MR microscopy and high resolution small animal MRI: applications in neuroscience research

Analyzing the cortical fine structure as revealed by ex-vivo anatomical MRI

The human cortex has a rich fiber structure as revealed by myelin-staining of histological slices. Myelin also contributes to the image contrast in Magnetic Resonance Imaging (MRI). Recent advances in Magnetic Resonance (MR) scanner and imaging technology allowed the acquisition of an ex-vivo data set at an isotropic resolution of 100 µm. This study focused on a computational analysis of this data set with the aim of bridging between histological knowledge and MRI-based results. This work highlights: (1) the design and implementation of a processing chain that extracts intracortical features from a high-resolution MR image; (2) a demonstration of the correspondence between MRI-based cortical intensity profiles and the myelo-architectonic layering of the cortex; (3) the characterization and classification of four basic myelo-architectonic profile types; (4) the distinction of cortical regions based on myelo-architectonic features; and (5) the segmentation of cortical modules in the entorhinal cortex.

Tissue optimization strategies for high-quality ex vivo diffusion imaging

Ex vivo diffusion imaging can be used to study healthy and pathological tissue microstructure in the rodent brain with high resolution, providing a link between in vivo MRI and ex vivo microscopy techniques. Major challenges for the successful acquisition of ex vivo diffusion imaging data however are changes in the relaxivity and diffusivity of brain tissue following perfusion fixation. In this study we address this question by examining the combined effects of tissue preparation factors that influence signal-to-noise ratio (SNR) and consequently image quality, including fixative concentration, contrast agent concentration and tissue rehydration time. We present an optimization strategy combining these factors to manipulate theT 1 andT 2 of fixed tissue and maximize SNR efficiency. We apply this strategy in the rat brain, for a diffusion-weighted spin echo protocol with TE = 27 ms on a 9.4 T scanner with a 39 mm volume coil and 660 mT/m 114 mm gradient insert. We used a reduced fixative concentration of 2% paraformaldehyde (PFA), rehydration time more than 20 days, 15 mM Gd-DTPA in perfusate and TR 250 ms. This resulted in a doubling of SNR and an increase in SNR per unit time of 135% in cortical grey matter and 88% in white matter compared with 4% PFA and no contrast agent. This improved SNR efficiency enabled the acquisition of excellent-quality high-resolution (78 μ m isotropic voxel size) diffusion data with b = 4000 s/mm2 , 30 diffusion directions and a field of view of 40 × 13 × 18 mm3 in less than 4 days. It was also possible to achieve comparable data quality for a standard resolution (150 μ m) diffusion dataset in 2 1 4 h. In conclusion, the tissue optimization strategy presented here may be used to improve SNR, increase spatial resolution and/or allow faster acquisitions in preclinical ex vivo diffusion MRI experiments.

Fluids and flows in brain cancer and neurological disorders

Interstitial fluid (IF) and cerebrospinal fluid (CSF) are an integral part of the brain, serving to cushion and protect the brain parenchymal cells against damage and aid in their function. The brain IF contains various ions, nutrients, waste products, peptides, hormones, and neurotransmitters. IF moves primarily by pressure-dependent bulk flow through brain parenchyma, draining into the ventricular CSF. The brain ventricles and subarachnoid spaces are filled with CSF which circulates through the perivascular spaces. It also flows into the IF space regulated, in part, by aquaporin channels, removing waste solutes through a process of IF-CSF mixing. During disease development, the composition, flow, and volume of these fluids changes and can lead to brain cell dysfunction. With the improvement of imaging technology and the help of genomic profiling, more information has been and can be obtained from brain fluids; however, the role of CSF and IF in brain cancer and neurobiological disease is still limited. Here we outline recent advances of our knowledge of brain fluid flow in cancer and neurodegenerative disease based on our understanding of its dynamics and composition. This article is categorized under: Cancer > Biomedical Engineering Neurological Diseases > Biomedical Engineering.

In vivo molecular imaging in preclinical research

In vivo molecular imaging is a research field in which molecular biology and advanced imaging techniques are combined for imaging molecular-level biochemical and physiological changes that occur in a living body. For biomolecular imaging, the knowledge of molecular biology, cell biology, biochemistry, and physiology must be applied. Imaging techniques such as fluorescence, luminescence, single-photon emission computed tomography (SPECT), positron emission tomography (PET), computed tomography (CT), and magnetic resonance imaging (MRI) are used for biomolecular imaging. These imaging techniques are used in various fields, i.e., diagnosis of various diseases, development of new drugs, development of treatments, and evaluation of effects. Moreover, as biomolecular imaging can repeatedly acquire images without damaging biological tissues or sacrificing the integrity of objects, changes over time can be evaluated.

Phenotypes or diseases in a living body are caused by the accumulation of various biological phenomena. Genetic differences cause biochemical and physiological differences, which accumulate and cause anatomical or structural changes. Biomolecular imaging techniques are suitable for each step. In evaluating anatomical or structural changes, MRI, CT, and ultrasound have advantages in obtaining high-resolution images. SPECT and MRI are advantageous for the evaluation of various physiological phenomena. PET and magnetic resonance spectroscopy can be used to image biochemical phenomena in vivo. Although various biomolecular imaging techniques can be used to evaluate various biological phenomena, it is important to use imaging techniques suitable for each purpose.

Simulation Study of Radio Frequency Safety and the Optimal Size of a Single-Channel Surface Radio Frequency Coil for Mice at 9.4 T Magnetic Resonance Imaging

The optimized size of a single-channel surface radio frequency (RF) coil for mouse body images in a 9.4 T magnetic resonance imaging (MRI) system was determined via electromagnetic-field analysis of the signal depth according to the size of a single-channel coil. The single-channel surface RF coils used in electromagnetic field simulations were configured to operate in transmission/reception mode at a frequency of 9.4 T–400 MHz. Computational analysis using the finite-difference time-domain method was used to assess the single-channel surface RF coil by comparing single-channel surface RF coils of varying sizes in terms of |B₁|-, |B₁⁺|-, |B₁⁻|- and |E|-field distribution. RF safety for the prevention of burn injuries to small animals was assessed using an analysis of the specific absorption rate. A single-channel surface RF coil with a 20 mm diameter provided optimal B₁-field distribution and RF safety, thus confirming that single-channel surface RF coils with ≥25 mm diameter could not provide typical B₁-field distribution. A single-channel surface RF coil with a 20 mm diameter for mouse body imaging at 9.4 T MRI was recommended to preserve the characteristics of single-channel surface RF coils, and ensured that RF signals were applied correctly to the target point within RF safety guidelines.

MR-compatible optical microscope for in-situ dual-mode MR-optical microscopy

We present the development of a dual-mode imaging platform that combines optical microscopy with magnetic resonance microscopy. Our microscope is designed to operate inside a 9.4T small animal scanner with the option to use a 72mm bore animal RF coil or different integrated linear micro coils. With a design that minimizes the magnetic distortions near the sample, we achieved a field inhomogeneity of 19 ppb RMS. We further integrated a waveguide in the optical layout for the electromagnetic shielding of the camera, which minimizes the noise increase in the MR and optical images below practical relevance. The optical layout uses an adaptive lens for focusing, 2 × 2 modular combinations of objectives with 0.6mm to 2.3mm field of view and 4 configurable RGBW illumination channels and achieves a plano-apochromatic optical aberration correction with 0.6μm to 2.3μm resolution. We present the design, implementation and characterization of the prototype including the general optical and MR-compatible design strategies, a knife-edge optical characterization and different concurrent imaging demonstrations.

Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging

G Protein-Coupled Receptor Kinase-Interacting Protein-1 (GIT1) regulates neuronal functions, including cell and axon migration and synapse formation and maintenance, and GIT1 knockout (KO) mice exhibit learning and memory deficits. We noted that male and female GIT1-KO mice exhibit neuroimaging phenotypes including microcephaly, and altered cortical layering, with a decrease in neuron density in cortical layer V. Micro-CT and magnetic resonance microscopy (MRM) were used to identify morphometric phenotypes for the skulls and throughout the GIT1-KO brains. High field MRM of actively-stained mouse brains from GIT1-KO and wild type (WT) controls (n = 6 per group) allowed segmenting 37 regions, based on co-registration to the Waxholm Space atlas. Overall brain size in GIT1-KO mice was ~32% smaller compared to WT controls. After correcting for brain size, several regions were significantly different in GIT1-KO mice relative to WT, including the gray matter of the ventral thalamic nuclei and the rest of the thalamus, the inferior colliculus, and pontine nuclei. GIT1-KO mice had reduced volume of white matter tracts, most notably in the anterior commissure (~26% smaller), but also in the cerebral peduncle, fornix, and spinal trigeminal tract. On the other hand, the basal ganglia appeared enlarged in GIT1-KO mice, including the globus pallidus, caudate putamen, and particularly the accumbens - supporting a possible vulnerability to addiction. Volume based morphometry based on high-resolution MRM (21.5 μm isotropic voxels) was effective in detecting overall, and local differences in brain volumes in GIT1-KO mice, including in white matter tracts. The reduced relative volume of specific brain regions suggests a critical, but not uniform, role for GIT1 in brain development, conducive to brain microcephaly, and aberrant connectivity.

Magnetic resonance microscopy of samples with translational symmetry with FOVs smaller than sample size

In MRI, usually the Field of View (FOV) has to cover the entire object. If this condition is not fulfilled, an infolding image artifact is observed, which suppresses visualization. In this study it is shown that for samples with translational symmetry, i.e., those consisting of identical objects in periodic unit cells, the FOV can be reduced to match the unit cell which enables imaging of an average object, of which the signal is originated from all unit cells of the sample, with no punishment by a loss in signal-to-noise ratio (SNR). This theoretical prediction was confirmed by experiments on a test sample with a 7 × 7 mm² unit cell arranged in a 3 × 3 matrix which was scanned by the spin-echo and by single point imaging methods. Effects of experimental imperfections in size and orientation mismatch between FOV and unit cell were studied as well. Finally, this method was demonstrated on a 3D periodic sample of tablets, which yielded well-resolved images of moisture distribution in an average tablet, while single tablet imaging provided no results. The method can be applied for SNR increase in imaging of any objects with inherently low signals provided they can be arranged in a periodic structure.

Assessing spatial resolution, acquisition time and signal-to-noise ratio for commercial microimaging systems at 14.1, 17.6 and 22.3 T

This work provides a systematic comparison of the signal-to-noise ratio (SNR), spatial resolution, acquisition time and metabolite limits-of-detection for magnetic resonance microscopy and spectroscopy at three different magnetic field strengths of 14.1 T, 17.6 T and 22.3 T (the highest currently available for imaging), utilizing commercially available hardware. We find an SNR increase of a factor 5.9 going from 14.1 T to 22.3 T using 5 mm radiofrequency (saddle and birdcage) coils, which results in a 24-fold acceleration in acquisition time and deviates from the theoretically expected increase of factor 2.2 due to differences in hardware. This underlines the importance of not only the magnetic field strengths but also hardware optimization. In addition, using a home-built 1.5 mm solenoid coil, we can achieve an isotropic resolution of (5.5 µm)³ over a field-of-view of 1.58 mm × 1.05 mm × 1.05 mm with an SNR of 12:1 using 44 signal averages in 58 h 34 min acquisition time at 22.3 T. In light of these results, we discuss future perspectives for ultra-high field Magnetic Resonance Microscopy and Spectroscopy.

3D Monte Carlo simulation of light distribution in mouse brain in quantitative photoacoustic computed tomography

Background

Photoacoustic computed tomography (PACT) detects light-induced ultrasound (US) waves to reconstruct the optical absorption contrast of the biological tissues. Due to its relatively deep penetration (several centimeters in soft tissue), high spatial resolution, and inherent functional sensitivity, PACT has great potential for imaging mouse brains with endogenous and exogenous contrasts, which is of immense interest to the neuroscience community. However, conventional PACT either assumes homogenous optical fluence within the brain or uses a simplified attenuation model for optical fluence estimation. Both approaches underestimate the complexity of the fluence heterogeneity and can result in poor quantitative imaging accuracy.

Methods

To optimize the quantitative performance of PACT, we explore for the first time 3D Monte Carlo (MC) simulation to study the optical fluence distribution in a complete mouse brain model. We apply the MCX MC simulation package on a digital mouse (Digimouse) brain atlas that has complete anatomy information. To evaluate the impact of the brain vasculature on light delivery, we also incorporate the whole-brain vasculature in the Digimouse atlas. k-wave toolbox was used to investigate the effect of inhomogeneous illumination on the reconstructed images and chromophore concentration estimation.

Results

The simulation results clearly show that the optical fluence in the mouse brain is heterogeneous at the global level and can decrease by a factor of five with increasing depth. Moreover, the strong absorption and scattering of the brain vasculature also induce the fluence disturbance at the local level.

Conclusions

Both global and local fluence heterogeneity contributes to the reduced quantitative accuracy of the reconstructed PACT images of mouse brain. Correcting the optical fluence distribution can improve the quantitative accuracy of PACT.

Non-invasive quantification of cardiac stroke volume in the edible crab Cancer pagurus

Background

Brachyuran crabs can effectively modulate cardiac stroke volume independently of heart rate in response to abiotic drivers. Non-invasive techniques can help to improve the understanding of cardiac performance parameters of these animals. This study demonstrates the in vivo quantification of cardiac performance parameters through magnetic resonance imaging (MRI) on the edible crab Cancer pagurus. Furthermore, the suitability of signal integrals of infra-red photoplethysmographs as a qualitative tool is assessed under severe hypoxia.

Results

Multi-slice self-gated cardiac cinematic (CINE) MRI revealed the structure and motion of the ventricle to quantify heart rates, end-diastolic volume, end-systolic volume, stroke volume and ejection fraction. CINE MRI showed that stroke volumes increased under hypoxia because of a reduction of end-systolic volumes at constant end-diastolic volumes. Plethysmograph recordings allowed for automated heart rate measurements but determination of a qualitative stroke volume proxy strongly depended on the position of the sensor on the animal. Both techniques revealed a doubling in stroke volumes after 6 h under severe hypoxia (water PO₂ = 15% air saturation).

Conclusions

MRI has allowed for detailed descriptions of cardiac performance in intact animals under hypoxia. The temporal resolution of quantitative non-invasive CINE MRI is limited but should encourage further refining. The stroke volume proxy based on plethysmograph recordings is feasible to complement other cardiac measurements over time. The presented methods allow for non-destructive in vivo determinations of multiple cardiac performance parameters, with the possibility to study neuro-hormonal or environmental effects on decapod cardio physiology.

Non-sedated functional imaging based on deep synchronization of PROPELLER MRI and NIRS

BACKGROUND AND OBJECTIVE

Periodically rotated overlapping parallel lines with enhanced reconstruction-echo planar imaging (PROPELLER-EPI) is a promising technique for non-sedated functional imaging due to its unique advantage of motion correction. However, its multiple-blades sampling blood-oxygen-level dependent (BOLD) signal leads to low sampling rate and aliasing of higher frequency physiological signal components such as the cardiac pulsation.

METHODS

In this study, we use near infrared spectroscopy (NIRS) synchronized with pulse sequences of PROPELLER-EPI, utilizing the fact that the optical sensing speed is inherently high. NIRS measures changes of oxyhemoglobin and deoxyhemoglobin to identify the transient states of on-BOLD and off-BOLD, and then labels each blade by temporal co-registration. The labeled blades from multiple epochs of a functional experiment are then used for the k-space data combination and subsequent image reconstruction. An eigenfunction model is proposed for temporal co-registration and to quantify the temporal resolution of the hemodynamic response.

RESULT

The experiment of NIRS labeled PROPELLER-EPI was carried out with the optical sampling rate of 10 Hz and the magnetic pulses repetition time of 1000 ms, and the temporal resolution is 20 times better than that of the state-of-the-art sliding-window PROPELLER-EPI. We compared the functional imaging results against the conventional magnetic resonance echo planar imaging-measured activity and achieved an accuracy of 0.9.

CONCLUSIONS

Using the synchronization of NIRS, the proposed imaging scheme provides an effective way to implement PROPELLER-EPI, which features motion free, high SNR, and enhanced spatial-temporal resolution.

Studying the cardiovascular system of a marine crustacean with magnetic resonance imaging at 9.4 T

OBJECTIVES

An approach is presented for high-field MRI studies of the cardiovascular system (CVS) of a marine crustacean, the edible crab Cancer pagurus, submerged in highly conductive seawater.

MATERIALS AND METHODS

Structure and function of the CVS were investigated at 9.4 T. Cardiac motion was studied using self-gated CINE MRI. Imaging protocols and radio-frequency coil arrangements were tested for anatomical imaging. Haemolymph flow was quantified using phase-contrast angiography. Signal-to-noise-ratios and flow velocities in afferent and efferent branchial veins were compared with Student's t test (n = 5).

RESULTS

Seawater induced signal losses were dependent on imaging protocols and RF coil setup. Internal cardiac structures could be visualized with high spatial resolution within 8 min using a gradient-echo technique. Variations in haemolymph flow in different vessels could be determined over time. Maximum flow was similar within individual vessels and corresponded to literature values from Doppler measurements. Heart contractions were more pronounced in lateral and dorso-ventral directions than in the anterior-posterior direction.

DISCUSSION

Choosing adequate imaging protocols in combination with a specific RF coil arrangement allows to monitor various parts of the crustacean CVS with exceptionally high spatial resolution despite the adverse effects of seawater at 9.4 T.

Emerging Applications of Porphyrins and Metalloporphyrins in Biomedicine and Diagnostic Magnetic Resonance Imaging

In recent years, scientific advancements have constantly increased at a significant rate in the field of biomedical science. Keeping this in view, the application of porphyrins and metalloporphyrins in the field of biomedical science is gaining substantial importance. Porphyrins are the most widely studied tetrapyrrole-based compounds because of their important roles in vital biological processes. The cavity of porphyrins containing four pyrrolic nitrogens is well suited for the binding majority of metal ions to form metalloporphyrins. Porphyrins and metalloporphyrins possess peculiar photochemical, photophysical, and photoredox properties which are tunable through structural modifications. Their beneficial photophysical properties, such as the long wavelength of emission and absorption, high singlet oxygen quantum yield, and low in vivo toxicity, have drawn scientists' interest to discover new dimensions in the biomedical field. Applications of porphyrins and metalloporphyrins have been pursued in the perspective of contrast agents for magnetic resonance imaging (MRI), photodynamic therapy (PDT) of cancer, bio-imaging, and other biomedical applications. This review discusses photophysics and the photochemistry of porphyrins and their metal complexes. Secondly, it explains the current developments and mode of action for contrast agents for MRI. Moreover, the application of porphyrin and metalloporphyrin-based molecules as a photosensitizer in PDT of cancer, the mechanism of the generation of reactive oxygen species (ROS), factors that determine the efficiency of PDT, and the developments to improve this technology are delineated. The last part explores the most recent research and developments on metalloporphyrin-based materials in bio-imaging, drug delivery, and the determination of ferrochelatase in bone marrow indicating their prospective clinical applications.

Micro-imaging of Brain Cancer Radiation Therapy Using Phase-contrast Computed Tomography

PURPOSE

Experimental neuroimaging provides a wide range of methods for the visualization of brain anatomic morphology down to subcellular detail. Still, each technique-specific detection mechanism presents compromises among the achievable field-of-view size, spatial resolution, and nervous tissue sensitivity, leading to partial sample coverage, unresolved morphologic structures, or sparse labeling of neuronal populations and often also to obligatory sample dissection or other sample invasive manipulations. X-ray phase-contrast imaging computed tomography (PCI-CT) is an experimental imaging method that simultaneously provides micrometric spatial resolution, high soft-tissue sensitivity, and ex vivo full organ rodent brain coverage without any need for sample dissection, staining or labeling, or contrast agent injection. In the present study, we explored the benefits and limitations of PCI-CT use for in vitro imaging of normal and cancerous brain neuromorphology after in vivo treatment with synchrotron-generated x-ray microbeam radiation therapy (MRT), a spatially fractionated experimental high-dose radiosurgery. The goals were visualization of the MRT effects on nervous tissue and a qualitative comparison of the results to the histologic and high-field magnetic resonance imaging findings.

METHODS AND MATERIALS

MRT was administered in vivo to the brain of both healthy and cancer-bearing rats. At 45 days after treatment, the brain was dissected out and imaged ex vivo using propagation-based PCI-CT.

RESULTS

PCI-CT visualizes the brain anatomy and microvasculature in 3 dimensions and distinguishes cancerous tissue morphology, necrosis, and intratumor accumulation of iron and calcium deposits. Moreover, PCI-CT detects the effects of MRT throughout the treatment target areas (eg, the formation of micrometer-thick radiation-induced tissue ablation). The observed neurostructures were confirmed by histologic and immunohistochemistry examination and related to the micro-magnetic resonance imaging data.

CONCLUSIONS

PCI-CT enabled a unique 3D neuroimaging approach for ex vivo studies on small animal models in that it concurrently delivers high-resolution insight of local brain tissue morphology in both normal and cancerous micro-milieu, localizes radiosurgical damage, and highlights the deep microvasculature. This method could assist experimental small animal neurology studies in the postmortem evaluation of neuropathology or treatment effects.

Tissue magnetic susceptibility mapping as a marker of tau pathology in Alzheimer's disease

Alzheimer's disease is connected to a number of other neurodegenerative conditions, known collectively as 'tauopathies', by the presence of aggregated tau protein in the brain. Neuroinflammation and oxidative stress in AD are associated with tau pathology and both the breakdown of axonal sheaths in white matter tracts and excess iron accumulation grey matter brain regions. Despite the identification of myelin and iron concentration as major sources of contrast in quantitative susceptibility maps of the brain, the sensitivity of this technique to tau pathology has yet to be explored. In this study, we perform Quantitative Susceptibility Mapping (QSM) and T2* mapping in the rTg4510, a mouse model of tauopathy, both in vivo and ex vivo. Significant correlations were observed between histological measures of myelin content and both mean regional magnetic susceptibility and T2* values. These results suggest that magnetic susceptibility is sensitive to tissue myelin concentrations across different regions of the brain. Differences in magnetic susceptibility were detected in the corpus callosum, striatum, hippocampus and thalamus of the rTg4510 mice relative to wild type controls. The concentration of neurofibrillary tangles was found to be low to intermediate in these brain regions indicating that QSM may be a useful biomarker for early stage detection of tau pathology in neurodegenerative diseases.

Ex vivo tissue imaging for radiology-pathology correlation: a pilot study with a small bore 7-T MRI in a rare pigmented ganglioglioma exhibiting complex MR signal characteristics associated with melanin and hemosiderin

To advance magnetic resonance imaging (MRI) technologies further for in vivo tissue characterization with histopathologic validation, we investigated the feasibility of ex vivo tissue imaging of a surgically removed human brain tumor as a comprehensive approach for radiology–pathology correlation in histoanatomically identical fashion in a rare case of pigmented ganglioglioma with complex paramagnetic properties. Pieces of surgically removed ganglioglioma, containing melanin and hemosiderin pigments, were imaged with a small bore 7-T MRI scanner to obtain T1-, T2-, and T2*-weighted image and diffusion tensor imaging (DTI). Corresponding histopathological slides were prepared for routine hematoxylin and eosin stain and special stains for melanin and iron/hemosiderin to correlate with MRI signal characteristics. Furthermore, mean diffusivity (MD) maps were generated from DTI data and correlated with cellularity using image analysis. While the presence of melanin was difficult to interpret in in vivo MRI with certainty due to concomitant hemosiderin pigments and calcium depositions, ex vivo tissue imaging clearly demonstrated pieces of tissue exhibiting the characteristic MR signal pattern for melanin with pathologic confirmation in a histoanatomically identical location. There was also concordant correlation between MD and cellularity. Although it is still in an initial phase of development, ex vivo tissue imaging is a promising approach, which offers radiology–pathology correlation in a straightforward and comprehensive manner.

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study

Very preterm newborns have an increased risk of developing an inflammatory cerebral white matter injury that may lead to severe neuro-cognitive impairment. In this study we performed functional connectivity (fc) analysis using resting-state optical imaging of intrinsic signals (rs-OIS) to assess the impact of inflammation on resting-state networks (RSN) in a pre-clinical model of perinatal inflammatory brain injury. Lipopolysaccharide (LPS) or saline injections were administered in postnatal day (P3) rat pups and optical imaging of intrinsic signals were obtained 3 weeks later. (rs-OIS) fc seed-based analysis including spatial extent were performed. A support vector machine (SVM) was then used to classify rat pups in two categories using fc measures and an artificial neural network (ANN) was implemented to predict lesion size from those same fc measures. A significant decrease in the spatial extent of fc statistical maps was observed in the injured group, across contrasts and seeds (^*p = 0.0452 for HbO₂ and ^**p = 0.0036 for HbR). Both machine learning techniques were applied successfully, yielding 92% accuracy in group classification and a significant correlation r = 0.9431 in fractional lesion volume prediction (^**p = 0.0020). Our results suggest that fc is altered in the injured newborn brain, showing the long-standing effect of inflammation.

Scanning laser optical tomography for in toto imaging of the murine cochlea

The mammalian cochlea is a complex macroscopic structure due to its helical shape and the microscopic arrangements of the individual layers of cells. To improve the outcomes of hearing restoration in deaf patients, it is important to understand the anatomic structure and composition of the cochlea ex vivo. Hitherto, only one histological technique based on confocal laser scanning microscopy and optical clearing has been developed for in toto optical imaging of the murine cochlea. However, with a growing size of the specimen, e.g., human cochlea, this technique reaches its limitations. Here, we demonstrate scanning laser optical tomography (SLOT) as a valuable imaging technique to visualize the murine cochlea in toto without any physical slicing. This technique can also be applied in larger specimens up to cm³ such as the human cochlea. Furthermore, immunolabeling allows visualization of inner hair cells (otoferlin) or spiral ganglion cells (neurofilament) within the whole cochlea. After image reconstruction, the 3D dataset was used for digital segmentation of the labeled region. As a result, quantitative analysis of position, length and curvature of the labeled region was possible. This is of high interest in order to understand the interaction of cochlear implants (CI) and cells in more detail.

Dry coupling for whole-body small-animal photoacoustic computed tomography

We have enhanced photoacoustic computed tomography with dry acoustic coupling that eliminates water immersion anxiety and wrinkling of the animal and facilitates incorporating complementary modalities and procedures. The dry acoustic coupler is made of a tubular elastic membrane enclosed by a closed transparent water tank. The tubular membrane ensures water-free contact with the animal, and the closed water tank allows pressurization for animal stabilization. The dry coupler was tested using a whole-body small-animal ring-shaped photoacoustic computed tomography system. Dry coupling was found to provide image quality comparable to that of conventional water coupling.

Comparison of In Vivo and Ex Vivo MRI for the Detection of Structural Abnormalities in a Mouse Model of Tauopathy

With increasingly large numbers of mouse models of human disease dedicated to MRI studies, compromises between in vivo and ex vivo MRI must be fully understood in order to inform the choice of imaging methodology. We investigate the application of high resolution in vivo and ex vivo MRI, in combination with tensor-based morphometry (TBM), to uncover morphological differences in the rTg4510 mouse model of tauopathy. The rTg4510 mouse also offers a novel paradigm by which the overexpression of mutant tau can be regulated by the administration of doxycycline, providing us with a platform on which to investigate more subtle alterations in morphology with morphometry. Both in vivo and ex vivo MRI allowed the detection of widespread bilateral patterns of atrophy in the rTg4510 mouse brain relative to wild-type controls. Regions of volume loss aligned with neuronal loss and pathological tau accumulation demonstrated by immunohistochemistry. When we sought to investigate more subtle structural alterations in the rTg4510 mice relative to a subset of doxycycline-treated rTg4510 mice, ex vivo imaging enabled the detection of more regions of morphological brain changes. The disadvantages of ex vivo MRI may however mitigate this increase in sensitivity: we observed a 10% global shrinkage in brain volume of the post-mortem tissues due to formalin fixation, which was most notable in the cerebellum and olfactory bulbs. However, many central brain regions were not adversely affected by the fixation protocol, perhaps due to our “in-skull” preparation. The disparity between our TBM findings from in vivo and ex vivo MRI underlines the importance of appropriate study design, given the trade-off between these two imaging approaches. We support the utility of in vivo MRI for morphological phenotyping of mouse models of disease; however, for subtler phenotypes, ex vivo offers enhanced sensitivity to discrete morphological changes.

The Neuromelanin-related T2* Contrast in Postmortem Human Substantia Nigra with 7T MRI

High field magnetic resonance imaging (MRI)-based delineation of the substantia nigra (SN) and visualization of its inner cellular organization are promising methods for the evaluation of morphological changes associated with neurodegenerative diseases; however, corresponding MR contrasts must be matched and validated with quantitative histological information. Slices from two postmortem SN samples were imaged with a 7 Tesla (7T) MRI with T₁ and T₂* imaging protocols and then stained with Perl’s Prussian blue, Kluver-Barrera, tyrosine hydroxylase, and calbindin immunohistochemistry in a serial manner. The association between T₂* values and quantitative histology was investigated with a co-registration method that accounts for histology slice preparation. The ventral T₂* hypointense layers between the SNr and the crus cerebri extended anteriorly to the posterior part of the crus cerebri, which demonstrates the difficulty with an MRI-based delineation of the SN. We found that the paramagnetic hypointense areas within the dorsolateral SN corresponded to clusters of neuromelanin (NM). These NM-rich zones were distinct from the hypointense ventromedial regions with high iron pigments. Nigral T₂* imaging at 7T can reflect the density of NM-containing neurons as the metal-bound NM macromolecules may decrease T₂* values and cause hypointense signalling in T₂* imaging at 7T.

Regional Specificity of Magnetic Resonance Imaging and Histopathology Following Cerebral Ischemia in Preterm Fetal Sheep

Early and accurate evaluation of the nature and extent of cerebral injury in the preterm infant brain is important for prognostication and decision making in the neonatal intensive care unit. The capability of magnetic resonance imaging (MRI) to define acute ischemic changes in white and gray matter in comparison to contemporaneous histopathology has not been adequately ascertained. The aim of this study is to assess whether postmortem MRI predicts the nature and extent of brain injury in a preterm fetal sheep model of cerebral hypoperfusion. MRI examinations were performed on fetal sheep brains (d99-100 gestation), perfusion fixed 72 hours after an ischemic insult (n = 7) with left-hemispheric placement of a microdialysis probe and compared with sham-occlusion (n = 3) and unoperated-control fetuses (n = 4). Cerebral ischemia was associated with MRI changes including global cerebral injury and diffuse white matter signal abnormality, which corresponded closely with histological damage. However, histological changes in deep structures, including the corona radiata, thalamus, and globus pallidus were not reliably detected on MRI. These findings confirm that in preterm fetal sheep, MRI can accurately assess cortical gray matter and subcortical and periventricular white matter abnormalities 3 days after hypoxic-ischemic injury but appears to have limited sensitivity to detect injury to deep structures.

Three-dimensional image analysis of the mouse cochlea

The mouse has proven to be an essential model system for studying hearing loss. A key advantage of the mouse is the ability to image the sensory cells in the cochlea. Many different protocols exist for the dissection and imaging of the cochlea. Here we describe a method that utilizes confocal imaging of whole-mount preparations followed by 3D analysis using the Imaris software. The 3D analysis of confocal stacks has been successfully used for investigating a number of mouse tissues and developmental processes. We propose that this method is also a valuable tool to analyze the cellular and tissue organization of the sensory hair cells in the cochlea.

Magnetic resonance spectroscopy and imaging on fresh human brain tumor biopsies at microscopic resolution

The metabolic composition and concentration knowledge provided by magnetic resonance spectroscopy (MRS) liquid and high-resolution magic angle spinning spectroscopy (HR-MAS) has a relevant impact in clinical practice during magnetic resonance imaging (MRI) monitoring of human tumors. In addition, the combination of morphological and chemical information by MRI and MRS has been particularly useful for diagnosis and prognosis of tumor evolution. MRI spatial resolution reachable in human beings is limited for safety reasons and the demanding necessary conditions are only applicable on experimental model animals. Nevertheless, MRS and MRI can be performed on human biopsies at high spatial resolution, enough to allow a direct correlation between the chemical information and the histological features observed in such biopsies. Although HR-MAS is nowadays a well-established technique for spectroscopic analysis of tumor biopsies, with this approach just a mean metabolic profile of the whole sample can be obtained and thus the high histological heterogeneity of some important tumors is mostly neglected. The value of metabolic HR-MAS data strongly depends on a wide statistical analysis and usually the microanatomical rationale for the correlation between histology and spectroscopy is lost. We present here a different approach for the combined use of MRI and MRS on fresh human brain tumor biopsies with native contrast. This approach has been designed to achieve high spatial (18 × 18 × 50 μm) and spectral (0.031 μL) resolution in order to obtain as much spatially detailed morphological and metabolical information as possible without any previous treatment that can alter the sample. The preservation of native tissue conditions can provide information that can be translated to in vivo studies and additionally opens the possibility of performing other techniques to obtain complementary information from the same sample.

Mouse brain magnetic resonance microscopy: Applications in Alzheimer disease

Over the past two decades, various Alzheimer's disease (AD) trangenetic mice models harboring genes with mutation known to cause familial AD have been created. Today, high-resolution magnetic resonance microscopy (MRM) technology is being widely used in the study of AD mouse models. It has greatly facilitated and advanced our knowledge of AD. In this review, most of the attention is paid to fundamental of MRM, the construction of standard mouse MRM brain template and atlas, the detection of amyloid plaques, following up on brain atrophy and the future applications of MRM in transgenic AD mice. It is believed that future testing of potential drugs in mouse models with MRM will greatly improve the predictability of drug effect in preclinical trials.

Default mode network, motor network, dorsal and ventral basal ganglia networks in the rat brain: comparison to human networks using resting state-fMRI

Rodent models are developed to enhance understanding of the underlying biology of different brain disorders. However, before interpreting findings from animal models in a translational aspect to understand human disease, a fundamental step is to first have knowledge of similarities and differences of the biological systems studied. In this study, we analyzed and verified four known networks termed: default mode network, motor network, dorsal basal ganglia network, and ventral basal ganglia network using resting state functional MRI (rsfMRI) in humans and rats. Our work supports the notion that humans and rats have common robust resting state brain networks and that rsfMRI can be used as a translational tool when validating animal models of brain disorders. In the future, rsfMRI may be used, in addition to short-term interventions, to characterize longitudinal effects on functional brain networks after long-term intervention in humans and rats.

Histologic validation of locus coeruleus MRI contrast in post-mortem tissue

The locus coeruleus (LC) noradrenergic system regulates arousal and modulates attention through its extensive projections across the brain. LC dysfunction has been implicated in a broad range of neurodevelopmental, neurodegenerative and psychiatric disorders, as well as in the cognitive changes observed during normal aging. Magnetic resonance imaging (MRI) has been used to characterize the human LC (elevated contrast relative to surrounding structures), but there is limited understanding of the factors underlying putative LC contrast that are critical to successful biomarker development and confidence in localizing nucleus LC. We used ultra-high-field 7 T magnetic resonance imaging (MRI) to acquire T1-weighted microscopy resolution images (78 μm in-plane resolution) of the LC from post-mortem tissue samples. Histological analyses were performed to characterize the distribution of tyrosine hydroxylase (TH) and neuromelanin in the scanned tissue, which allowed for direct comparison with MR microscopy images. Our results indicate that LC-MRI contrast corresponds to the location of neuromelanin cells in LC; these also correspond to norepinephrine neurons. Thus, neuromelanin appears to serve as a natural contrast agent for nucleus LC that can be used to localize nucleus LC and may have the potential to characterize neurodegenerative disease.

Post-mortem magnetic resonance microscopy (MRM) of the murine brain at 7 Tesla results in a gain of resolution as compared to in vivo MRM

Small-animal MRI with high field strength allows imaging of the living animal. However, spatial resolution in in vivo brain imaging is limited by the scanning time. Measurements of fixated mouse brains allow longer measurement time, but fixation procedures are time consuming, since the process of fixation may take several weeks. We here present a quick and simple post-mortem approach without fixation that allows high-resolution MRI even at 7 Tesla (T2-weighted MRI). This method was compared to in vivo scans with optimized spatial resolution for the investigation of anesthetized mice (T1-weighted MRI) as well as to ex situ scans of fixed brains (T1- and T2-weighted scans) by using standard MRI-sequences, along with anatomic descriptions of areas observable in the MRI, analysis of tissue shrinkage and post-processing procedures (intensity inhomogeneity correction, PCNN3D brain extract, SPMMouse segmentation, and volumetric measurement). Post-mortem imaging quality was sufficient to determine small brain substructures on the morphological level, provided fast possibilities for volumetric acquisition and for automatized processing without manual correction. Moreover, since no fixation was used, tissue shrinkage due to fixation does not occur as it is, e.g., the case by using ex vivo brains that have been kept in fixatives for several days. Thus, the introduced method is well suited for comparative investigations, since it allows determining small structural alterations in the murine brain at a reasonable high resolution even by MRI performed at 7 Tesla.

Complementary molecular imaging technologies: High resolution SPECT, PET and MRI

Molecular imaging has emerged as a powerful approach for studying drug interactions with cellular targets noninvasively in animal models and humans. Most large pharmaceutical companies are now building capacity for molecular imaging or seeking partnerships with research facilities. Therefore, it is timely to review the features and capabilities of the key technologies - single photon emission computed tomography (SPECT), positron emission tomography (PET) and magnetic resonance imaging (MRI). Owing to the differences in the information they convey and the time scales on which they are able to measure the kinetics of labelled drugs, they form a highly complementary set of technologies.:

Noninvasive assessment of cardiac abnormalities in experimental autoimmune myocarditis by magnetic resonance microscopy imaging in the mouse

Myocarditis is an inflammation of the myocardium, but only -10% of those affected show clinical manifestations of the disease. To study the immune events of myocardial injuries, various mouse models of myocarditis have been widely used. This study involved experimental autoimmune myocarditis (EAM) induced with cardiac myosin heavy chain (Myhc)-α 334-352 in A/J mice; the affected animals develop lymphocytic myocarditis but with no apparent clinical signs. In this model, the utility of magnetic resonance microscopy (MRM) as a non-invasive modality to determine the cardiac structural and functional changes in animals immunized with Myhc-α 334-352 is shown. EAM and healthy mice were imaged using a 9.4 T (400 MHz) 89 mm vertical core bore scanner equipped with a 4 cm millipede radio-frequency imaging probe and 100 G/cm triple axis gradients. Cardiac images were acquired from anesthetized animals using a gradient-echo-based cine pulse sequence, and the animals were monitored by respiration and pulse oximetry. The analysis revealed an increase in the thickness of the ventricular wall in EAM mice, with a corresponding decrease in the interior diameter of ventricles, when compared with healthy mice. The data suggest that morphological and functional changes in the inflamed hearts can be non-invasively monitored by MRM in live animals. In conclusion, MRM offers an advantage of assessing the progression and regression of myocardial injuries in diseases caused by infectious agents, as well as response to therapies.

Small-animal whole-body photoacoustic tomography: a review

With the wide use of small animals for biomedical studies, in vivo small-animal whole-body imaging plays an increasingly important role. Photoacoustic tomography (PAT) is an emerging whole-body imaging modality that shows great potential for preclinical research. As a hybrid technique, PAT is based on the acoustic detection of optical absorption from either endogenous tissue chromophores, such as oxyhemoglobin and deoxyhemoglobin, or exogenous contrast agents. Because ultrasound scatters much less than light in tissue, PAT generates high-resolution images in both the optical ballistic and diffusive regimes. Using near-infrared light, which has relatively low blood absorption, PAT can image through the whole body of small animals with acoustically defined spatial resolution. Anatomical and vascular structures are imaged with endogenous hemoglobin contrast, while functional and molecular images are enabled by the wide choice of exogenous optical contrasts. This paper reviews the rapidly growing field of small-animal whole-body PAT and highlights studies done in the past decade.

Comparison of divalent transition metal ion paraCEST MRI contrast agents

Transition-metal-ion-based paramagnetic chemical exchange saturation transfer (paraCEST) agents are a promising new class of compounds for magnetic resonance imaging (MRI) contrast. Members in this class of compounds include paramagnetic complexes of Fe(II), Co(II), and Ni(II). The development of the coordination chemistry for these paraCEST agents is presented with an emphasis on the choice of the azamacrocycle backbone and pendent groups with the goals of controlling the oxidation state, spin state, and stability of the complexes. Chemical exchange saturation transfer spectra and images are compared for different macrocyclic complexes containing amide or heterocyclic pendent groups. The potential of paraCEST agents that function as pH- and redox-activated MRI probes is discussed.

High-resolution photoacoustic tomography of resting-state functional connectivity in the mouse brain

The increasing use of mouse models for human brain disease studies presents an emerging need for a new functional imaging modality. Using optical excitation and acoustic detection, we developed a functional connectivity photoacoustic tomography system, which allows noninvasive imaging of resting-state functional connectivity in the mouse brain, with a large field of view and a high spatial resolution. Bilateral correlations were observed in eight functional regions, including the olfactory bulb, limbic, parietal, somatosensory, retrosplenial, visual, motor, and temporal regions, as well as in several subregions. The borders and locations of these regions agreed well with the Paxinos mouse brain atlas. By subjecting the mouse to alternating hyperoxic and hypoxic conditions, strong and weak functional connectivities were observed, respectively. In addition to connectivity images, vascular images were simultaneously acquired. These studies show that functional connectivity photoacoustic tomography is a promising, noninvasive technique for functional imaging of the mouse brain.

Cell layers and neuropil: contrast-enhanced MRI of mouse brain in vivo

Contrast-enhanced T₁- and T₂-weighted MRI at 9.4 T and in-plane resolutions of 25 and 30 µm has been demonstrated to differentiate between neural tissues in mouse brain in vivo, including granule cell layers, principal cell layers, general neuropil, specialized neuropil and white matter. In T₁-weighted MRI of the olfactory bulb, hippocampus and cerebellum, contrast obtained by the intracranial administration of gadopentetate dimeglumine (Gd-DTPA) reflects the extra- and intracellular spaces of gray matter in agreement with histological data. General neuropil areas are highlighted, whereas other tissues present with lower signal intensities. The induced contrast is similar to that in plain T₂-weighted MRI, but offers a 16-30-fold higher contrast-to-noise ratio. Systemic administration of manganese chloride increases the signal-to-noise ratio in T₁-weighted MRI to a significantly greater extent in principal cell layers and specialized neuropil than in granule cell layers, whereas gadolinium-enhanced MRI indicates no larger intracellular spaces in these tissues. Granule cell layers are enhanced no more than general neuropil by manganese, whereas gadolinium-enhanced MRI indicates significantly larger intracellular spaces in the cell layers. These discrepancies suggest that the signal increase after manganese administration reflects cellular activity which is disproportionate to the intracellular space. As a result, principal cell layers and specialized neuropil become highlighted, whereas granule cell layers, general neuropil and white matter present with lower signal intensities.

Structural layers of ex vivo rat hippocampus at 7T MRI

Magnetic resonance imaging (MRI) applied to the hippocampus is challenging in studies of the neurophysiology of memory and the physiopathology of numerous diseases such as epilepsy, Alzheimer’s disease, ischemia, and depression. The hippocampus is a well-delineated cerebral structure with a multi-layered organization. Imaging of hippocampus layers is limited to a few studies and requires high magnetic field and gradient strength. We performed one conventional MRI sequence on a 7T MRI in order to visualize and to delineate the multi-layered hippocampal structure ex vivo in rat brains. We optimized a volumic three-dimensional T2 Rapid Acquisition Relaxation Enhancement (RARE) sequence and quantified the volume of the hippocampus and one of its thinnest layers, the stratum granulare of the dentate gyrus. Additionally, we tested passive staining by gadolinium with the aim of decreasing the acquisition time and increasing image contrast. Using appropriated settings, six discrete layers were differentiated within the hippocampus in rats. In the hippocampus proper or Ammon’s Horn (AH): the stratum oriens, the stratum pyramidale of, the stratum radiatum, and the stratum lacunosum moleculare of the CA1 were differentiated. In the dentate gyrus: the stratum moleculare and the stratum granulare layer were seen distinctly. Passive staining of one brain with gadolinium decreased the acquisition time by four and improved the differentiation between the layers. A conventional sequence optimized on a 7T MRI with a standard receiver surface coil will allow us to study structural layers (signal and volume) of hippocampus in various rat models of neuropathology (anxiety, epilepsia, neurodegeneration).

A comprehensive neuropsychological mapping battery for functional magnetic resonance imaging

Existing batteries for FMRI do not precisely meet the criteria for comprehensive mapping of cognitive functions within minimum data acquisition times using standard scanners and head coils. The goal was to develop a battery of neuropsychological paradigms for FMRI that can also be used in other brain imaging techniques and behavioural research. Participants were 61 healthy, young adult volunteers (48 females and 13 males, mean age: 22.25 ± 3.39 years) from the university community. The battery included 8 paradigms for basic (visual, auditory, sensory-motor, emotional arousal) and complex (language, working memory, inhibition/interference control, learning) cognitive functions. Imaging was performed using standard functional imaging capabilities (1.5-T MR scanner, standard head coil). Structural and functional data series were analysed using Brain Voyager QX2.9 and Statistical Parametric Mapping-8. For basic processes, activation centres for individuals were within a distance of 3-11 mm of the group centres of the target regions and for complex cognitive processes, between 7 mm and 15 mm. Based on fixed-effect and random-effects analyses, the distance between the activation centres was 0-4 mm. There was spatial variability between individual cases; however, as shown by the distances between the centres found with fixed-effect and random-effects analyses, the coordinates for individual cases can be used to represent those of the group. The findings show that the neuropsychological brain mapping battery described here can be used in basic science studies that investigate the relationship of the brain to the mind and also as functional localiser in clinical studies for diagnosis, follow-up and pre-surgical mapping.

Ex vivo MR volumetry of human brain hemispheres

PURPOSE

The aims of this work were to (a) develop an approach for ex vivo MR volumetry of human brain hemispheres that does not contaminate the results of histopathological examination, (b) longitudinally assess regional brain volumes postmortem, and (c) investigate the relationship between MR volumetric measurements performed in vivo and ex vivo.

METHODS

An approach for ex vivo MR volumetry of human brain hemispheres was developed. Five hemispheres from elderly subjects were imaged ex vivo longitudinally. All datasets were segmented. The longitudinal behavior of volumes measured ex vivo was assessed. The relationship between in vivo and ex vivo volumetric measurements was investigated in seven elderly subjects imaged both antemortem and postmortem.

RESULTS

This approach for ex vivo MR volumetry did not contaminate the results of histopathological examination. For a period of 6 months postmortem, within-subject volume variation across time points was substantially smaller than intersubject volume variation. A close linear correspondence was detected between in vivo and ex vivo volumetric measurements.

CONCLUSION

Regional brain volumes measured with this approach for ex vivo MR volumetry remain relatively unchanged for a period of 6 months postmortem. Furthermore, the linear relationship between in vivo and ex vivo MR volumetric measurements suggests that this approach captures information linked to antemortem macrostructural brain characteristics.

Wireless amplified nuclear MR detector (WAND) for high-spatial-resolution MR imaging of internal organs: preclinical demonstration in a rodent model

PURPOSE

To assess the feasibility of imaging deep-lying internal organs at high spatial resolution by imaging kidney glomeruli in a rodent model with use of a newly developed, wireless amplified nuclear magnetic resonance (MR) detector.

MATERIALS AND METHODS

This study was approved by the Animal Care and Use Committee at the National Institutes of Health/National Institute of Neurologic Disorder and Stroke. As a preclinical demonstration of this new detection technology, five different millimeter-scale wireless amplified nuclear MR detectors configured as double frequency resonators were chronically implanted on the medial surface of the kidney in five Sprague-Dawley rats for MR imaging at 11.7 T. Among these rats, two were administered gadopentetate dimeglumine to visualize renal tubules on T1-weighted gradient-refocused echo (GRE) images, two were administered cationized ferritin to visualize glomeruli on T2*-weighted GRE images, and the remaining rat was administered both gadopentetate dimeglumine and cationized ferritin to visualize the interleaved pattern of renal tubules and glomeruli. The image intensity in each pixel was compared with the local tissue signal intensity average to identify regions of hyper- or hypointensity.

RESULTS

T1-weighted images with 70-μm in-plane resolution and 200-μm section thickness were obtained within 3.2 minutes to image renal tubules, and T2*-weighted images of the same resolution were obtained within 5.8 minutes to image the glomeruli. Hyperintensity from gadopentetate dimeglumine enabled visualization of renal tubules, and hypointensity from cationic ferritin enabled visualization of the glomeruli.

CONCLUSION

High-spatial-resolution images have been obtained to observe kidney microstructures in vivo with a wireless amplified nuclear MR detector.

Multimodal imaging of human cerebellum - merging X-ray phase microtomography, magnetic resonance microscopy and histology

Imaging modalities including magnetic resonance imaging and X-ray computed tomography are established methods in daily clinical diagnosis of human brain. Clinical equipment does not provide sufficient spatial resolution to obtain morphological information on the cellular level, essential for applying minimally or non-invasive surgical interventions. Therefore, generic data with lateral sub-micrometer resolution have been generated from histological slices post mortem. Sub-cellular spatial resolution, lost in the third dimension as a result of sectioning, is obtained using magnetic resonance microscopy and micro computed tomography. We demonstrate that for human cerebellum grating-based X-ray phase tomography shows complementary contrast to magnetic resonance microscopy and histology. In this study, the contrast-to-noise values of magnetic resonance microscopy and phase tomography were comparable whereas the spatial resolution in phase tomography is an order of magnitude better. The registered data with their complementary information permit the distinct segmentation of tissues within the human cerebellum.

Implanted, inductively-coupled, radiofrequency coils fabricated on flexible polymeric material: application to in vivo rat brain MRI at 7 T

Combined with high-field MRI scanners, small implanted coils allow for high resolution imaging with locally improved SNR, as compared to external coils. Small flexible implantable coils dedicated to in vivo MRI of the rat brain at 7 T were developed. Based on the Multi-turn Transmission Line Resonator design, they were fabricated with a Teflon substrate using copper micromolding process and a specific metal-polymer adhesion treatment. The implanted coils were made biocompatible by PolyDimethylSiloxane (PDMS) encapsulation. The use of low loss tangent material achieves low dielectric losses within the substrate and the use of the PDMS layer reduces the parasitic coupling with the surrounding media. An implanted coil was implemented in a 7 T MRI system using inductive coupling and a dedicated external pick-up coil for signal transmission. In vivo images of the rat brain acquired with in plane resolution of (150 μm)(2) thanks to the implanted coil revealed high SNR near the coil, allowing for the visualization of fine cerebral structures.

In vivo structural imaging of the cerebellum, the contribution of ultra-high fields

This review covers some of the contributions to date from cerebellar imaging studies performed at ultra-high magnetic fields. A short overview of the general advantages and drawbacks of the use of such high field systems for imaging is given. One of the biggest advantages of imaging at high magnetic fields is the improved spatial resolution, achievable thanks to the increased available signal-to-noise ratio. This high spatial resolution better matches the dimensions of the cerebellar substructures, allowing a better definition of such structures in the images. The implications of the use of high field systems is discussed for several imaging sequences and image contrast mechanisms. This review covers studies which were performed in vivo in both rodents and humans, with a special focus on studies that were directed towards the observation of the different cerebellar layers.

A parallel imaging approach to wide-field MR microscopy

Magnetic resonance microscopy, suggested in the earliest papers on MRI, has always been limited by the low signal-to-noise ratio resulting from the small voxel size. Magnetic resonance microscopy has largely been enabled by the use of microcoils that provide the signal-to-noise ratio improvement required to overcome this limitation. Concomitant with the small coils is a small field-of-view, which limits the use of magnetic resonance microscopy as a histological tool or for imaging large regions in general. This article describes initial results in wide field-of-view magnetic resonance microscopy using a large array of narrow, parallel coils, which provides a signal-to-noise ratio enhancement as well as the ability to use parallel imaging techniques. Comparison images made between a volume coil and the proposed technique demonstrate reductions in imaging time of more than 100 with no loss in signal-to-noise ratio or resolution.

In vivo magnetic resonance microscopy of Drosophilae at 9.4 T

In preclinical research, genetic studies have made considerable progress as a result of the development of transgenic animal models of human diseases. Consequently, there is now a need for higher resolution MRI to provide finer details for studies of small animals (rats, mice) or very small animals (insects). One way to address this issue is to work with high-magnetic-field spectrometers (dedicated to small animal imaging) with strong magnetic field gradients. It is also necessary to develop a complete methodology (transmit/receive coil, pulse sequence, fixing system, air supply, anesthesia capabilities, etc.). In this study, we developed noninvasive protocols, both in vitro and in vivo (from coil construction to image generation), for drosophila MRI at 9.4 T. The 10 10 80-μm resolution makes it possible to visualize whole drosophila (head, thorax, abdomen) and internal organs (ovaries, longitudinal and transverse muscles, bowel, proboscis, antennae and optical lobes). We also provide some results obtained with a Drosophila model of muscle degeneration. This opens the way for new applications of structural genetic modification studies using MRI of drosophila.