Manipulation of tissue contrast using contrast agents for enhanced MR microscopy in ex vivo mouse brain

Deep brain stimulation of the anterior cingulate cortex reduces opioid addiction in preclinical studies

Substance Use Disorder (SUD) is a medical condition where an individual compulsively misuses drugs or alcohol despite knowing the negative consequences. The anterior cingulate cortex (ACC) has been implicated in various types of SUDs, including nicotine, heroin, and alcohol use disorders. Our research aimed to investigate the effects of deep brain stimulation (DBS) in the ACC as a potential therapeutic approach for morphine use disorder. Additionally, we measured c-Fos protein expression as an indicator of neural activity in the nucleus accumbens (NAc) and prefrontal cortex (PFC). Our findings indicate that high-frequency (130 Hz) DBS at different amperages, 150 µA and 200 µA in the ACC during the acquisition phase of morphine conditioned place preference (CPP) inhibited the rewarding properties of morphine. Furthermore, DBS at these intensities during the extinction phase facilitated the extinction and mitigated the reinstatement of morphine CPP triggered by drug priming. Morphine conditioning was associated with impaired novel object conditioning (NOR) and locomotor activity. While DBS in the acquisition and extinction phases at both intensities restored NOR memory, only DBS at 200 µA recovered locomotor activity in the open field test. Treatment with DBS at 200 µA decreased c-Fos protein expression in the NAc and PFC (compared to morphine-only group). In conclusion, our data indicate an intensity-dependent effect of ACC DBS on the acquisition, extinction, and reinstatement of morphine-induced CPP in rats. These findings suggest that ACC DBS could be a potential intervention for the treatment of morphine use disorder.

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.

Mouse Brain MRI: Including In Vivo, Ex Vivo, and fcMRI for the Study of Microcephaly

With its sensitivity to soft tissue, MRI is a powerful tool for the study of the neuroanatomical manifestations of a variety of conditions, such as microcephaly-related morbidities that are not easily visualized by other imaging techniques, such as CT. In addition to structural imaging, more recently, researchers have found changes in brain function in a wide range of neurological conditions-highlighting the utility of MRI for the study of microcephaly.In this methods chapter, basic mouse preparation and the acquisition of data for in vivo anatomical MRI will be discussed. Additionally, we will provide our protocol for the perfusion and fixation of brain tissue with gadolinium contrast agent. Following that, the process of optimization of system parameters will be shown for anatomical imaging of in vivo and ex vivo brain tissue. Lastly, the chapter will detail a protocol for fcMRI along with a discussion of considerations specific to functional imaging.

The brains of aged mice are characterized by altered tissue diffusion properties and cerebral microbleeds

Background

Brain aging is a major risk factor in the progression of cognitive diseases including Alzheimer’s disease (AD) and vascular dementia. We investigated a mouse model of brain aging up to 24 months old (mo).

Methods

A high field (11.7T) MRI protocol was developed to characterize specific features of brain aging including the presence of cerebral microbleeds (CMBs), morphology of grey and white matter, and tissue diffusion properties. Mice were selected from age categories of either young (3 mo), middle-aged (18 mo), or old (24 mo) and fed normal chow over the duration of the study. Mice were imaged in vivo with multimodal MRI, including conventional T2-weighted (T2W) and T2*-weighted (T2*W) imaging, followed by ex vivo diffusion-weighted imaging (DWI) and T2*W MR-microscopy to enhance the detection of microstructural features.

Results

Structural changes observed in the mouse brain with aging included reduced cortical grey matter volume and enlargement of the brain ventricles. A remarkable age-related change in the brains was the development of CMBs found starting at 18 mo and increasing in total volume at 24 mo, primarily in the thalamus. CMBs presence was confirmed with high resolution ex vivo MRI and histology. DWI detected further brain tissue changes in the aged mice including reduced fractional anisotropy, increased radial diffusion, increased mean diffusion, and changes in the white matter fibers visualized by color-coded tractography, including around a large cortical CMB.

Conclusions

The mouse is a valuable model of age-related vascular contributions to cognitive impairment and dementia (VCID). In composite, these methods and results reveal brain aging in older mice as a multifactorial process including CMBs and tissue diffusion alterations that can be well characterized by high field MRI.

Isotropic 25-Micron 3D Neuroimaging Using ex vivo Microstructural Manganese-Enhanced MRI (MEMRI)

MRI observations following in vivo administration of Mn²⁺ [manganese (Mn)-enhanced MRI, MEMRI] have been used as an excellent morphological and functional MRI tool for in vivo preclinical studies. To detect brain three-dimensional (3D) microstructures, we improved the ex vivo MEMRI method for mouse brains after in vivo Mn administration and obtained high-resolution MRIs using a cryogenic radiofrequency (RF) coil. Male C57BL/6 mice (n = 8) were injected with 50 mM MnCl₂ intravenously and MEMRIs of the brain were acquired in vivo after 24 h, followed by perfusion fixation with a 4% paraformaldehyde (PFA) solution. High-resolution 25-μm isotropic MRIs were successfully acquired from the extracted brain tissue and could identify the brain microstructures, especially in the hippocampus [the pyramidal cell layer through CA1–3 and the dentate gyrus (DG) granular layers (GLs)], cell layers of cerebellum, three sub-regions of the deep cerebellar nucleus, and white matter (WM) structures [e.g., the fasciculus retroflexus (fr) and optic tract in the thalamus]. The following technical conditions were also examined: (i) the longitudinal stability of Mn-enhanced ex vivo tissue after in vivo administration; and (ii) the effects of mixing glutaraldehyde (GA) with the fixative solution for the preservation of in vivo MEMRI contrast. Our results indicate that ex vivo MEMRI observations made shortly after fixation maintain the contrast observed in vivo. This research will be useful for non-destructive whole-brain pathological analysis.

Comparative analysis of high field MRI and histology for ex vivo whole organ imaging: assessment of placental functional morphology in a murine model

OBJECTIVES

The purpose of our study was to evaluate MRI as a tool to examine placental morphology in a murine model in comparison to classical histology techniques.

METHODS

Assessment of placental samples (n = 24) from C57Bl/6 J mice was performed using MR imaging and histomorphological analyses. To optimize image contrast for MRI, a protocol for gadolinium-mediated enhancement of placental tissue was established. To test method sensitivity, placental zone assessment with MRI and histology was applied to a model of prenatal stress exposure known to affect placental morphology (n = 10). Mean data acquisition time for both methods was estimated. Difference between groups was calculated using the Mann-Whitney U test.

RESULTS

Tissue fixation with formaldehyde and staining with gadolinium resulted in the best image quality. Placental functional zones were identified and measured with both MRI and histology. MRI and histology were able to detect changes in the L/Jz ratio upon a prenatal stress challenge (p = 0.001; p = 0.003). Data acquisition time was shorter using MRI assessment.

CONCLUSIONS

Ex vivo MRI analyses of murine placental functional morphology with MRI are feasible and results are comparable to time-consuming histology. Both MRI and histology allow the detection of experimentally induced morphological tissue alterations.

Ex vivo mouse brain microscopy at 15T with loop-gap RF coil

The design of a loop-gap-resonator RF coil optimized for ex vivo mouse brain microscopy at ultra high fields is described and its properties characterized using simulations, phantoms and experimental scans of mouse brains fixed in 10% formalin containing 4 mM Magnevist™. The RF (B₁) and magnetic field (B₀) homogeneities are experimentally quantified and compared to electromagnetic simulations of the coil. The coil's performance is also compared to a similarly sized surface coil and found to yield double the sensitivity. A three-dimensional gradient-echo (GRE) sequence is used to acquire high resolution mouse brain scans at (47 μm)³ resolution in 1.8 h and a 20 × 20 × 19 μm³ resolution in 27 h. The high resolution obtained permitted clear visualization and identification of multiple structures in the ex vivo mouse brain and represents, to our knowledge, the highest resolution ever achieved for a whole mouse brain. Importantly, the coil design is simple and easy to construct.

MRI in the Study of Animal Models of Neurodegenerative Diseases

Magnetic Resonance Imaging (MRI) is an important tool to study various animal models of degenerative diseases. This chapter describes routine protocols of T ₁-, T ₂-, and T ₂*-weighted and diffusion-weighted MRI for rodent brain and spinal cord. These protocols can be used to measure atrophy, axonal and myelin injury and changes in white matter connectivity.

Long-Term Anesthetic-Dependent Hypoactivity after Repetitive Mild Traumatic Brain Injuries in Adolescent Mice

Recent evidence supports the hypothesis that repetitive mild traumatic brain injuries (rmTBIs) culminate in neurological impairments and chronic neurodegeneration, which have wide-ranging implications for patient management and return-to-play decisions for athletes. Adolescents show a high prevalence of sports-related head injuries and may be particularly vulnerable to rmTBIs due to ongoing brain maturation. However, it remains unclear whether rmTBIs, below the threshold for acute neuronal injury or symptomology, influence long-term outcomes. To address this issue, we first defined a very mild injury in adolescent mice (postnatal day 35) as evidenced by an increase in Iba-1- labeled microglia in white matter in the acutely injured brain, in the absence of indices of cell death, axonal injury, and vasogenic edema. Using this level of injury severity and Avertin (2,2,2-tribromoethanol) as the anesthetic, we compared mice subjected to either a single mTBI or 2 rmTBIs, each separated by 48 h. Neurobehavioral assessments were conducted at 1 week and at 1 and 3 months postimpact. Mice subjected to rmTBIs showed transient anxiety and persistent and pronounced hypoactivity compared to sham control mice, alongside normal sensorimotor, cognitive, social, and emotional function. As isoflurane is more commonly used than Avertin in animal models of TBI, we next examined long-term outcomes after rmTBIs in mice that were anesthetized with this agent. However, there was no evidence of abnormal behaviors even with the addition of a third rmTBI. To determine whether isoflurane may be neuroprotective, we compared the acute pathology after a single mTBI in mice anesthetized with either Avertin or isoflurane. Pathological findings were more pronounced in the group exposed to Avertin compared to the isoflurane group. These collective findings reveal distinct behavioral phenotypes (transient anxiety and prolonged hypoactivity) that emerge in response to rmTBIs. Our findings further suggest that selected anesthetics may confer early neuroprotection after rmTBIs, and as such mask long-term abnormal phenotypes that may otherwise emerge as a consequence of acute pathogenesis.

Parametric Probability Distribution Functions for Axon Diameters of Corpus Callosum

Axon diameter is an important neuroanatomical characteristic of the nervous system that alters in the course of neurological disorders such as multiple sclerosis. Axon diameters vary, even within a fiber bundle, and are not normally distributed. An accurate distribution function is therefore beneficial, either to describe axon diameters that are obtained from a direct measurement technique (e.g., microscopy), or to infer them indirectly (e.g., using diffusion-weighted MRI). The gamma distribution is a common choice for this purpose (particularly for the inferential approach) because it resembles the distribution profile of measured axon diameters which has been consistently shown to be non-negative and right-skewed. In this study we compared a wide range of parametric probability distribution functions against empirical data obtained from electron microscopy images. We observed that the gamma distribution fails to accurately describe the main characteristics of the axon diameter distribution, such as location and scale of the mode and the profile of distribution tails. We also found that the generalized extreme value distribution consistently fitted the measured distribution better than other distribution functions. This suggests that there may be distinct subpopulations of axons in the corpus callosum, each with their own distribution profiles. In addition, we observed that several other distributions outperformed the gamma distribution, yet had the same number of unknown parameters; these were the inverse Gaussian, log normal, log logistic and Birnbaum-Saunders distributions.

Recent Progress in Magnetic Resonance Imaging of the Embryonic and Neonatal Mouse Brain

The laboratory mouse has been widely used as a model system to investigate the genetic control mechanisms of mammalian brain development. Magnetic resonance imaging (MRI) is an important tool to characterize changes in brain anatomy in mutant mouse strains and injury progression in mouse models of fetal and neonatal brain injury. Progress in the last decade has enabled us to acquire MRI data with increasing anatomical details from the embryonic and neonatal mouse brain. High-resolution ex vivo MRI, especially with advanced diffusion MRI methods, can visualize complex microstructural organizations in the developing mouse brain. In vivo MRI of the embryonic mouse brain, which is critical for tracking anatomical changes longitudinally, has become available. Applications of these techniques may lead to further insights into the complex and dynamic processes of brain development.

Towards higher sensitivity and stability of axon diameter estimation with diffusion-weighted MRI

Diffusion-weighted MRI is an important tool for in vivo and non-invasive axon morphometry. The ActiveAx technique utilises an optimised acquisition protocol to infer orientationally invariant indices of axon diameter and density by fitting a model of white matter to the acquired data. In this study, we investigated the factors that influence the sensitivity to small-diameter axons, namely the gradient strength of the acquisition protocol and the model fitting routine. Diffusion-weighted ex. vivo images of the mouse brain were acquired using 16.4-T MRI with high (Gmax of 300 mT/m) and ultra-high (Gmax of 1350 mT/m) gradient strength acquisitions. The estimated axon diameter indices of the mid-sagittal corpus callosum were validated using electron microscopy. In addition, a dictionary-based fitting routine was employed and evaluated. Axon diameter indices were closer to electron microscopy measures when higher gradient strengths were employed. Despite the improvement, estimated axon diameter indices (a lower bound of ~ 1.8 μm) remained higher than the measurements obtained using electron microscopy (~1.2 μm). We further observed that limitations of pulsed gradient spin echo (PGSE) acquisition sequences and axonal dispersion could also influence the sensitivity with which axon diameter indices could be estimated. Our results highlight the influence of acquisition protocol, tissue model and model fitting, in addition to gradient strength, on advanced microstructural diffusion-weighted imaging techniques. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Enhancing magnetic resonance imaging with contrast agents for ultra-high field strengths

Contrast agents are diagnostic tools that often complement magnetic resonance imaging. At ultra-high field strengths (≥7 T), magnetic resonance imaging is capable of generating desirable high signal-to-noise ratios, but clinically available contrast agents are less effective at ultra-high field strengths relative to lower fields. This gap in effectiveness demands the development of contrast agents for ultra-high field strengths. In this minireview, we summarize contrast agents reported during the last three years that focused on ultra-high field strengths.

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.

Response of the primary auditory and non-auditory cortices to acoustic stimulation: a manganese-enhanced MRI study

Structural and functional features of various cerebral cortices have been extensively explored in neuroscience research. We used manganese-enhanced MRI, a non-invasive method for examining stimulus-dependent activity in the whole brain, to investigate the activity in the layers of primary cortices and sensory, such as auditory and olfactory, pathways under acoustic stimulation. Male Sprague-Dawley rats, either with or without exposure to auditory stimulation, were scanned before and 24-29 hour after systemic MnCl2 injection. Cortex linearization and layer-dependent signal extraction were subsequently performed for detecting layer-specific cortical activity. We found stimulus-dependent activity in the deep layers of the primary auditory cortex and the auditory pathways. The primary sensory and visual cortices also showed the enhanced activity, whereas the olfactory pathways did not. Further, we performed correlation analysis of the signal intensity ratios among different layers of each cortex, and compared the strength of correlations between with and without the auditory stimulation. In the primary auditory cortex, the correlation strength between left and right hemisphere showed a slight but not significant increase with the acoustic simulation, whereas, in the primary sensory and visual cortex, the correlation coefficients were significantly smaller. These results suggest the possibility that even though the primary auditory, sensory, and visual cortices showed enhanced activity to the auditory stimulation, these cortices had different associations for auditory processing in the brain network.

Manganese-enhanced MRI of minimally gadolinium-enhancing breast tumors

PURPOSE

To investigate the potential of manganese (Mn)-enhanced MRI for sensitive detection and delineation of tumors that demonstrate little enhancement on Gd-DTPA.

MATERIALS AND METHODS

Eighteen nude rats bearing 1 to 2 cm in diameter orthotopic breast tumors (ZR75 and LM2) were imaged on a 3 Tesla (T) clinical scanner. Gd-DTPA was administered intravenously and MnCl2 subcutaneously, both at 0.05 mmol/kg. T1 -weighted imaging and T1 measurements were performed precontrast, 10 min post-Gd-DTPA, and 24 h post-MnCl2 . Tumors were excised and histologically assessed using H&E (composition and necrosis) and CD34 (vascularity).

RESULTS

Most tumors (78%) demonstrated little enhancement (< 20% change in R1 ) on Gd-DTPA. MnCl2 administration achieved greater and more uniform enhancement throughout the tumor mass (i.e., not restricted to the tumor periphery), with R1 changing over 20% in 72% of tumors. MnCl2 -induced R1 changes compared with Gd-induced changes were significantly greater in both ZR75 (P < 0.01) and LM2 tumors (P < 0.05). Histology confirmed very low vascularity in both tumor models, and necrotic areas were well delineated only on Mn-enhanced MRI.

CONCLUSION

Mn-enhanced MRI is a promising approach for detection of low-Gd-enhancing tumors.

Anatomical MRI templates of tree shrew brain for volumetric analysis and voxel-based morphometry

BACKGROUND

Tree shrews are close relatives of primates, and are increasingly used as models in the research of vision, social stress and neurological/psychiatric diseases. However, neuroimaging techniques, for example magnetic resonance (MR) imaging, are only rarely applied to this species to study the structure and function of the brain. A template MR image set, which is essential for morphometry/volumetric analysis, of tree shrew brain has been lacking in the literature.

NEW METHOD

High-resolution anatomical MR images and diffusion tensor images of the brain were acquired from male Chinese tree shrews (Tupaia belangeri chinensis), and resampled to an isotropic resolution of 200 μm × 200 μm × 200 μm. Population-based image templates of tree shrew brain, including gray matter/white matter/cerebrospinal fluid probability maps and a fractional anisotropy template, were constructed at this spatial resolution, all in a reference space. Digital masks of representative anatomical structures, including hippocampus, amygdala and cingulum bundle, were created.

RESULT

With the templates constructed, the volumes of bilateral hippocampus and amygdala were measured using a template-facilitated semi-automated approach to be 59.8 ± 8.3 and 64.3 ± 3.4 mm(3), respectively.

COMPARISON WITH EXISTING METHOD(S)

For the first time, high-resolution MR image templates of tree shrew brain were reported. The average volume of bilateral hippocampus measured with the template-facilitated semi-automated approach was found to be similar to the result obtained by the much more labor-intensive manual approach.

CONCLUSIONS

The MR image templates obtained in this study are useful for analyzing neuroimage data of tree shrew brain. The templates are freely available to the scientific community upon request.

Highlighting manganese dynamics in the nervous system of Aplysia californica using MEMRI at ultra-high field

Exploring the pathways of manganese (Mn(2+)) transport in the nervous system becomes of interest as many recent studies use Mn(2+) as a neural tract tracer in mammals. In this study, we performed manganese enhanced MRI (MEMRI) at 17.2 T on the buccal ganglia of Aplysia californica. The main advantage of this model over mammalian systems is that it contains networks of large identified neurons. Using Mn(2+) retrograde transport along selected nerves, we first validated the mapping of motor neurons' axonal projections into peripheral nerves, previously obtained from optical imaging (Morton et al., 1991). This protocol was found not to alter the functional properties of the neuronal network. Second, we compared the Mn(2+) dynamics inside the ganglia in the presence or absence of chemical stimulation. We found that 2h of stimulation with the modulatory transmitter dopamine increased the extent of areas of intermediate signal enhancement caused by manganese accumulation. In the absence of dopamine, an overall decrease of the enhanced areas in favor of non-enhanced areas was found, as a result of natural Mn(2+) washout. This supports the hypothesis that, upon activation, Mn(2+) is released from labeled neurons and captured by other, initially unlabeled, neurons. However, the latter could not be clearly identified due to lack of sensitivity and multiplicity of possible pathways starting from labeled cells. Nonetheless, the Aplysia buccal ganglia remain a well-suited model for attempting to visualize Mn(2+) transport from neuron to neuron upon activation, as well as for studying dopaminergic modulation in a motor network.

Mouse brain fixation to preserve In vivo manganese enhancement for ex vivo manganese-enhanced MRI

PURPOSE

To develop a tissue fixation method that preserves in vivo manganese enhancement for ex vivo magnetic resonance imaging (MRI). The needs are clear, as conventional in vivo manganese-enhanced MRI (MEMRI) applied to live animals is time-limited, hence limited in spatial resolution and signal-to-noise ratio (SNR). Ex vivo applications can achieve superior spatial resolution and SNR through increased signal averaging and optimized radiofrequency coil designs. A tissue fixation method that preserves in vivo Mn(2+) enhancement postmortem is necessary for ex vivo MEMRI.

MATERIALS AND METHODS

T1 measurements and T1 -weighted MRI were performed on MnCl2 -administered mice. The mice were then euthanized and the brains were fixed using one of two brain tissue fixation methods: aldehyde solution or focused beam microwave irradiation (FBMI). MRI was then performed on the fixed brains.

RESULTS

T1 values and T1 -weighted signal contrasts were comparable between in vivo and ex vivo scans on aldehyde-fixed brains. FBMI resulted in the loss of Mn(2+) enhancement.

CONCLUSION

Aldehyde fixation, not FBMI, maintained in vivo manganese enhancement for ex vivo MEMRI.

Segmentation propagation using a 3D embryo atlas for high-throughput MRI phenotyping: comparison and validation with manual segmentation

Effective methods for high-throughput screening and morphometric analysis are crucial for phenotyping the increasing number of mouse mutants that are being generated. Automated segmentation propagation for embryo phenotyping is an emerging application that enables noninvasive and rapid quantification of substructure volumetric data for morphometric analysis. We present a study to assess and validate the accuracy of brain and kidney volumes generated via segmentation propagation in an ex vivo mouse embryo MRI atlas comprising three different groups against the current "gold standard"--manual segmentation. Morphometric assessment showed good agreement between automatically and manually segmented volumes, demonstrating that it is possible to assess volumes for phenotyping a population of embryos using segmentation propagation with the same variation as manual segmentation. As part of this study, we have made our average atlas and segmented volumes freely available to the community for use in mouse embryo phenotyping studies. These MRI datasets and automated methods of analyses will be essential for meeting the challenge of high-throughput, automated embryo phenotyping.

Structural correlates of active-staining following magnetic resonance microscopy in the mouse brain

Extensive worldwide efforts are underway to produce knockout mice for each of the ~25,000 mouse genes, which may give new insights into the underlying pathophysiology of neurological disease. Microscopic magnetic resonance imaging (μMRI) is a key method for non-invasive morphological phenotyping, capable of producing high-resolution 3D images of ex-vivo brains, after fixation with an MR contrast agent. These agents have been suggested to act as active-stains, enhancing structures not normally visible on MRI. In this study, we investigated the structural correlates of the MRI agent Gd-DTPA, together with the optimal preparation and scan parameters for contrast-enhanced gradient-echo imaging of the mouse brain. We observed that in-situ preparation was preferential to ex-situ due to the degree of extraction damage. In-situ brains scanned with optimised parameters, enabled images with a high signal-to-noise-ratio (SNR ~30) and comprehensive anatomical delineation. Direct correlation of the MR brain structures to histology, detailed fine histoarchitecture in the cortex, cerebellum, olfactory bulb and hippocampus. Neurofilament staining demonstrated that regions of negative MR contrast strongly correlated to myelinated white-matter structures, whilst structures of more positive MR contrast corresponded to areas with high grey matter content. We were able to identify many sub-regions, particularly within the hippocampus, such as the unmyelinated mossy fibres (stratum lucidum) and their region of synapse in the stratum pyramidale, together with the granular layer of the dentate gyrus, an area of densely packed cell bodies, which was clearly visible as a region of hyperintensity. This suggests that cellular structure influences the site-specific distribution of the MR contrast agent, resulting in local variations in T(2)*, which leads to enhanced tissue discrimination. Our findings provide insights not only into the cellular distribution and mechanism of MR active-staining, but also allow for three dimensional analysis, which enables interpretation of magnetic resonance microscopy brain data and highlights cellular structure for investigation of disease processes in development and disease.

Magnetic resonance histology of the adult zebrafish brain: optimization of fixation and gadolinium contrast enhancement

Magnetic resonance histology (MRH) has become a widespread tool to examine brain morphology in situ or ex vivo. Samples are routinely fixed and stained to allow for longer scan times with increased contrast and resolution. Although the zebrafish is an important model for neuroscience, to date most MRH studies have focused almost exclusively on mice. In this paper, we examined, for the first time, the zebrafish brain using MRH. We compared a range of fixatives, contrast agents, and fixation/staining durations to determine optimal imaging of the zebrafish brain. By quantifying the T(1), T(2), and T(2)* relaxation values, we demonstrated that ethanol and potassium permanganate are unviable for imaging and significant differences exist between mono and di-aldehydes. Furthermore, we compared two commercially available gadolinium-based contrast agents, Magnevist® and Optimark®, at five different concentrations. For both contrast agents, a concentration of 0.5% was determined to be ideal as it significantly shortened the T(1) but maintained a relatively long T(2) and T(2)*. Subsequently, we analyzed the duration of fixation/staining and established a period of 12 h, which best minimized T(1) values but maintained T(2) and T(2)* values. Finally, using this optimized fixation and staining protocol, we performed a gradient-echo T(2)*-weighted imaging to obtain an image set of the adult zebrafish brain at an isotropic resolution of 10 µm.

A three-dimensional digital atlas of the zebrafish brain

In the past three decades, the zebrafish has become a vital animal model in a range of biological sciences. To augment current neurobiological research, we have developed the first three-dimensional digital atlas of the zebrafish brain from T2-weighted magnetic resonance histology (MRH) images acquired on a 16.4-T superconducting magnet. We achieved an isotropic resolution of 10 microm, which is the highest resolution achieved in a vertebrate brain and, for the first time, is comparable in slice thickness to conventional histology. By using manual segmentation, 53 anatomical structures, including fiber tracts as small as 40 microm, were delineated. Using Amira software, structures were also individually segmented and reconstructed to create three-dimensional animations. Additional quantitative information including, volume, surface areas, and mean gray scale intensities were also determined. Finally, we established a stereotaxic coordinate system as a framework in which maps created from other modalities can be incorporated into the atlas.

Porous Polymersomes with Encapsulated Gd-labeled Dendrimers as Highly Efficient MRI Contrast Agents

The use of nanovesicles with encapsulated Gd as MR contrast agents has largely been ignored due to the detrimental effects of the slow water exchange rate through the vesicle bilayer on the relaxivity of encapsulated Gd. Here, we describe the facile synthesis of a composite MR contrast platform, consisting of dendrimer conjugates encapsulated in porous polymersomes. These nanoparticles exhibit improved permeability to water flux and a large capacity to store chelated Gd within the aqueous lumen, resulting in enhanced longitudinal relaxivity. The porous polymersomes, ~130 nm in diameter, were produced through the aqueous assembly of the polymers, polyethylene oxide-b-polybutadiene (PBdEO), and polyethylene oxide-b-polycaprolactone (PEOCL). Subsequent hydrolysis of the caprolactone (CL) block resulted in a highly permeable outer membrane. To prevent the leakage of small Gd-chelate through the pores, Gd was conjugated to PAMAM dendrimer via diethylenetriaminepentaacetic acid dianhydride (DTPA dianhydride) prior to encapsulation. As a result of the slower rotational correlation time of Gd-labeled dendrimers, the porous outer membrane of the nanovesicle, and the high Gd payload, these functional nanoparticles were found to exhibit a relaxivity (R1) of 292,109 mM(-1) s(-1) per particle. The polymersomes were also found to exhibit unique pharmacokinetics with a circulation half-life of >3.5 hrs and predominantly renal clearance.