Small animal imaging with magnetic resonance microscopy

New insights into morphological adaptation in common mole-rats (Cryptomys hottentotus hottentotus) along an aridity gradient

Morphological adaptation is the change in the form of an organism that benefits the individual in its current habitat. Mole-rats (family Bathyergidae), despite being subterranean, are impacted by both local and broad-scale environmental conditions that occur above ground. Common mole-rats (Cryptomys hottentotus hottentotus) present an ideal mammalian model system for the study of morphological variation in response to ecology, as this species is found along an aridity gradient and thus can be sampled from geographically non-overlapping populations of the same species along an environmental longitudinal cline. Using the mass of five internal organs, ten skeletal measurements and 3D morphometric analyses of skulls, we assessed the morphology of wild non-breeding individuals from five common mole-rat populations in South Africa. We found that the body mass and mean relative mass of the spleen and kidneys in arid populations was larger, and individuals from arid regions possessed shorter legs and larger inter-shoulder widths compared to individuals from mesic regions. Additionally, arid populations demonstrated greater skull depth, and shape change of features such as angular processes of the lower jaw than mesic individuals, indicating that these distinct geographic populations show differences corresponding to the aridity gradient, potentially in response to environmental factors such as the variation in food sources found between different habitats, in addition to different soil compositions found in the different regions. Arid populations potentially require a stronger jaw and neck musculature associated with mastication to chew xeric-adapted plants and to dig through hard soil types, whereas mesic populations excavate through soft, looser soil and may make use of their front limbs to aid the movement of soils when digging. Aridity influences the morphology of this species and could indicate the impact of environmental changes on speciation and mammalian skull morphology.

Preclinical Models for Cryptococcosis of the CNS and Their Characterization Using In Vivo Imaging Techniques

Infections caused by Cryptococcus neoformans and Cryptococcus gattii remain a challenge to our healthcare systems as they are still difficult to treat. In order to improve treatment success, in particular for infections that have disseminated to the central nervous system, a better understanding of the disease is needed, addressing questions like how it evolves from a pulmonary to a brain disease and how novel treatment approaches can be developed and validated. This requires not only clinical research and research on the microorganisms in a laboratory environment but also preclinical models in order to study cryptococci in the host. We provide an overview of available preclinical models, with particular emphasis on models of cryptococcosis in rodents. In order to further improve the characterization of rodent models, in particular the dynamic aspects of disease manifestation, development, and ultimate treatment, preclinical in vivo imaging methods are increasingly used, mainly in research for oncological, neurological, and cardiac diseases. In vivo imaging applications for fungal infections are rather sparse. A second aspect of this review is how research on models of cryptococcosis can benefit from in vivo imaging methods that not only provide information on morphology and tissue structure but also on function, metabolism, and cellular properties in a non-invasive way.

An improved F98 glioblastoma rat model to evaluate novel treatment strategies incorporating the standard of care

Glioblastoma (GB) is the most common and malignant primary brain tumor in adults with a median survival of 12-15 months. The F98 Fischer rat model is one of the most frequently used animal models for GB studies. However, suboptimal inoculation leads to extra-axial and extracranial tumor formations, affecting its translational value. We aim to improve the F98 rat model by incorporating MRI-guided (hypo)fractionated radiotherapy (3 x 9 Gy) and concomitant temozolomide chemotherapy, mimicking the current standard of care. To minimize undesired tumor growth, we reduced the number of inoculated cells (starting from 20 000 to 500 F98 cells), slowed the withdrawal of the syringe post-inoculation, and irradiated the inoculation track separately. Our results reveal that reducing the number of F98 GB cells correlates with a diminished risk of extra-axial and extracranial tumor growth. However, this introduces higher variability in days until GB confirmation and uniformity in GB growth. To strike a balance, the model inoculated with 5000 F98 cells displayed the best results and was chosen as the most favorable. In conclusion, our improved model offers enhanced translational potential, paving the way for more accurate and reliable assessments of novel adjuvant therapeutic approaches for GB.

Accuracy of skull stripping in a single-contrast convolutional neural network model using eight-contrast magnetic resonance images

In automated analyses of brain morphometry, skull stripping or brain extraction is a critical first step because it provides accurate spatial registration and signal-intensity normalization. Therefore, it is imperative to develop an ideal skull-stripping method in the field of brain image analysis. Previous reports have shown that convolutional neural network (CNN) method is better at skull stripping than non-CNN methods. We aimed to evaluate the accuracy of skull stripping in a single-contrast CNN model using eight-contrast magnetic resonance (MR) images. A total of 12 healthy participants and 12 patients with a clinical diagnosis of unilateral Sturge-Weber syndrome were included in our study. A 3-T MR imaging system and QRAPMASTER were used for data acquisition. We obtained eight-contrast images produced by post-processing T1, T2, and proton density (PD) maps. To evaluate the accuracy of skull stripping in our CNN method, gold-standard intracranial volume (ICVG) masks were used to train the CNN model. The ICVG masks were defined by experts using manual tracing. The accuracy of the intracranial volume obtained from the single-contrast CNN model (ICVE) was evaluated using the Dice similarity coefficient [= 2(ICVE ⋂ ICVG)/(ICVE + ICVG)]. Our study showed significantly higher accuracy in the PD-weighted image (WI), phase-sensitive inversion recovery (PSIR), and PD-short tau inversion recovery (STIR) compared to the other three contrast images (T1-WI, T2-fluid-attenuated inversion recovery [FLAIR], and T1-FLAIR). In conclusion, PD-WI, PSIR, and PD-STIR should be used instead of T1-WI for skull stripping in the CNN models.

High-resolution imaging in studies of alcohol effect on prenatal development

Fetal alcohol syndrome represents the leading known preventable cause of mental retardation. FAS is on the most severe side of fetal alcohol spectrum disorders that stem from the deleterious effects of prenatal alcohol exposure. Affecting as many as 1 to 5 out of 100 children, FASD most often results in brain abnormalities that extend to structure, function, and cerebral hemodynamics. The present review provides an analysis of high-resolution imaging techniques that are used in animals and human subjects to characterize PAE-driven changes in the developing brain. Variants of magnetic resonance imaging such as magnetic resonance microscopy, magnetic resonance spectroscopy, diffusion tensor imaging, along with positron emission tomography, single-photon emission computed tomography, and photoacoustic imaging, are modalities that are used to study the influence of PAE on brain structure and function. This review briefly describes the aforementioned imaging modalities, the main findings that were obtained using each modality, and touches upon the advantages/disadvantages of each imaging approach.

In vivo intra-articular contrast enhanced μCT imaging of mouse knee cartilage

In vivo micro-Computed Tomography (μCT) is commonly used tool in the study of mouse bone architecture. However, in vivo imaging of mouse cartilage has been limited. Intra-articular contrast injection was evaluated for its utility in detecting mouse cartilage in μCT. Clinically used iodinated contrast agent was chosen for its widespread commercial availability. Imaging protocol was developed with wild type C57BL/6 mice for its ability to detect expected cartilage thinning that occurs with sexual maturity. The protocol was then validated with transgenic mouse model with known extracellular matrix loss. μCT findings showed good correspondence with histological assessment. In conclusion, in vivo intra-articular contrast-enhanced μCT arthrography is viable technique for evaluation of mouse cartilage. SUMMARY: In vivo intra-articular contrast enhanced μCT of the mouse knee joint can delineate cartilage thickness and extracellular matrix content. The imaging protocol may be useful for longitudinal evaluation of cartilage anomalies in transgenicmouse model.

Accessing lanthanide-based, in situ illuminated optical turn-on probes by modulation of the antenna triplet state energy

Luminescent lanthanides possess ideal properties for biological imaging, including long luminescent lifetimes and emission within the optical window. Here, we report a novel approach to responsive luminescent Tb(iii) probes that involves direct modulation of the antenna excited triplet state energy. If the triplet energy lies too close to the 5D4 Tb(iii) excited state (20 500 cm-1), energy transfer to 5D4 competes with back energy transfer processes and limits lanthanide-based emission. To validate this approach, a series of pyridyl-functionalized, macrocyclic lanthanide complexes were designed, and the corresponding lowest energy triplet states were calculated using density functional theory (DFT). Subsequently, three novel constructs L3 (nitro-pyridyl), L4 (amino-pyridyl) and L5 (fluoro-pyridyl) were synthesized. Photophysical characterization of the corresponding Gd(iii) complexes revealed antenna triplet energies between 25 800 and 30 400 cm-1 and a 500-fold increase in quantum yield upon conversion of Tb(L3) to Tb(L4) using the biologically relevant analyte H2S. The corresponding turn-on reaction can be monitored using conventional, small-animal optical imaging equipment in presence of a Cherenkov radiation emitting isotope as an in situ excitation source, demonstrating that antenna triplet state energy modulation represents a viable approach to biocompatible, Tb-based optical turn-on probes.

Preclinical MRI to Quantify Pulmonary Disease Severity and Trajectories in Poorly Characterized Mouse Models: A Pedagogical Example Using Data from Novel Transgenic Models of Lung Fibrosis

Structural remodeling in lung disease is progressive and heterogeneous, making temporally and spatially explicit information necessary to understand disease initiation and progression. While mouse models are essential to elucidate mechanistic pathways underlying disease, the experimental tools commonly available to quantify lung disease burden are typically invasive (e.g., histology). This necessitates large cross-sectional studies with terminal endpoints, which increases experimental complexity and expense. Alternatively, magnetic resonance imaging (MRI) provides information noninvasively, thus permitting robust, repeated-measures statistics. Although lung MRI is challenging due to low tissue density and rapid apparent transverse relaxation (T₂* <1 ms), various imaging methods have been proposed to quantify disease burden. However, there are no widely accepted strategies for preclinical lung MRI. As such, it can be difficult for researchers who lack lung imaging expertise to design experimental protocols-particularly for novel mouse models. Here, we build upon prior work from several research groups to describe a widely applicable acquisition and analysis pipeline that can be implemented without prior preclinical pulmonary MRI experience. Our approach utilizes 3D radial ultrashort echo time (UTE) MRI with retrospective gating and lung segmentation is facilitated with a deep-learning algorithm. This pipeline was deployed to assess disease dynamics over 255 days in novel, transgenic mouse models of lung fibrosis based on disease-associated, loss-of-function mutations in Surfactant Protein-C. Previously identified imaging biomarkers (tidal volume, signal coefficient of variation, etc.) were calculated semi-automatically from these data, with an objectively-defined high signal volume identified as the most robust metric. Beyond quantifying disease dynamics, we discuss common pitfalls encountered in preclinical lung MRI and present systematic approaches to identify and mitigate these challenges. While the experimental results and specific pedagogical examples are confined to lung fibrosis, the tools and approaches presented should be broadly useful to quantify structural lung disease in a wide range of mouse models.

A Review of Ex Vivo X-ray Microfocus Computed Tomography-Based Characterization of the Cardiovascular System

Cardiovascular malformations and diseases are common but complex and often not yet fully understood. To better understand the effects of structural and microstructural changes of the heart and the vasculature on their proper functioning, a detailed characterization of the microstructure is crucial. In vivo imaging approaches are noninvasive and allow visualizing the heart and the vasculature in 3D. However, their spatial image resolution is often too limited for microstructural analyses, and hence, ex vivo imaging is preferred for this purpose. Ex vivo X-ray microfocus computed tomography (microCT) is a rapidly emerging high-resolution 3D structural imaging technique often used for the assessment of calcified tissues. Contrast-enhanced microCT (CE-CT) or phase-contrast microCT (PC-CT) improve this technique by additionally allowing the distinction of different low X-ray-absorbing soft tissues. In this review, we present the strengths of ex vivo microCT, CE-CT and PC-CT for quantitative 3D imaging of the structure and/or microstructure of the heart, the vasculature and their substructures in healthy and diseased state. We also discuss their current limitations, mainly with regard to the contrasting methods and the tissue preparation.

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.

In vivo selection of the MDA-MB-231br/eGFP cancer cell line to obtain a clinically relevant rat model for triple negative breast cancer brain metastasis

Young triple negative breast cancer (TNBC) patients are at high risk for developing very aggressive brain metastases associated with a poor prognosis and a high mortality rate. Preclinical models that allow follow-up by magnetic resonance imaging (MRI) can contribute to the development of new therapeutic approaches for brain metastasis. To date, preclinical brain tumor research has almost exclusively relied on xenograft mouse models. Yet, rats are an ideal model for imaging of brain metastasis as their larger brain offers better relative spatial resolution compared to a mouse brain. For the development of a clinically relevant rat model for TNBC brain metastasis, the MDA-MB-231br/eGFP cancer cell line can be used. However, as a result of species-dependent extracranial features, the propensity of the MDA-MB-231br/eGFP cancer cell line to metastasize exclusively to the brain needs to be enhanced by in vivo selection. In this study, repeated sequential passages of metastatic cancer cells obtained from brain metastases in nude rats were performed. Brain metastasis formation was evaluated using preclinical MRI, while bone metastasis formation was assessed using high-resolution computed tomography (CT) and 2-deoxy-2-[¹⁸F] fluoro-D-glucose ([¹⁸F] FDG) positron emission tomography (PET) imaging. Our results demonstrated that the metastatic tumor burden in the rat brain (number and volume) significantly increased with increasing passage, while the metastatic tumor burden in the skeleton (i.e., number of metastasis-affected bones) significantly decreased with increasing passage. However, bone metastasis development was not reduced to a negligible amount. Consequently, despite in vivo selection, our rat model is not recommended for investigating brain metastasis as a single disease. Our findings highlight the importance of well-reasoned selection of both the preclinical model and the cancer cell line in order to obtain reliable and reproducible scientific results.

Detection of Cerebrovascular Loss in the Normal Aging C57BL/6 Mouse Brain Using in vivo Contrast-Enhanced Magnetic Resonance Angiography

Microvascular rarefaction, or the decrease in vascular density, has been described in the cerebrovasculature of aging humans, rats, and, more recently, mice in the presence and absence of age-dependent diseases. Given the wide use of mice in modeling age-dependent human diseases of the cerebrovasculature, visualization, and quantification of the global murine cerebrovasculature is necessary for establishing the baseline changes that occur with aging. To provide in vivo whole-brain imaging of the cerebrovasculature in aging C57BL/6 mice longitudinally, contrast-enhanced magnetic resonance angiography (CE-MRA) was employed using a house-made gadolinium-bearing micellar blood pool agent. Enhancement in the vascular space permitted quantification of the detectable, or apparent, cerebral blood volume (aCBV), which was analyzed over 2 years of aging and compared to histological analysis of the cerebrovascular density. A significant loss in the aCBV was detected by CE-MRA over the aging period. Histological analysis via vessel-probing immunohistochemistry confirmed a significant loss in the cerebrovascular density over the same 2-year aging period, validating the CE-MRA findings. While these techniques use widely different methods of assessment and spatial resolutions, their comparable findings in detected vascular loss corroborate the growing body of literature describing vascular rarefaction aging. These findings suggest that such age-dependent changes can contribute to cerebrovascular and neurodegenerative diseases, which are modeled using wild-type and transgenic laboratory rodents.

Design and construction of a gradient coil for high resolution marmoset imaging

A gradient coil with integrated second and third order shims has been designed and constructed for use inside an actively shielded 310 mm horizontal bore 9.4 T small animal MRI. An extension of the boundary element method, to minimise the power deposited in conducting surfaces, was used to design the gradients, and a boundary element method with a constraint on mutual inductance was used to design the shims. The gradient coil allows for improved imaging performance and was optimized for an imaging region appropriate for marmoset imaging studies. Efficiencies of 1.5 mT m^-1 A^-1 were achieved in a 15 cm wide bore while maintaining gradient uniformity ≤5% over the 8 cm region of interest. Two new cooling methods were implemented which allowed the gradient coil to operate at 100 A RMS, 25 % of max current with a temperature rise below 30 C.

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.

Imaging in mice and men: Pathophysiological insights into multiple sclerosis from conventional and advanced MRI techniques

Magnetic resonance imaging (MRI) is the most important tool for diagnosing multiple sclerosis (MS). However, MRI is still unable to precisely quantify the specific pathophysiological processes that underlie imaging findings in MS. Because autopsy and biopsy samples of MS patients are rare and biased towards a chronic burnt-out end or fulminant acute early stage, the only available methods to identify human disease pathology are to apply MRI techniques in combination with subsequent histopathological examination to small animal models of MS and to transfer these insights to MS patients. This review summarizes the existing combined imaging and histopathological studies performed in MS mouse models and humans with MS (in vivo and ex vivo), to promote a better understanding of the pathophysiology that underlies conventional MRI, diffusion tensor and magnetization transfer imaging findings in MS patients. Moreover, it provides a critical view on imaging capabilities and results in MS patients and mouse models and for future studies recommends how to combine those particular MR sequences and parameters whose underlying pathophysiological basis could be partly clarified. Further combined longitudinal in vivo imaging and histopathological studies on rationally selected, appropriate mouse models are required.

Processing Pipeline for Atlas-Based Imaging Data Analysis of Structural and Functional Mouse Brain MRI (AIDAmri)

Magnetic resonance imaging (MRI) is a key technology in multimodal animal studies of brain connectivity and disease pathology. In vivo MRI provides non-invasive, whole brain macroscopic images containing structural and functional information, thereby complementing invasive in vivo high-resolution microscopy and ex vivo molecular techniques. Brain mapping, the correlation of corresponding regions between multiple brains in a standard brain atlas system, is widely used in human MRI. For small animal MRI, however, there is no scientific consensus on pre-processing strategies and atlas-based neuroinformatics. Thus, it remains difficult to compare and validate results from different pre-clinical studies which were processed using custom-made code or individual adjustments of clinical MRI software and without a standard brain reference atlas. Here, we describe AIDAmri, a novel Atlas-based Imaging Data Analysis pipeline to process structural and functional mouse brain data including anatomical MRI, fiber tracking using diffusion tensor imaging (DTI) and functional connectivity analysis using resting-state functional MRI (rs-fMRI). The AIDAmri pipeline includes automated pre-processing steps, such as raw data conversion, skull-stripping and bias-field correction as well as image registration with the Allen Mouse Brain Reference Atlas (ARA). Following a modular structure developed in Python scripting language, the pipeline integrates established and newly developed algorithms. Each processing step was optimized for efficient data processing requiring minimal user-input and user programming skills. The raw data is analyzed and results transferred to the ARA coordinate system in order to allow an efficient and highly-accurate region-based analysis. AIDAmri is intended to fill the gap of a missing open-access and cross-platform toolbox for the most relevant mouse brain MRI sequences thereby facilitating data processing in large cohorts and multi-center studies.

Potential clinical benefits and limitations of fetal virtopsy using high-field MRI at 7 Tesla versus stereomicroscopic autopsy to assess first trimester fetuses

OBJECTIVE

The aim of this study was to establish the diagnostic accuracy of high-field magnetic resonance imaging (MRI) at 7 Tesla (T) compared with that of stereomicroscopic autopsy for assessing first trimester fetuses.

METHODS

Nine consecutive cases of first trimester fetuses resulting from spontaneous and therapeutic pregnancy termination were considered. The cases were divided into two groups according to gestational age: the Embryo Group with cases of nine to 10 gestational weeks (GWs) and the Fetus Group with cases of 13 GWs. The first group was scanned using three-dimensional fast imaging with steady state precession (3D FISP), and the second group was scanned using a two-dimensional (2D) turbo spin-echo high-resolution T2-weighted imaging (T2 WI) protocol. A radiologist and two embryologists interpreted the images. All cases were evaluated by invasive autopsy, with pathologist blinded to the imaging results. In total, the database included 270 items for evaluation (9 cases × 30 structures/case).

RESULTS

The global agreement between fetal high-field virtopsy and microscopic or stereomicroscopic autopsy was evaluated using 225 evaluation items visible by both methods. Overall, using microscopic examination and stereomicroscopic autopsy as the gold standard, fetal high-field virtopsy had a sensitivity of 94.6% [95% CI, 87.2-98.3] and a specificity of 97.6% [95% CI, 95-98.8]. The positive predictive value (PPV) was 93% [95% CI, 85.7-96.6], and the negative predictive value (NPV) was 98.2% [95% CI, 95.7-99.4]. Cohen kappa coefficient of agreement was k = 0.92 [95% CI, 0.82-0.97], and the McNemar test showed p = 1.00.

CONCLUSIONS

Virtual autopsy using high-field MRI at 7 T can be considered a safe alternative approach to stereomicroscopic autopsy for the assessment of fetal structural anomalies at the end of the first trimester of pregnancy.

Quantification of placental change in mouse models of preeclampsia using magnetic resonance microscopy

Abnormal development of the placenta is postulated to be central to the aetiology of preeclampsia. This study investigates changes in placental histopathology in mouse models of preeclampsia compared to the morphology using magnetic resonance microscopy (MRM) (11.7 T) of intact ex vivo tissue followed by 3D analysis of the image data. Here, C57BL/6JArc pregnant mice were subject to either normal pregnancy (n=3), or to one of two experimental models of preeclampsia; TNF-α infusion (n=3) or reduced uterine perfusion pressure (RUPP) (n=3). Placental tissue was collected at gestational day (gd) 17, fixed in formalin and incubated with Magnavist™ contrast agent, and high resolution images (50 μm × 50 μm × 50 μm voxels) obtained by magnetic resonance imaging at 11.74 T. Visual segmentation into placental subregions and three dimensional (3D) reconstruction followed by volume analysis was performed with Amira™ 3D analysis software. The significance of differences between treatment groups in total and regional volumes was assessed. In a single placenta the volumes measure by standard histology were compared. Three placentas from each animal were imaged, segmented into anatomical regions and 3D reconstructions generated. Total placental volume, labyrinth and decidual volume were not significantly different between groups. The junctional zone volume was found to be significantly larger in the RUPP animals (18.5±1.5 mm³) compared to TNF-α infused animals (15.8±1.5) or control animals (15.0±0.7, P<0.01). However, the decidual/junctional zone volume was smaller in the TNF-a compared to control animals (P<0.05). Placental structural change in experimental models of preeclampsia is able to be visualized and quantified using MRM and 3-D analysis. These techniques could prove to be a powerful tool in examining changes in placental morphology.

Anesthesia and Monitoring of Animals During MRI Studies

The use of imaging represents a major impact on the refinement and the reduction of in vivo studies in animal models, in particular for allowing longitudinal monitoring of the onset and the progression of disease within the same animal, and studying the biological effects of drug candidate and their therapeutic effectiveness. But the use of imaging procedures can affect animal physiology, and the need to anesthetize the animals for imaging entails potential health risks. During anesthesia, there is an inevitable autonomic nervous system depression which induces cardiovascular depression, respiratory depression, and hypothermia. Also other procedures associated with imaging such as animal preparation (e.g., fasting, premedication), blood sampling, and dosage/contrast agent injections can also affect physiology and animal welfare. All these factors are likely to have confounding effect on the outcome of the imaging studies and pose important concerns regarding the animal's well-being, particularly when imaging immune deprived animals or diseased animals. We will discuss these challenges and considerations during imaging to maximize efficacious data while promoting animal welfare.

Therapeutic activity of superoxide dismutase-containing enzymosomes on rat liver ischaemia-reperfusion injury followed by magnetic resonance microscopy

Liver ischaemia-reperfusion injury (IRI) may occur during hepatic surgery and is unavoidable in liver transplantation. Superoxide dismutase enzymosomes (SOD-enzymosomes), liposomes where SOD is at the liposomal surface expressing enzymatic activity in intact form without the need of liposomal disruption, were developed with the aim of having a better insight into its antioxidant therapeutic outcome in IRI. We also aimed at validating magnetic resonance microscopy (MRM) at 7T as a tool to follow IRI. SOD-enzymosomes were characterized and tested in a rat ischaemia-reperfusion model and the therapeutic outcome was compared with conventional long circulating SOD liposomes and free SOD using biochemical liver injury biomarkers, histology and MRM. MRM results correlated with those obtained using classical biochemical biomarkers of liver injury and liver histology. Moreover, MRM images suggested that the therapeutic efficacy of both SOD liposomal formulations used was related to prevention of peripheral biliary ductular damage and disrupted vascular architecture. Therefore, MRM at 7T is a useful technique to follow IRI. SOD-enzymosomes were more effective than conventional liposomes in reducing liver ischaemia-reperfusion injury and this may be due to a short therapeutic window.

In vivo imaging techniques: a new era for histochemical analysis

In vivo imaging techniques can be integrated with classical histochemistry to create an actual histochemistry of water. In particular, Magnetic Resonance Imaging (MRI), an imaging technique primarily used as diagnostic tool in clinical/preclinical research, has excellent anatomical resolution, unlimited penetration depth and intrinsic soft tissue contrast. Thanks to the technological development, MRI is not only capable to provide morphological information but also and more interestingly functional, biophysical and molecular. In this paper we describe the main features of several advanced imaging techniques, such as MRI microscopy, Magnetic Resonance Spectroscopy, functional MRI, Diffusion Tensor Imaging and MRI with contrast agent as a useful support to classical histochemistry.

In vivo imaging of CREB phosphorylation in awake-mouse brain

The cyclic adenosine monophosphate response element binding protein (CREB) is a phosphorylation-dependent transcription factor that plays important roles in memory consolidation and several neuropsychological disorders. Although analyzing the spatiotemporal pattern of CREB phosphorylation is required for elucidating the mechanism of memory consolidation, imaging of phosphorylation of a particular protein in the brain of live animals is impossible at present. Here, we developed a method for visualizing the CREB phosphorylation in the cerebral cortex of an awake mouse using a split luciferase technique. Using this technique, we demonstrated the correlation between the change in CREB phosphorylation at a particular region in the brain and behavioral consequences induced by the administration of reserpine, a psychotropic agent.

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.

Regional fractional ventilation mapping in spontaneously breathing mice using hyperpolarized ¹²⁹Xe MRI

The feasibility of ventilation imaging with hyperpolarized (HP) (129) Xe MRI has been investigated for quantitative and regional assessment of ventilation in spontaneously breathing mice. The multiple breath ventilation imaging technique was modified to the protocol of spontaneous inhalation of HP (129) Xe delivered continuously from a (129) Xe polarizer. A series of (129) Xe ventilation images was obtained by varying the number of breaths before the (129) Xe lung imaging. The fractional ventilation, r, was successfully evaluated for spontaneously breathing mice. An attempt was made to detect ventilation dysfunction in the emphysematous mouse lung induced by intratracheal administration of porcine pancreatic elastase (PPE). As a result, the distribution of fractional ventilation could be visualized by the r map. Significant dysfunction of ventilation was quantitatively identified in the PPE-treated group. The whole-lung r value of 0.34 ± 0.01 for control mice (N = 4) was significantly reduced, to 0.25 ± 0.07, in PPE-treated mice (N = 4) (p = 0.038). This study is the first application of multiple breath ventilation imaging to spontaneously breathing mice, and shows that this methodology is sensitive to differences in the pulmonary ventilation. This methodology is expected to improve simplicity as well as noninvasiveness when assessing regional ventilation in small rodents.

Postmortem microcomputed tomography (micro-CT) of small fetuses and hearts

OBJECTIVE

To assess the feasibility and utility of contrast-enhanced microcomputed tomography (micro-CT) for identifying structural anomalies in ex-vivo first- and second-trimester human fetuses and isolated fetal hearts.

METHODS

Radiopaque iodine staining and micro-CT scanning protocols were first developed in rodent studies and then used to examine routinely fixed whole human fetuses (n = 7, weight 0.1-90 g, gestational age, 7-17 weeks) and isolated fetal hearts (n = 14, weight 0.1-5.2 g, gestational age, 11-22 weeks). Samples were scanned using an isotropic resolution of 18 (and, if necessary, 9 or 35) µm and findings were interpreted jointly by four fetal pathologists, a fetal cardiologist and a radiologist. Samples with gestational ages ≥ 13 weeks also underwent conventional autopsy or dissection.

RESULTS

Micro-CT identified all anatomical structures and abnormalities documented by the macroscopic examination. In all seven cases involving fetuses ≤ 13 weeks (four fetuses, three isolated hearts), micro-CT excluded the presence of structural anomalies. In the remaining 14 cases, it provided all the information obtained with invasive autopsy or dissection and in seven of the 14 (two fetuses, five isolated hearts) it furnished additional diagnostic details.

CONCLUSIONS

This pilot study confirms the feasibility of postmortem contrast-enhanced micro-CT assessment of structural anomalies in whole small fetuses and fetal hearts. Further study is needed to confirm our findings, particularly in whole fetuses, and to define the extent to which this virtual examination might be used instead of conventional invasive autopsy.

Multimodal cell tracking of a spontaneous metastasis model: comparison between MRI, electron paramagnetic resonance and bioluminescence

MRI cell tracking is a promising technique for tracking various cell types in living animals. Usually, cells are incubated with iron oxides so that the particles are taken up before the cells are injected in vivo. In the present study, we aimed to monitor migration of luciferase-expressing mouse renal cancer cells (RENCA-luc) after intrarenal or intrasplenic injection. These cells were labelled using Molday Ion Rhodamine B (MIRB) fluorescent superparamagnetic iron oxide particles. Their fate after injection was first assessed using ex vivo X-band electron paramagnetic resonance (EPR) spectroscopy. This biodistribution study showed that RENCA-luc cells quickly colonized the lungs and the liver after intrarenal and intrasplenic injection, respectively. Bioluminescence imaging (BLI) studies confirmed that this cell line preferentially metastasized to these organs. Early tracking of labelled RENCA-luc cells in the liver using high-field MRI (11.7 T) was not feasible because of a lack of sensitivity. MRI of MIRB-labelled RENCA-luc cells after injection in the left kidney was then performed. T2 - and T2 *-weighted images showed that the labelled cells induced hypointense signals at the injection site. Nevertheless, the hypointense regions tended to disappear after several days, mainly owing to dilution of the MIRB iron oxides with cell proliferation. In conclusion, EPR is well adapted to ex vivo analysis of tissues after cell tracking experiments and allows short-term monitoring of metastasizing cells. MRI is a suitable tool for checking labelled cells at their injection site, but dilution of the iron oxides owing to cell division remains a major limitation. BLI remains the most suitable technique for long-term monitoring of metastatic cells.

A digital multigate Doppler method for high frequency ultrasound

Noninvasive visualization of blood flow with high frequency Doppler ultrasound has been extensively used to assess the morphology and hemodynamics of the microcirculation. A completely digital implementation of multigate pulsed-wave (PW) Doppler method was proposed in this paper for high frequency ultrasound applications. Analog mixer was eliminated by a digital demodulator and the same data acquisition path was shared with traditional B-mode imaging which made the design compact and flexible. Hilbert transform based quadrature demodulation scheme was employed to achieve the multigate Doppler acquisition. A programmable high frequency ultrasound platform was also proposed to facilitate the multigate flow visualization. Experimental results showed good performance of the proposed method. Parabolic velocity gradient inside the vessel and velocity profile with different time slots were acquired to demonstrate the functionality of the multigate Doppler. Slow wall motion was also recorded by the proposed method.

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.

A red fluorescent nude mouse model of human endometriosis: advantages of a non-invasive imaging method

OBJECTIVES

To establish red fluorescent human endometriosis lesions in a nude mouse model and dynamically and non-invasively to compare intraperitoneal and subcutaneous injection models.

STUDY DESIGN

Primary cultures of endometrial stromal cells (ESCs) and epithelial cells (EECs) isolated from 24 patients with a normal uterine cavity were transfected with 2.5×10(8) (Group 1) and 1.25×10(8) (Group 2) plaque-forming units (PFU) of adenovirus encoding red fluorescent protein (Ad-RFP). Transfection efficiencies, fluorescence intensity and apoptosis rate of the two types of cells were compared in vitro. A mixture of 2.5×10(8) PFU Ad-RFP-infected approximately 400 EECs cell mass and 2×10(6) ESCs for 36h was injected individually into 24 female nude mice subcutaneously (Group A) or intraperitoneally (Group B). From Day 5 after injection, an in vivo imaging system (IVIS) was used to non-invasively observe and compare the lesions of the two groups every week until Day 33. Specifically, the fluorescent intensity, positive rates, persistence time and lesion weight in the implanted human endometriosis lesions were compared. A parametric Student's t-test and two-way analysis of variance were used for statistical analysis.

RESULTS

Compared with 1.25×10(8) PFU RFP, a titre of 2.5×10(8) PFU RFP ESCs and EECs incubated for 36h exhibited higher transfection efficiencies and higher fluorescence intensities in vitro. In vivo imaging of the fluorescent human endometriosis lesions originating from an RFP titre of 2.5×10(8) PFU showed that the intensity and lesion weight in Group A were significantly higher than in Group B. However, the two groups had the same RFP-positive rates and fluorescence persistence. The structure of each lesion was evaluated by immunohistochemistry to confirm its human endometrial origin.

CONCLUSIONS

The red fluorescent human endometriosis model established by subcutaneously injecting 2.5×10(8) PFU RFP-transfected stromal cells and epithelial cells into nude mice had a higher fluorescent positive rate from Day 5, higher intensity and weight but the same persistence as the intraperitoneal injection model.

Imaging the hard/soft tissue interface

Interfaces between different tissues play an essential role in the biomechanics of native tissues and their recapitulation is now recognized as critical to function. As a consequence, imaging the hard/soft tissue interface has become increasingly important in the area of tissue engineering. Particularly as several biotechnology based products have made it onto the market or are close to human trials and an understanding of their function and development is essential. A range of imaging modalities have been developed that allow a wealth of information on the morphological and physical properties of samples to be obtained non-destructively in vivo or via destructive means. This review summarizes the use of a selection of imaging modalities on interfaces to date considering the strengths and weaknesses of each. We will also consider techniques which have not yet been utilized to their full potential or are likely to play a role in future work in the area.

MRI compatible small animal monitoring and trigger system for whole body scanners

Performing magnetic resonance imaging (MRI) experiments with small animals requires continuous monitoring of vital parameters, especially the respiration rate. Clinical whole-body MR scanners represent an attractive option for preclinical imaging as dedicated animal scanners are cost-intensive in both investment and maintenance, thus limiting their availability. Even though impressive image quality is achievable with clinical MR systems in combination with special coils, their built-in physiologic monitoring and triggering units are often not suited for small animal imaging. In this work, we present a simple, MRI compatible low cost solution to monitor the respiration and heart rate of small animals in a clinical whole-body MR scanner. The recording and processing of the biosignals as well as the optimisation of the respiratory trigger generation is decribed. Additionally rat and mouse in-vivo MRI experiments are presented to illustrate the effectiveness of the monitoring and respiratory trigger system in suppressing motion artifacts.

Whole body MRI and fluorescent microscopy for detection of stem cells labeled with superparamagnetic iron oxide (SPIO) nanoparticles and DiI following intramuscular and systemic delivery

Methods to monitor transplanted stem cells in vivo are of great importance for potential therapeutic applications. Of particular interest are methods allowing noninvasive detection of stem cells throughout the body. Magnetic resonance imaging (MRI) is a tool that would allow detection of cells in nearly any tissue in the body and is already commonly used in the clinic. MRI tracking of stem cells is therefore feasible and likely to be easily adapted to patients receiving donor cells. Patients with Duchenne muscular dystrophy are good candidates for stem cell therapy, given the naturally regenerative nature of skeletal muscle, which repairs damage by employing endogenous stem cells from the muscle interstitium to regenerate muscle fibers throughout adulthood. We describe methods for labeling stem cells with superparamagnetic iron oxide nanoparticles (SPIO) to enhance MRI contrast, injecting them locally into skeletal and cardiac muscle, or systemically in mouse models for Duchenne muscular dystrophy, and tracking them in muscle tissue of live mice following injection. We focus on the use of whole body MRI to detect stem cells, as this is necessary for conditions such as muscular dystrophy, in which affected tissues are present throughout the body and systemic delivery of stem cells may be necessary. Emphasis is placed on the development of an MRI coil that is field of view (FOV) adjustable and can be used for both whole body imaging to determine stem cell localization as well as subsequent focusing on smaller, local regions where stem cells are present to obtain high-resolution images. We discuss the coil design and its significance for stem cell tracking. We also describe methods for labeling stem cells with a fluorescent dye and for tracking them in postmortem tissue specimens with fluorescent microscopy to correlate, compare, and contrast with results of whole body MRI in preclinical studies.

Mouse atlas registration with non-tomographic imaging modalities-a pilot study based on simulation

PURPOSE

This study investigates methodologies for the estimation of small animal anatomy from non-tomographic modalities, such as planar X-ray projections, optical cameras, and surface scanners. The key goal is to register a digital mouse atlas to a combination of non-tomographic modalities, in order to provide organ-level anatomical references of small animals in 3D.

PROCEDURES

A 2D/3D registration method was developed to register the 3D atlas to the combination of non-tomographic imaging modalities. Eleven combinations of three non-tomographic imaging modalities were simulated, and the registration accuracy of each combination was evaluated.

RESULTS

Comparing the 11 combinations, the top-view X-ray projection combined with the side-view optical camera yielded the best overall registration accuracy of all organs. The use of a surface scanner improved the registration accuracy of skin, spleen, and kidneys.

CONCLUSIONS

The methodologies and evaluation presented in this study should provide helpful information for designing preclinical atlas-based anatomical data acquisition systems.

Long-term left ventricular remodelling in rat model of nonreperfused myocardial infarction: sequential MR imaging using a 3T clinical scanner

Purpose. To evaluate whether 3T clinical MRI with a small-animal coil and gradient-echo (GE) sequence could be used to characterize long-term left ventricular remodelling (LVR) following nonreperfused myocardial infarction (MI) using semi-automatic segmentation software (SASS) in a rat model. Materials and Methods. 5 healthy rats were used to validate left ventricular mass (LVM) measured by MRI with postmortem values. 5 sham and 7 infarcted rats were scanned at 2 and 4 weeks after surgery to allow for functional and structural analysis of the heart. Measurements included ejection fraction (EF), end-diastolic volume (EDV), end-systolic volume (ESV), and LVM. Changes in different regions of the heart were quantified using wall thickness analyses. Results. LVM validation in healthy rats demonstrated high correlation between MR and postmortem values. Functional assessment at 4 weeks after MI revealed considerable reduction in EF, increases in ESV, EDV, and LVM, and contractile dysfunction in infarcted and noninfarcted regions. Conclusion. Clinical 3T MRI with a small animal coil and GE sequence generated images in a rat heart with adequate signal-to-noise ratio (SNR) for successful semiautomatic segmentation to accurately and rapidly evaluate long-term LVR after MI.

A template-based automatic skull-stripping approach for mouse brain MR microscopy

Small animal magnetic resonance microscopy (MRM) has been widely used today in computational neuroanatomy. Accurate identification of brain tissue in a mouse MRM is a critical fundamental step in neuroimaging processing, which is given less attention. This study presents an automatic skull-stripping technique based on template models and histogram analysis. Results were evaluated by calculating the Jaccard similarity index (JSI) and boundary concordance ratio (BCR) between the automatically segmented and manually traced brain volumes. Results demonstrate that this technique accurately extracts the brain volume (mean JSI = 97.1%, BC = 94.4%). The brain extraction method presented in this study will greatly facilitate analysis of neuroimaging studies of rodent animals in neurodegenerative diseases.

MARS: a mouse atlas registration system based on a planar x-ray projector and an optical camera

This paper introduces a mouse atlas registration system (MARS), composed of a stationary top-view x-ray projector and a side-view optical camera, coupled to a mouse atlas registration algorithm. This system uses the x-ray and optical images to guide a fully automatic co-registration of a mouse atlas with each subject, in order to provide anatomical reference for small animal molecular imaging systems such as positron emission tomography (PET). To facilitate the registration, a statistical atlas that accounts for inter-subject anatomical variations was constructed based on 83 organ-labeled mouse micro-computed tomography (CT) images. The statistical shape model and conditional Gaussian model techniques were used to register the atlas with the x-ray image and optical photo. The accuracy of the atlas registration was evaluated by comparing the registered atlas with the organ-labeled micro-CT images of the test subjects. The results showed excellent registration accuracy of the whole-body region, and good accuracy for the brain, liver, heart, lungs and kidneys. In its implementation, the MARS was integrated with a preclinical PET scanner to deliver combined PET/MARS imaging, and to facilitate atlas-assisted analysis of the preclinical PET images.

Anaesthesia and physiological monitoring during in vivo imaging of laboratory rodents: considerations on experimental outcomes and animal welfare

The implementation of imaging technologies has dramatically increased the efficiency of preclinical studies, enabling a powerful, non-invasive and clinically translatable way for monitoring disease progression in real time and testing new therapies. The ability to image live animals is one of the most important advantages of these technologies. However, this also represents an important challenge as, in contrast to human studies, imaging of animals generally requires anaesthesia to restrain the animals and their gross motion. Anaesthetic agents have a profound effect on the physiology of the animal and may thereby confound the image data acquired. It is therefore necessary to select the appropriate anaesthetic regime and to implement suitable systems for monitoring anaesthetised animals during image acquisition. In addition, repeated anaesthesia required for longitudinal studies, the exposure of ionising radiations and the use of contrast agents and/or imaging biomarkers may also have consequences on the physiology of the animal and its response to anaesthesia, which need to be considered while monitoring the animals during imaging studies. We will review the anaesthesia protocols and monitoring systems commonly used during imaging of laboratory rodents. A variety of imaging modalities are used for imaging rodents, including magnetic resonance imaging, computed tomography, positron emission tomography, single photon emission computed tomography, high frequency ultrasound and optical imaging techniques such as bioluminescence and fluorescence imaging. While all these modalities are implemented for non-invasive in vivo imaging, there are certain differences in terms of animal handling and preparation, how the monitoring systems are implemented and, importantly, how the imaging procedures themselves can affect mammalian physiology. The most important and critical adverse effects of anaesthetic agents are depression of respiration, cardiovascular system disruption and thermoregulation. When anaesthetising rodents, one must carefully consider if these adverse effects occur at the therapeutic dose required for anaesthesia, if they are likely to affect the image acquisitions and, importantly, if they compromise the well-being of the animals. We will review how these challenges can be successfully addressed through an appropriate understanding of anaesthetic protocols and the implementation of adequate physiological monitoring systems.

An FPGA-based open platform for ultrasound biomicroscopy

Ultrasound biomicroscopy (UBM) has been extensively applied to preclinical studies in small animal models. Individual animal study is unique and requires different utilization of the UBM system to accommodate different transducer characteristics, data acquisition strategies, signal processing, and image reconstruction methods. There is a demand for a flexible and open UBM platform to allow users to customize the system for various studies and have full access to experimental data. This paper presents the development of an open UBM platform (center frequency 20 to 80 MHz) for various preclinical studies. The platform design was based on a field-programmable gate array (FPGA) embedded in a printed circuit board to achieve B-mode imaging and directional pulsed-wave Doppler. Instead of hardware circuitry, most functions of the platform, such as filtering, envelope detection, and scan conversion, were achieved by FPGA programs; thus, the system architecture could be easily modified for specific applications. In addition, a novel digital quadrature demodulation algorithm was implemented for fast and accurate Doppler profiling. Finally, test results showed that the platform could offer a minimum detectable signal of 25 μV, allowing a 51 dB dynamic range at 47 dB gain, and real-time imaging at more than 500 frames/s. Phantom and in vivo imaging experiments were conducted and the results demonstrated good system performance.

Quantitative in vivo imaging of embryonic development: opportunities and challenges

Animal models are critically important for a mechanistic understanding of embryonic morphogenesis. For decades, visualizing these rapid and complex multidimensional events has relied on projection images and thin section reconstructions. While much insight has been gained, fixed tissue specimens offer limited information on dynamic processes that are essential for tissue assembly and organ patterning. Quantitative imaging is required to unlock the important basic science and clinically relevant secrets that remain hidden. Recent advances in live imaging technology have enabled quantitative longitudinal analysis of embryonic morphogenesis at multiple length and time scales. Four different imaging modalities are currently being used to monitor embryonic morphogenesis: optical, ultrasound, magnetic resonance imaging (MRI), and micro-computed tomography (micro-CT). Each has its advantages and limitations with respect to spatial resolution, depth of field, scanning speed, and tissue contrast. In addition, new processing tools have been developed to enhance live imaging capabilities. In this review, we analyze each type of imaging source and its use in quantitative study of embryonic morphogenesis in small animal models. We describe the physics behind their function, identify some examples in which the modality has revealed new quantitative insights, and then conclude with a discussion of new research directions with live imaging.

The Digital Fish Library: using MRI to digitize, database, and document the morphological diversity of fish

Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D) digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org), an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI) scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators.

Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images

Micro-CT is widely used in preclinical studies of small animals. Due to the low soft-tissue contrast in typical studies, segmentation of soft tissue organs from noncontrast enhanced micro-CT images is a challenging problem. Here, we propose an atlas-based approach for estimating the major organs in mouse micro-CT images. A statistical atlas of major trunk organs was constructed based on 45 training subjects. The statistical shape model technique was used to include inter-subject anatomical variations. The shape correlations between different organs were described using a conditional Gaussian model. For registration, first the high-contrast organs in micro-CT images were registered by fitting the statistical shape model, while the low-contrast organs were subsequently estimated from the high-contrast organs using the conditional Gaussian model. The registration accuracy was validated based on 23 noncontrast-enhanced and 45 contrast-enhanced micro-CT images. Three different accuracy metrics (Dice coefficient, organ volume recovery coefficient, and surface distance) were used for evaluation. The Dice coefficients vary from 0.45 ± 0.18 for the spleen to 0.90 ± 0.02 for the lungs, the volume recovery coefficients vary from 0.96 ± 0.10 for the liver to 1.30 ± 0.75 for the spleen, the surface distances vary from 0.18 ± 0.01 mm for the lungs to 0.72 ± 0.42 mm for the spleen. The registration accuracy of the statistical atlas was compared with two publicly available single-subject mouse atlases, i.e., the MOBY phantom and the DIGIMOUSE atlas, and the results proved that the statistical atlas is more accurate than the single atlases. To evaluate the influence of the training subject size, different numbers of training subjects were used for atlas construction and registration. The results showed an improvement of the registration accuracy when more training subjects were used for the atlas construction. The statistical atlas-based registration was also compared with the thin-plate spline based deformable registration, commonly used in mouse atlas registration. The results revealed that the statistical atlas has the advantage of improving the estimation of low-contrast organs.