A diffusion MRI-based spatiotemporal continuum of the embryonic mouse brain for probing gene-neuroanatomy connections.

The embryonic mouse brain undergoes drastic changes in establishing basic anatomical compartments and laying out major axonal connections of the developing brain. Correlating anatomical changes with gene-expression patterns is an essential step toward understanding the mechanisms regulating brain development. Traditionally, this is done in a cross-sectional manner, but the dynamic nature of development calls for probing gene-neuroanatomy interactions in a combined spatiotemporal domain. Here, we present a four-dimensional (4D) spatiotemporal continuum of the embryonic mouse brain from E10.5 to E15.5 reconstructed from diffusion magnetic resonance microscopy (dMRM) data. This study achieved unprecedented high-definition dMRM at 30- to 35-µm isotropic resolution, and together with computational neuroanatomy techniques, we revealed both morphological and microscopic changes in the developing brain. We transformed selected gene-expression data to this continuum and correlated them with the dMRM-based neuroanatomical changes in embryonic brains. Within the continuum, we identified distinct developmental modes comprising regional clusters that shared developmental trajectories and similar gene-expression profiles. Our results demonstrate how this 4D continuum can be used to examine spatiotemporal gene-neuroanatomical interactions by connecting upstream genetic events with anatomical changes that emerge later in development. This approach would be useful for large-scale analysis of the cooperative roles of key genes in shaping the developing brain.

High-field magnetic resonance microscopy of aortic plaques in a mouse model of atherosclerosis.

OBJECTIVES: Pre-clinical models of human atherosclerosis are extensively used; however, traditional histological methods do not allow for a holistic view of vascular lesions. We describe an ex-vivo, high-resolution MRI method that allows the 3 dimensional imaging of the vessel for aortic plaque visualization and quantification. MATERIALS AND METHODS: Aortas from apolipoprotein-E-deficient (apoE-/-) mice fed an atherogenic diet (group 1) or a control diet (group 2) were subjected to 14 T MR imaging using a 3D gradient echo sequence. The obtained data sets were reconstructed (Matlab), segmented, and analyzed (Avizo). The aortas were further sectioned and subjected to traditional histological analysis (Oil-Red O and hematoxylin staining) for comparison. RESULTS: A resolution up to 15 × 10x10 µm3 revealed that plaque burden (mm3) was significantly (p < 0.05) higher in group 1 (0.41 ± 0.25, n = 4) than in group 2 (0.01 ± 0.01, n = 3). The achieved resolution provided similar detail on the plaque and the vessel wall morphology compared with histology. Digital image segmentation of the aorta's lumen, plaque, and wall offered three-dimensional visualizations of the entire, intact aortas. DISCUSSION: 14 T MR microscopy provided histology-like details of pathologically relevant vascular lesions. This work may provide the path research needs to take to enable plaque characterization in clinical applications.

Transverse Relaxation Anisotropy of the Achilles and Patellar Tendon Studied by MR Microscopy.

BACKGROUND: T2 * anisotropy affects the clinical assessment of tendons (magic-angle artifact) and may be a source of T2 *-misinterpretation. PURPOSE: To analyze T2 *-anisotropy and T2 *-decay of Achilles and patellar tendons in vitro at microscopic resolution using a variable-echo-time (vTE) sequence. STUDY TYPE: Prospective. SPECIMEN: Four human Achilles and four patellar tendons. FIELD STRENGTH/SEQUENCE: A 7 T MR-microscopy; 3D-vTE spoiled-gradient-echo-sequence (T2 *-mapping). ASSESSMENT: All tendons were measured at 0° and 55° relative to B0 . Additional angles were measured for one Achilles and one patellar tendon for a total of 11 angles ranging from 0° to 90°. T2 *-decay was analyzed with mono- and bi-exponential signal fitting. Mono-exponential T2 *-values (T2 *m ), short and long T2 *-components (T2 *s , T2 *l ), and the fraction of the short component Fs of the bi-exponential T2 *-fit were calculated. T2 *-decay characteristics were compared with morphological MRI and histologic findings based on a region-of-interest analysis. STATISTICAL TESTS: Akaike information criterion (AICC ), F-test, and paired t-test. A P value smaller than the α-level of 0.05 was considered statistically significant. RESULTS: T2 *m -values between fiber-to-field angles of 0° and 55° were increased on average from T2 *m (0°) = 1.92 msec to T2 *m (55°) = 29.86 msec (15.5-fold) in the Achilles and T2 *m (0°) = 1.46 msec to T2 *m (55°) = 23.33 msec (16.0-fold) in the patellar tendons. The changes in T2 *m -values were statistically significant. For the whole tendon, according to F-test and AICC , a bi-exponential model was preferred for angles close to 0°, while the mono-exponential model tended to be preferred at angles close to 55°. CONCLUSION: MR-microscopy provides a deeper insight into the relationship between T2 *-decay (mono- vs. bi-exponential model) and tendon heterogeneity. Changes in fiber-to-field angle result in significant changes in T2 *-values. Thus, we conclude that awareness of T2 *-anisotropy should be noted in quantitative T2 *-mapping of tendons to avoid T2 *-misinterpretation such as a false positive detection of degeneration due to large fiber-to-field angles. EVIDENCE LEVEL: 2 TECHNICAL EFFICACY: Stage 2.

A multicontrast MR atlas of the Wistar rat brain.

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/mm2 yielding 50 um isotropic spatial resolution. The higher angular sampling allows use of the GQI algorithm improving 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 spatial 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.

Variability and heritability of mouse brain structure: Microscopic MRI atlases and connectomes for diverse strains.

Genome-wide association studies have demonstrated significant links between human brain structure and common DNA variants. Similar studies with rodents have been challenging because of smaller brain volumes. Using high field MRI (9.4 T) and compressed sensing, we have achieved microscopic resolution and sufficiently high throughput for rodent population studies. We generated whole brain structural MRI and diffusion connectomes for four diverse isogenic lines of mice (C57BL/6J, DBA/2J, CAST/EiJ, and BTBR) at spatial resolution 20,000 times higher than human connectomes. We measured narrow sense heritability (h2) I.e. the fraction of variance explained by strains in a simple ANOVA model for volumes and scalar diffusion metrics, and estimates of residual technical error for 166 regions in each hemisphere and connectivity between the regions. Volumes of discrete brain regions had the highest mean heritability (0.71 ± 0.23 SD, n = 332), followed by fractional anisotropy (0.54 ± 0.26), radial diffusivity (0.34 ± 0.022), and axial diffusivity (0.28 ± 0.19). Connection profiles were statistically different in 280 of 322 nodes across all four strains. Nearly 150 of the connection profiles were statistically different between the C57BL/6J, DBA/2J, and CAST/EiJ lines. Microscopic whole brain MRI/DTI has allowed us to identify significant heritable phenotypes in brain volume, scalar DTI metrics, and quantitative connectomes.

Ex vivo MR microscopy of a human brain with multiple sclerosis: Visualizing individual cells in tissue using intrinsic iron.

PURPOSE: To perform magnetic resonance microscopy (MRM) on human cortex and a cortical lesion as well as the adjacent normal appearing white matter. To shed light on the origins of MRI contrast by comparison with histochemical and immunostaining. METHODS: 3D MRM at a nominal isotropic resolution of 15 and 18 µm was performed on 2 blocks of tissue from the brain of a 77-year-old man who had MS for 47 years. One block contained normal appearing cortical gray matter (CN block) and adjacent normal appearing white matter (NAWM), and the other also included a cortical lesion (CL block). Postmortem ex-vivo MRI was performed at 11.7T using a custom solenoid coil and T2*-weighted 3D GRE sequence. Histochemical and immunostaining were done after paraffin embedding for iron, myelin, oligodendrocytes, neurons, blood vessels, macrophages and microglia, and astrocytes. RESULTS: MRM could identify individual iron-laden oligodendrocytes with high sensitivity (70% decrease in signal compared to surrounding) in CN and CL blocks, as well as some iron-laden activated macrophages and microglia. Iron-deficient oligodendrocytes seemed to cause relative increase in MRI signal within the cortical lesion. High concentration of myelin in the white matter was primarily responsible for its hypointense appearance relative to the cortex, however, signal variations within NAWM could be attributed to changes in density of iron-laden oligodendrocytes. CONCLUSION: Changes in iron accumulation within cells gave rise to imaging contrast seen between cortical lesions and normal cortex, as well as the patchy signal in NAWM. Densely packed myelin and collagen deposition also contributed to MRM signal changes. Even though we studied only one block each from normal appearing and cortical lesions, such studies can help better understand the origins of histopathological and microstructural correlates of MRI signal changes in multiple sclerosis and contextualize the interpretation of lower-resolution in vivo MRI scans.

On the application of balanced steady-state free precession to MR microscopy.

OBJECTIVE: The applicability of the balanced steady-state free precession (bSSFP) sequence to the field of MR microscopy was investigated, since the potentially high SNR makes bSSFP attractive. However, particularly at ultra-high magnetic fields, a number of constraints emerge: the frequency sensitivity of the bSSFP signal, the duty cycle of the imaging gradients, and the intrinsic diffusion attenuation of the steady state due to the imaging gradients. MATERIALS AND METHODS: Optimization of the bSSFP sequence was performed on three imaging systems (7 T and 9.4 T) suited for MR microscopy. Since biological samples are often imaged in the very proximity of materials from sample containers/holder or devices such as electrodes, several microscopy phantoms representing such circumstances were fabricated and examined with 3D bSSFP. RESULTS: Artifact-free microscopic bSSFP images could be obtained with voxel sizes down to 16 µm × 16 µm × 78 µm and with an SNR gain of 25% over standard gradient echo images. CONCLUSION: With appropriate choice of phantom materials, optimization of the flip angle to the diffusion-attenuated steady state and protocols considering duty-cycle limitations, bSSFP can be a valuable tool in MR microscopy.

In vivo MRI of the human finger at 7 T.

PURPOSE: To demonstrate a dedicated setup for ultrahigh resolution MR imaging of the human finger in vivo. METHODS: A radiofrequency coil was designed for optimized signal homogeneity and sensitivity in the finger at ultrahigh magnetic field strength (7 T), providing high measurement sensitivity. Imaging sequences (2D turbo-spin echo (TSE) and 3D magnetization-prepared rapid acquisition gradient echo (MPRAGE)) were adapted for high spatial resolution and good contrast of different tissues in the finger, while keeping acquisition time below 10 minutes. Data was postprocessed to display finger structures in three dimensions. RESULTS: 3D MPRAGE data with isotropic resolution of 200 µm, along with 2D TSE images with in-plane resolutions of 58 × 78 µm2 and 100 × 97 µm2 , allowed clear identification of various anatomical features such as bone and bone marrow, tendons and annular ligaments, cartilage, arteries and veins, nerves, and Pacinian corpuscles. CONCLUSION: Using this dedicated finger coil at 7 T, together with adapted acquisition sequences, it is possible to depict the internal structures of the human finger in vivo within patient-compatible measurement time. It may serve as a tool for diagnosis and treatment monitoring in pathologies ranging from inflammatory or erosive joint diseases to injuries of tendons and ligaments to nervous or vascular disorders in the finger. Magn Reson Med 79:588-592, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

9.4T and 17.6T MRI of Retinoblastoma: Ex Vivo evaluation of microstructural anatomy and disease extent compared with histopathology.

BACKGROUND: Retinoblastoma is the most common intraocular tumor in childhood with a good prognosis in terms of mortality, but detailed information about tumor morphology and disease extent in retinoblastoma is important for treatment decision making. PURPOSE: To demonstrate ultrahigh-field MRI tumor morphology and tumor extent in retinoblastoma correlating with in and ex vivo images with histopathology. STUDY TYPE: Prospective case series. POPULATION: Six retinoblastoma patients (median age 5.5 months, range 2-14) were prospectively included in this study. Median time between diagnosis and enucleation was 8 days (range 7-19). FIELD STRENGTH/SEQUENCE: In vivo pre-enucleation at 1.5T MRI with a circular surface coil. Ex vivo imaging (FLASH T1 -weighted and RARE T2 -weighted) was performed at field strengths of 9.4T and 17.6T. ASSESSMENT: After ex vivo imaging, the eyes were histopathologically analyzed and morphologically matched with MRI findings by three authors (two with respectively 14 and 4 years of experience in ocular MRI and one with 16 years of experience in ophthalmopathology). RESULTS: Small submillimeter morphological aspects of intraocular retinoblastoma were successfully depicted with higher-resolution MRI and matched with histopathology images. With ex vivo MRI a small subretinal tumor seed (300 µm) adjacent to the choroid was morphologically matched with histopathology. Also, a characteristic geographical pattern of vital tumor tissue (400 µm) surrounding a central vessel interspersed with necrotic areas correlated with histopathology images. Tumor invasion into the optic nerve showed a higher signal intensity on T1 -weighted higher-resolution MRI. DATA CONCLUSION: Higher-resolution MRI allows for small morphological aspects of intraocular retinoblastoma and extraocular disease extent not visible on currently used clinical in vivo MRI to be depicted. LEVEL OF EVIDENCE: 4 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:1487-1497.

MR microscopy of the human fetal upper extremity - a proof-of-principle study.

BACKGROUND: Current knowledge of the human fetal and embryonic development relies on early descriptive studies of humans and from experimental studies of laboratory animals and embryos. Taking the upper extremity as an example, this study explores the potential of magnetic resonance microscopy (MRM) for the assessment of the development of the fetal upper extremity and discusses its correlation with histological findings. METHODS: Ex vivo MRM at 7.1 T (Clin Scan, Bruker Biospin, Germany) was performed in 10 human specimens at 8 to 12 weeks of gestational age (GA). In-plane resolution was 20 µm with a slice thickness of 70 µm. MRM was followed by histological work-up of the specimens. MRM images were then correlated with conventional histology with a focus on the presence of chondrification and ossification. RESULTS: Ossification of the upper human extremity is detectable at 8 weeks GA in the humerus and the long bones of the forearm. There is excellent correlation for location and size of ossification between MRM and conventional histology. MRM imaging is in accordance with historical studies. CONCLUSION: Ex vivo MRM for the non-invasive assessment of the embryonic and fetal development of the upper human extremity is feasible. It may provide an accurate complementary tool for the evaluation of embryological development.

Intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence.

The purpose of this work was to analyze the intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence, meaning the observation of diffusion-induced attenuation of the bSSFP steady-state signal due to the imaging gradients. Although these diffusion effects are usually neglected for most clinical gradient systems, such strong gradient systems are employed for high resolution imaging of small animals or MR Microscopy. The impact on the bSSFP signal of the imaging gradients characterized by their b-values was analyzed with simulations and experiments at a 7T animal scanner using a gradient system with maximum gradient amplitude of approx. 700 mT/m. It was found that the readout gradients have a stronger impact on the attenuation than the phase encoding gradients. Also, as the PE gradients are varying with each repetition interval, the diffusion effects induce strong modulations of the bSSFP signal over the sequence repetition cycles depending on the phase encoding gradient table. It is shown that a signal gain can be obtained through a change of flip angle as a new optimal flip angle maximizing the signal can be defined. The dependency of the diffusion effects on relaxation times and b-values were explored with simulations. The attenuation increases with T2. In conclusion, diffusion attenuation of the bSSFP signal becomes significant for high resolution imaging voxel size (roughly < 100 µm) of long T2 substances.

4D MRI of polycystic kidneys from rapamycin-treated Glis3-deficient mice.

Polycystic kidney disease (PKD) is a life-threatening disease that leads to a grotesque enlargement of the kidney and significant loss of function. Several imaging studies with MRI have demonstrated that cyst size in polycystic kidneys can determine disease severity and progression. In the present study, we found that, although kidney volume and cyst volume decreased with drug treatment, renal function did not improve with treatment. Here, we applied dynamic contrast-enhanced MRI to study PKD in a Glis3 (GLI-similar 3)-deficient mouse model. Cysts from this model have a wide range of sizes and develop at an early age. To capture this crucial stage and assess cysts in detail, we imaged during early development (3-17 weeks) and applied high spatiotemporal resolution MRI (125 × 125 × 125 cubic microns every 7.7 s). A drug treatment with rapamycin (also known as sirolimus) was applied to determine whether disease progression could be halted. The effect and synergy (interaction) of aging and treatment were evaluated using an analysis of variance (ANOVA). Structural measurements, including kidney volume, cyst volume and cyst-to-kidney volume ratio, changed significantly with age. Drug treatment significantly decreased these metrics. Functional measurements of time-to-peak (TTP) mean and TTP variance were determined. TTP mean did not change with age, whereas TTP variance increased with age. Treatment with rapamycin generally did not affect these functional metrics. Synergistic effects of treatment and age were not found for any measurements. Together, the size and volume ratio of cysts decreased with drug treatment, whereas renal function remained the same. The quantification of renal structure and function with MRI can comprehensively assess the pathophysiology of PKD and response to treatment.

Phased-array of microcoils allows MR microscopy of ex vivo human skin samples at 9.4 T.

PURPOSE: The aim of this study was to demonstrate the feasibility of a custom-made phased-array microcoil within a 400 MHz animal system for the morphological characterization of human skin tissue in correlation with histopathology. MATERIALS AND METHODS: A dedicated 7-channel microcoil-based MR detector arranged in a phased-array geometry was developed to combine the advantages of both a large field of view and a high signal-to-noise ratio. Standard gradient echo sequences were adapted for the characterization of skin morphology ex vivo. RESULTS: In this study, the feasibility of using this type of microdetector, combined with specially manufactured sample holders, to achieve high-resolution MR images of fresh and formalin-fixed, normal and hidradenitis suppurativa diseased skin was successfully demonstrated. The setup presented in this work allows reliable acquisitions of high-resolution images with in-plane resolution up to 25 × 25 µm², and 100 µm in the orthogonal direction, thereby allowing the differentiation of typical layers of the skin, sebaceous glands and hair follicle. CONCLUSION: This study demonstrates that MR microscopy on skin biopsies can be applied at low cost on a standard animal MR imaging system. The successful imaging of different skin structures ex vivo is a prerequisite for non-invasive, in vivo application of skin MR microscopy for accurate complementary disease diagnosis in dermatology.

Evaluation of coils for imaging histological slides: signal-to-noise ratio and filling factor.

PURPOSE: To investigate the relative gain in sensitivity of five histology coils designed in-house to accommodate tissue sections of various sizes and compare with commercial mouse head coils. METHODS: The coil set was tailored to house tissue sections ranging from 5 to1000 µm encased in either glass slides or coverslips. RESULTS: Our simulations and experimental measurements demonstrated that although the sensitivity of this flat structure consistently underperforms relative to a birdcage head coil based on the gain expected from their respective filling factor ratios, our results demonstrate that it can still provide a remarkable gain in sensitivity. Our study also describes preparation protocols for freshly excised sections, as well as premounted tissue slides of both mouse and human specimens. Examples of the exceptional level of tissue detail and the near-perfect magnetic resonance imaging to light microscopic image coregistration are provided. CONCLUSION: The increase in filling factor achieved by the histology radiofrequency (RF) probe overcomes the losses associated with electric leaks inherent to this structure, leading to a 6.7-fold improvement in performance for the smallest coil implemented. Alternatively, the largest histology coil design exhibited equal sensitivity to the mouse head coil while nearly doubling the RF planar area coverage.

Four-dimensional MRI of renal function in the developing mouse.

The major roles of filtration, metabolism and high blood flow make the kidney highly vulnerable to drug-induced toxicity and other renal injuries. A method to follow kidney function is essential for the early screening of toxicity and malformations. In this study, we acquired high spatiotemporal resolution (four dimensional) datasets of normal mice to follow changes in kidney structure and function during development. The data were acquired with dynamic contrast-enhanced MRI (via keyhole imaging) and a cryogenic surface coil, allowing us to obtain a full three-dimensional image (isotropic resolution, 125 microns) every 7.7 s over a 50-min scan. This time course permitted the demonstration of both contrast enhancement and clearance. Functional changes were measured over a 17-week course (at 3, 5, 7, 9, 13 and 17 weeks). The time dimension of the MRI dataset was processed to produce unique image contrasts to segment the four regions of the kidney: cortex (CO), outer stripe (OS) of the outer medulla (OM), inner stripe (IS) of the OM and inner medulla (IM). Local volumes, time-to-peak (TTP) values and decay constants (DC) were measured in each renal region. These metrics increased significantly with age, with the exception of DC values in the IS and OS. These data will serve as a foundation for studies of normal renal physiology and future studies of renal diseases that require early detection and intervention.

MR microscopy of the human finger and correlation with histology--a proof-of-principle study.

Magnetic resonance imaging (MRI) with small surface coils is a well established method for the diagnostic evaluation of finger masses. Until now, histological examination has been required to reliably assess tumor extent and infiltration of surrounding structures. Ultra-high-field MR microscopy (MRM) allows evaluation of anatomical structures and pathologies with submillimeter resolution. This study describes the diagnostic prospects and potential of MRM based on the ex-vivo examination of different finger pathologies. Ten human digits were examined by ex-vivo MRM at 7.1 Tesla (ClinScan, Bruker BioScan) using a T2-weighted turbo spin echo (TSE) sequence. Imaging parameters were: TE 48 ms; TR 8370 ms; slice thickness 700 µm; matrix size 1024 × 1024 pixels; FOV 37 × 37 mm; in-plane resolution 36 × 36 µm/voxel. Afterwards specimens were examined histologically. Histology and MRM were correlated. MRM allowed evaluation of the anatomy of the nail, the tendon insertions, the distal interphalangeal joint, and the neurovascular bundles. Finger abnormalities evaluated by MRM included osteomyelitis and metastatic disease. Subsequent histological examination confirmed MRM findings regarding origin, internal makeup, and extent of the structures visualized. This study demonstrates the potential of MRM for imaging small anatomical structures and pathologies of the human finger. Our ex-vivo findings correlate strongly with histology, suggesting that MRM may gain a central role in assessing anatomical structures and pathology in terms of morphology, extent, and infiltration of surrounding structures. Therefore, with increasing availability, MRM is expected to become an essential tool not only in experimental studies but also for daily routine.

High-resolution MRI for human embryos with isotropic 10 µm resolution at 9.4 T.

Magnetic resonance (MR) microscopy of human embryos has contributed significantly to the development of human embryology. Higher-resolution MR microscopy will have obvious benefits, for example, in visualizing small structures that are blurred or lost in lower-resolution images, providing detailed information on the development and growth of various organs, and improving the accuracy of MR volumetry. However, high-resolution MR microscopy has yet to be realized because of many technical challenges. In this study, therefore, we have performed high-resolution MR microscopy for human embryos with isotropic resolutions of (12 µm)3 at full sampling and (10 µm)3 at compressed sensing, which far exceeds the resolution of previous embryonic MR studies. The hardware and the pulse sequence were improved to achieve higher spatial resolution. Line profile, signal-to-noise ratio, and histogram analysis using phantom images were performed to verify that the resolution and the voxel size were identical. Comparison with optical microscopy images of embryo specimens at the same developmental stage was performed to confirm that the microstructures were well delineated. Our results show that imaging at this high resolution effectively depicts the microstructures of human embryos. This technology is the cornerstone for constructing an unprecedented high-quality atlas that will contribute to the development of human embryology.

Corrigendum: Histological Correlates of Diffusion-Weighted Magnetic Resonance Microscopy in a Mouse Model of Mesial Temporal Lobe Epilepsy.

[This corrects the article DOI: 10.3389/fnins.2020.00543.].

Inner SPACE: 400-Micron Isotropic Resolution MRI of the Human Brain.

OBJECTIVES: Clinically relevant neuroanatomy is challenging to teach, learn and remember since many functionally important structures are visualized best using histology stains from serial 2D planar sections of the brain. In clinical patients, the locations of specific structures then must be inferred from spatial position and surface anatomy. A 3D MRI dataset of neuroanatomy has several advantages including simultaneous multi-planar visualization in the same brain, direct end-user manipulation of the data and image contrast identical to clinical MRI. We created 3D MRI datasets of the postmortem brain with high spatial and contrast resolution for simultaneous multi-planar visualization of complex neuroanatomy. MATERIALS AND METHODS: Whole human brains (N = 6) were immersion-fixed in 4% formaldehyde for 4 weeks, then washed continuously in water for 48 h. The brains were imaged on a clinical 3-T MRI scanner with a 64-channel head and neck coil using a 3D T2-weighted sequence with 400-micron isotropic resolution (voxel = 0.064 mm3; time = 7 h). Besides resolution, this sequence has multiple adjustments to improve contrast compared to a clinical protocol, including 93% reduced turbo factor and 77% reduced effective echo time. RESULTS: This MRI microscopy protocol provided excellent contrast resolution of small nuclei and internal myelinated pathways within the basal ganglia, thalamus, brainstem, and cerebellum. Contrast was sufficient to visualize the presence and variation of horizontal layers in the cerebral cortex. 3D isotropic resolution datasets facilitated simultaneous multi-planar visualization and efficient production of specific tailored oblique image orientations to improve understanding of complex neuroanatomy. CONCLUSION: We created an unlabeled high-resolution digital 3D MRI dataset of neuroanatomy as an online resource for readers to download, manipulate, annotate and use for clinical practice, research, and teaching that is complementary to traditional histology-based atlases. Digital MRI contrast is quantifiable, reproducible across brains and could help validate novel MRI strategies for in vivo structure visualization.

Histological Correlates of Diffusion-Weighted Magnetic Resonance Microscopy in a Mouse Model of Mesial Temporal Lobe Epilepsy.

Mesial temporal lobe epilepsy (MTLE) is the most common type of focal epilepsy. It is frequently associated with abnormal MRI findings, which are caused by underlying cellular, structural, and chemical changes at the micro-scale. In the current study, it is investigated to which extent these alterations correspond to imaging features detected by high resolution magnetic resonance imaging in the intrahippocampal kainate mouse model of MTLE. Fixed hippocampal and whole-brain sections of mouse brain tissue from nine animals under physiological and chronically epileptic conditions were examined using structural and diffusion-weighted MRI. Microstructural details were investigated based on a direct comparison with immunohistochemical analyses of the same specimen. Within the hippocampal formation, diffusion streamlines could be visualized corresponding to dendrites of CA1 pyramidal cells and granule cells, as well as mossy fibers and Schaffer collaterals. Statistically significant changes in diffusivities, fractional anisotropy, and diffusion orientations could be detected in tissue samples from chronically epileptic animals compared to healthy controls, corresponding to microstructural alterations (degeneration of pyramidal cells, dispersion of the granule cell layer, and sprouting of mossy fibers). The diffusion parameters were significantly correlated with histologically determined cell densities. These findings demonstrate that high-resolution diffusion-weighted MRI can resolve subtle microstructural changes in epileptic hippocampal tissue corresponding to histopathological features in MTLE.