A method for rapid morphologic phenotyping is demonstrated by using magnetic resonance microscopy. Whole fixed C57BL/6J mice were imaged at 110-microm isotropic resolution; limited volumes of the intact specimen, at 50-microm isotropic resolution; and isolated organs, at 25-microm isotropic resolution. The three-dimensional imaging technique was applied to uricase knockout mice to demonstrate the method for the evaluation of morphologic phenotype.

The quantification of cochlear fluid spaces provided by this study will enable the more accurate calculation of drug and other solute movements in fluids of the inner ear during experimental or clinical manipulations.

The Mouse Bioinformatics Research Network (MBIRN) has been established to integrate imaging studies of the mouse brain ranging from three-dimensional (3D) studies of the whole brain to focused regions at a sub-cellular scale. Magnetic resonance (MR) histology provides the entry point for many morphologic comparisons of the whole brain. We describe a standardized protocol that allows acquisition of 3D MR histology (43-micron resolution) images of the fixed, stained mouse brain with acquisition times < 30 minutes. A higher-resolution protocol with isotropic spatial resolution of 21.5 microns can be executed in 2 hours. A third acquisition protocol provides an alternative image contrast (at 43-micron isotropic resolution), which is exploited in a statistically driven algorithm that segments 33 of the most critical structures in the brain. The entire process, from specimen perfusion, fixation and staining, image acquisition and reconstruction, post-processing, segmentation, archiving, and analysis is integrated through a structured workflow. This yields a searchable database for archive and query of the very large (1.2 GB) images acquired with this standardized protocol. These methods have been applied to a collection of both male and female adult murine brains ranging over 4 strains and 6 neurologic knockout models. This collection and acquisition methods are now available to the neuroscience community as a standard web-deliverable service.

Magnetic resonance histology (MRH) images of the whole mouse have been acquired at 100-micron isotropic resolution at 2.0T with image arrays of 256 ϫ 256 ϫ 1024. Higher resolution (50 ϫ 50 ϫ 50 microns) of limited volumes has been acquired at 7.1T with image arrays of 512 ϫ 512 ϫ 512. Even higher resolution images (20 ϫ 20 ϫ 20 microns) of isolated organs have been acquired at 9.4T. The volume resolution represents an increase of 625,000ϫ over conventional clinical MRI. The technological basis is summarized that will allow basic scientists to begin using MRH as a routine method for morphologcic phenotyping of the mouse. MRH promises four unique attributes over conventional histology: 1) MRH is non-destructive; 2) MRH exploits the unique contrast mechanisms that have made MRI so successful clinically; 3) MRH is 3-dimensional; and 4) the data are inherently digital. We demonstrate the utility in morphologic phenotyping a whole C57BL/6J mouse.

Projection reconstruction has been implemented with self-refocused selection pulses on a small bore, 2.0 T MR microscope, to allow imaging of lung parenchyma. Scan synchronous ventilation and cardiac gating have been integrated with the sequence to minimize motion artifacts. A systematic survey of the pulse sequence parameters has been undertaken in conjunction with the biological gating parameters to optimize resolution and signal-to-noise (SNR). The resulting projection images with effective echo time of < 300 microseconds allow definition of lung parenchyma with an SNR improvement of approximately 15 x over a more conventional 2DFT short echo gradient sequence.

Radial acquisition (RA) techniques have been extended to produce isotropic, three-dimensional images of lung in live laboratory animals at spatial resolution down to 0.013 mm3 with a signal-to-noise ratio of 30:1. The pulse sequence and reconstruction algorithm have been adapted to allow acquisition of image matrices of up to 256(3) in less than 15 min. Scan-synchronous ventilation has been incorporated to limit breathing motion artifacts. The imaging sequence permits randomizing and/or discarding selected views to minimize the consequences of breathing motion. The signal in lung parenchyma was measured as a function of flip angle (alpha) for different repetition times and found to follow the predictions for which there is an optimum excitation (Ernst) angle. A single T1 relaxation value of 780 +/- 54 ms fits all data from six guinea pigs at 2.0 T. This T1 value parameterizes the signal and allows for a priori optimization, such as calculation of the Ernst angle appropriate for lung imaging.

Sophisticated image analysis methods have been developed for the human brain, but such tools still need to be adapted and optimized for quantitative small animal imaging. We propose a framework for quantitative anatomical phenotyping in mouse models of neurological and psychiatric conditions. The framework encompasses an atlas space, image acquisition protocols, and software tools to register images into this space. We show that a suite of segmentation tools (Avants, Epstein et al., 2008) designed for human neuroimaging can be incorporated into a pipeline for segmenting mouse brain images acquired with multispectral magnetic resonance imaging (MR) protocols. We present a flexible approach for segmenting such hyperimages, optimizing registration, and identifying optimal combinations of image channels for particular structures. Brain imaging with T1, T2* and T2 contrasts yielded accuracy in the range of 83% for hippocampus and caudate putamen (Hc and CPu), but only 54% in white matter tracts, and 44% for the ventricles. The addition of diffusion tensor parameter images improved accuracy for large gray matter structures (by >5%), white matter (10%), and ventricles (15%). The use of Markov random field segmentation further improved overall accuracy in the C57BL/6 strain by 6%; so Dice coefficients for Hc and CPu reached 93%, for white matter 79%, for ventricles 68%, and for substantia nigra 80%. We demonstrate the segmentation pipeline for the widely used C57BL/6 strain, and two test strains (BXD29, APP/TTA). This approach appears promising for characterizing temporal changes in mouse models of human neurological and psychiatric conditions, and may provide anatomical constraints for other preclinical imaging, e.g. fMRI and molecular imaging. This is the first demonstration that multiple MR imaging modalities combined with multivariate segmentation methods lead to significant improvements in anatomical segmentation in the mouse brain.

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