Supplemental Materials

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Manuscript Description Link
Johnson GA, Laoprasert R, Anderson RJ, Cofer G, Cook J, Pratson F, White LE. A multicontrast MR atlas of the Wistar rat brain. Neuroimage

We describe a multi-contrast, multi-dimensional atlas of the Wistar rat acquired at microscopic spatial resolution using magnetic resonance histology (MRH). Diffusion weighted images, and associated scalar images were acquired of a single specimen with a fully sampled Fourier reconstruction, 61 angles and b = 3000 s/mm 2 yielding 50 um isotropic spatial resolution. The higher angular sampling allows use of the GQI algorithm im- proving the angular invariance of the scalar images and yielding an orientation distribution function to assist in delineating subtle boundaries where there are crossing fibers and track density images providing insight into local fiber architecture. A multigradient echo image of the same specimen was acquired at 25 um isotropic spa- tial resolution. A quantitative susceptibility map enhances fiber architecture relative to the magnitude images. An accompanying multi-specimen atlas (n = 6) was acquired with compressed sensing with the same diffusion protocol as used for the single specimen atlas. An average was created using diffeomorphic mapping. Scalar volumes from the diffusion data, a T2 ∗ weighted volume, a quantitative susceptibility map, and a track density volume, all registered to the same space provide multiple contrasts to assist in anatomic delineation. The new template provides significantly increased contrast in the scalar DTI images when compared to previous atlases. A compact interactive viewer based on 3D Slicer is provided to facilitate comparison among the contrasts in the multiple volumes. The single volume and average atlas with multiple 3D volumes provide an improved template for anatomic interrogation of the Wistar rat brain. The improved contrast to noise in the scalar DTI images and the addition of other volumes (eg. QA,QSM,TDI ) will facilitate automated label registration for MR histology and preclinical imaging.

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Manuscript Description Link
Syed M.Adil, Evan Calabrese, Lefko T.Charalambous, JamesJ.Cook, Shervin Rahimpour, Ahmet F. Atik, Gary P.Cofer, Beth A.Parente, G.Allan Johnson, Shivanand P. Lad, Leonard E.White. A high-resolution interactive atlas of the human brainstem using magnetic resonance imaging NeuroImage

Conventional atlases of the human brainstem are limited by the inflexible, sparsely-sampled, two-dimensional nature of histology, or the low spatial resolution of conventional magnetic resonance imaging (MRI). Postmortem high-resolution MRI circumvents the challenges associated with both modalities. A single human brainstem specimen extending from the rostral diencephalon through the caudal medulla was prepared for imaging after the brain was removed from a 65-year-old male within 24 h of death. The specimen was formalin-fixed for two weeks, then rehydrated and placed in a custom-made MRI compatible tube and immersed in liquid fluorocarbon. MRI was performed in a 7-Tesla scanner with 120 unique diffusion directions. Acquisition time for anatomic and diffusion images were 14 h and 208 h, respectively. Segmentation was performed manually. This atlas presents multiple contrasting datasets and selected tract reconstruction with unprecedented resolution for MR imaging of the human brainstem.

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Manuscript Description Link
Nian Wang, Robert J Anderson, David G Ashbrook, Vivek Gopalakrishnan, Youngser Park, Carey E Priebe, Yi Qi, Rick Laoprasert, Joshua T Vogelstein, Robert W Williams, G Allan Johnson. Variability and Heritability of Mouse Brain Structure: Microscopic MRI Atlases and Connectomes for Diverse Strains. NeuroImage PrePub

We acquired high spatial & angular resolution DTI images on 4 diverse strains of mice allowing measure of heritability in multiple neuro imaging phenotypes.

• Volume of 254 of 322 regions were highly heritable

• Significant strain variance in FA was seen across 298 of the 322 regions

• connection profiles of 280 of 322 nodes were heritable for all 4 strains

• connection profiles of 150 nodes were heritable in the three “normal" strains

Nian Wang, Leonard E.White, Yi Qi, Gary Cofer, G. Allan Johnson. Cytoarchitecture of the mouse brain by high resolution diffusion magnetic resonance imaging. neuroimage.2020.116876 MRI has been widely used to probe the neuroanatomy of the mouse brain, directly correlating MRI findings to histology is still challenging due to the limited spatial resolution and various image contrasts derived from water relaxation or diffusion properties. View
Nian Wang, Anthony J. Mirando, Gary Cofer, Yi Qi, Matthew J. Hilton, G. Allan Johnson. Magnetic Resonance in Medicine 21January2020 28181 MRM 28181 Characterization complex collagen fiber architecture in knee joint using high‐resolution diffusion imaging View


Manuscript Description Link
Nian Wang Anthony J. Mirando Gary Cofer Yi Qi Matthew J. Hilton G. Allan Johnson Magnetic Resonance in Medicine 22 January 2019 27652 MRM 27652 Diffusion tractography of the rat knee at microscopic resolution View
Nian Wang, Jieying Zhang, Gary Cofer, Yi Qi, Robert J. Anderson, Leonard E. White, G. Allan Johnson Brain. Structure and Function 20 April 2019Structure and Function 20 April 2019 Neurite orientation dispersion and density imaging of mouse brain microstructure View


Manuscript Description Link
Nian Wang, Farid Badar, Yang Xia PubMed 3 January 2018 PMCID: PMC6585296 Experimental Influences in the Accurate Measurement of Cartilage Thickness in MRI View


Manuscript Description Link
Hongjiang Wei, Russell Dibb, Kyle Decker, Nian Wang, Yuyao Zhang, Xiaopeng Zong, Weili Lin, Daniel B. Nissman, Chunlei Liu Investigating magnetic susceptibility of human knee joint at 7 Tesla. PMCID: PMC5513801 To evaluate the magnetic susceptibility properties of different anatomical structures within the knee joint using quantitative susceptibility mapping (QSM) View


Manuscript Description Link
Robert J Anderson, et al.,A high-performance computing voxel-based analysis pipeline for the rodent brain with a formal validation framework. Neuroinformatics volume 17, pages451–472(2019).Open Access An automated VBA processing pipeline running on a high-performance computing cluster View
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. ajprenal.00351.2015 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. View


Manuscript Description Link
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 Method to register 3D CT images of intact rat brains implanted with metal electrode bundles to an MR histology atlas View
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 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 View
E Calabrese, et al., A diffusion tensor MRI atlas of the postmortem rhesus macaque brain, Neuroimage 117: 408-416, 2015. PMCID: PMC4512905 Previous MR DTI rhesus brain atlases limited by low contrast / low spatial resolution. This atlas extends prior analyses by including high-resolution multi-contrast image data View
L Xie, et al., Susceptibility tensor imaging of the kidney and its microstructural underpinnings, Magn Reson Med 73 (3):1270-81, 2015. PMCID: PMC4183741 Susceptibility tensor imaging (STI) tracks tubules throughout the kidney, and diffusion tensor imaging for inner medulla View
L Xie, et al., 4D MRI of polycystic kidneys from rapamycin-treated Glis3-deficient mice, NMR in Biomedicine 2015 May;28(5):546-554 PMCID: PMC4400264 Dynamic contrast-enhanced (DCE) MRI capture crucial stages of cyst development and rapamycin treatment used to see if disease progression can be halted View


Manuscript Description Link
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. [Article first published online: 5 JUL 2014] DOI: 10.1002/hbm.22578PMCID: PMC4206697 Temporal tradeoff effects between spatial resolution and diffusion sampling on tractography in rhesus macaque brain View
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 Voxelwise analysis of diffusion tensor imaging to quantify white matter injury in a rat model of repetitive primary blast exposure View
GA Johnson, et al., Quantitative mapping of trimethyltin in the rat brain using MR histology, Neurotoxicology, 11;42C:12-23 2014. PMCID: PMC4053477 MR histology shows DTI detection of changes in rat brains exposed to trimethyltin (8 mg/Kg and 12 mg/Kg) View
L Xie, et al., 4D MRI of renal function in the developing mouse, NMR Biomed 2014; 27(9):1094-102. PMCID: PMC4134394


125-micron isotropic resolution 3D images show enhanced contrast / clearance over 17 weeks of development View
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 In vivo mouse study compares 4D microSPECT to microCT to quantitatively assess cardiac function / myocardial perfusion View


Manuscript Description Link
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 Developmental neuro-ontology tracks regional changes in MR biomarkers through Wistar rat postnatal neurodevelopment View
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 MR histology atlas to analyze regional morphometric changes / variability through rat neurodevelopment View
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 QSM offers new MR contrast mechanism to detect pathology caused by small focal inflammation and fibrosis View
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 Novel post-reconstruction spectral filtration scheme; 3D iodine and gold maps measure fractional blood volume /vascular permeability of active tumor growth over 5 days View


Manuscript Description Link
E Calabrese, GA Johnson, Diffusion tensor MR histology reveals microstructural changes in the developing rat brain, Neuroimage 79:329-39, 2013. PMCID: PMC3690820 MR histology rat atlas to analyze regional changes in diffusion tensor parameters through postnatal neurodevelopment View
GA Johnson, E Calabrese, A Badea, G Paxinos, C Watson, A multidimensional MR histology atlas of the Wistar rat brain, PMCID: PMC3408821 MR histology atlas aligned with Paxinos-Watson atlas, based on optical sections, compares histochemical and immuno-marker data View
A Badea, et al.. Quantitative mouse brain phenotyping based on single and multispectral MR protocols, Neuroimage 63: 1633-1645, 2012.PMCID: PMC3604698 Segmentation tools for human neuroimaging adapted / streamlined for mouse brain segmentation using multispectral MR protocols. View
L Xie, et al., MR histology of age-related nephropathy in the Sprague Dawley rat, Toxicol Path 40(5):764-778, 2012. PMCID: PMC3515870 MR histology for background pathology in kidneys. Contrast mechanisms optimize scanning protocols. View
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: PMC3615410 Pipeline for registration-based segmentation and functional analysis of 4D cardiac micro-CT mouse data for quantitative analysis of cardiac images View
SM Johnston, GA Johnson, CT Badea, Temporal and spectral imaging with micro-CT. Med Phys 39(8): 4943-4968, 2012. PMCID: PMC3416878 Retrospectively-gated dual energy CT to reconstruct data in 5D volumetric images distinguishes different materials at different time points View


Manuscript Description Link
Y Jiang, GA Johnson, Microscopic diffusion tensor atlas of the mouse brain, Neuroimage 56(3): 1235-1243, 2011. PMCID: PMC3085633 Critical addition to Waxholm Space online mouse brain atlas. Averaged values of DTI indices in 9 white matter structures. View
J Nouls, et al., A constant-volume ventilator and gas recapture system for hyperpolarized gas MRI of mouse and rat lungs,

Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering, 39B(2): 78-88, 2011 PMCID: PMC3103138

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 View


Manuscript Description Link
GA Johnson, et al., Waxholm Space: An image-based reference for coordinating mouse brain research, Neuroimage, 53(2): 365-372, 2010. PMCID: PMC2930145 Normal adult mouse brain atlas using streamlined protocol (specimen fixation, staining, image acquisition, reconstruction, normalization to Waxholm Space) View
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 Automated MR analyses for longitudinal view of volumetric changes in transgenic mouse model of AD from earliest amyloid deposits to remote volumetric changes View
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. Magnetic Resonance in Medicine 63(4):979-87, 2010 PMCID: PMC2852272 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 View


Manuscript Description Link
GP Howles, et al., Rapid production of specialized animal handling devices using computer-aided design and solid freeform fabrication, Journal of Magnetic Resonance Imaging 30(2):466-471, 2009 PMCID: PMC2746045 Computer-aided design process and solid freeform fabrication for fast, inexpensive production of sophisticated animal handling devices View


Manuscript Description Link
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 Online atlas of high-resolution normal, transgenic, and mutant mouse models at embryonic and neonatal stages View


Manuscript Description Link
A Badea, et al., Neuroanatomical phenotypes in the Reeler mouse, Neuroimage 34(4): 1363-1374, 2007. PMCID: PMC1945208 Contrast-enhanced 9.4 T MR scans of perfusion-fixed mouse brains View
GA Johnson, et al., Morphologic phenotyping by MR microscopy: the visible mouse, Radiology 222(3): 789-793, 2002. PMCID: PMC1994723 MR microscopy active staining protocol for 3D imaging of C57BL/6J mouse View