT to microCT to quantitatively assess cardiac function / myocardial perfusion - 4D cardiac microCT dataset
- 2 4D cardiac microSPECT datasets
- movies show comparison
NT Befera, CT Badea, GA Johnson, Comparison of 4D microSPECT and microCT for murine cardiac function, Mol Imag Biol 16(2): 235-245, 2014. PMCID: PMC4061569
Schematics / parts - to build a constant-volume ventilator and gas recapture system For high-resolution proton and hyperpolarized gas MR of mice and rats, this ventilator differs from others by eliminating need for a custom pneumatic valve located near trachea - schematics for ventilator and power distribution
- parts list, manufacturers, contacts
- illustrations and photos
- LabVIEW code
J Nouls, et al., A constant-volume ventilator and gas recapture system for hyperpolarized gas MRI of mouse and rat lungs, Concepts in Magn Reson Part B, 39B(2): 78–88, 2011. PMCID: PMC3103138
Constructing animal handling devices Computer-aided design process and solid freeform fabrication for fast, inexpensive production of sophisticated animal handling devices Device includes head fixation and integrated anesthesia and monitoring
- nose cone; cradle; draw bar; procedure bed
GP Howles, et al., Rapid production of specialized animal handling devices using computer-aided design and solid freeform fabrication, J Magn Reson Imag 30(2):466-471, 2009. PMCID: PMC2746045

more to come...



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