Three-dimensional atlas system for mouse and rat brain imaging data

Abstract

Tomographic neuroimaging techniques allow visualization of functionally and structurally specific signals in the mouse and rat brain. The interpretation of the image data relies on accurate determination of anatomical location, which is frequently obstructed by the lack of structural information in the data sets. Positron emission tomography (PET) generally yields images with low spatial resolution and little structural contrast, and many experimental magnetic resonance imaging (MRI) paradigms give specific signal enhancements but often limited anatomical information. Side-by-side comparison of image data with conventional atlas diagram is hampered by the 2-D format of the atlases, and by the lack of an analytical environment for accumulation of data and integrative analyses. We here present a method for reconstructing 3-D atlases from digital 2-D atlas diagrams, and exemplify 3-D atlas-based analysis of PET and MRI data. The reconstruction procedure is based on two seminal mouse and brain atlases, but is applicable to any stereotaxic atlas. Currently, 30 mouse brain structures and 60 rat brain structures have been reconstructed. To exploit the 3-D atlas models, we have developed a multi-platform atlas tool (available via The Rodent Workbench, http://rbwb.org) which allows combined visualization of experimental image data within the 3-D atlas space together with 3-D viewing and user-defined slicing of selected atlas structures. The tool presented facilitates assignment of location and comparative analysis of signal location in tomographic images with low structural contrast.

Statistical Parametric Mapping for Effects of Verapamil on Olfactory Connections of Rat Brain in Vivo using Manganese-enhanced MR Imaging

“…[13][14][15][16][17][18] With these techniques, spatial normalization of the brain permits voxel-based analysis of the entire brain and more objective results than those of conventional ROI/VOI analysis. The results are less susceptible to changes in subject shape and size, and position, shape, and size of the ROI/VOI do not vary between observers.…”

“…An FWHM value that is too large for smoothing prevents detection of small regions enhanced by Mn 2＋ , and one that is too small reduces the statistical power, as described. Because recent studies made no reference to the smoothing parameter for statistical mapping of the rat brain using MEMRI, [11][12][13][14][15][16][17][18] we set the parameter such that the t-score was increased. Figure 7 shows that smoothing increased the t-score.…”

“…However, the spatial normalization (anatomical standardization) technique used in this mapping method enables an objective ROI/VOI analysis that can measure the intensities. The 3-dimensional stereotaxic rat brain regions (ROIs/VOIs) predeˆned in the rat brain atlas 17,18 allow the ROI/VOI analysis. The analysis with the 3-dimensional stereotaxic ROI/VOI has been used in theˆeld of the human clinical assessment for quantitative cerebral blood ‰ow by using single-photon emission computed tomography (SPECT) or positron emission tomography (PET).…”

Network analysis of mesoscale optical recordings to assess regional, functional connectivity

“…Recently, there has been great interest in quantifying aspects of the connectome, which refers to a complete description of the structural or functional connections between elements of the nervous system. 1,2 There have been a number of efforts to reconstruct the structural connectivity of the entire brain through detailed anatomical tracing studies in the mouse [3][4][5][6] and rat 7 brain. Such intense research effort is indicative of the great potential of the connectome to reshape our framework for understanding the brain in health and disease.…”

Estudio de la conectividad funcional en cerebros de animales de experimentación a partir del análisis de imágenes de resonancia magnética mediante técnicas de clasificación no supervisada

“…El registro de las imágenes experimentales y el atlas como volúmenes tridimensionales no es una tarea sencilla. Por ejemplo, en Hjornevik et al [147] las imágenes experimentales se corregistran en base a puntos de referencia reconocibles del cerebro y/o cráneo, por lo que la calidad del registro (y por tanto, del análisis regional) reside fundamentalmente en la habilidad de encontrar buenos puntos de referencia. Aunque la utilidad de los análisis regionales que utilicen un corregistro manual no se pone en duda [148] la tendencia actual es la de realizar un corregistro automático mediante algún software específico (por ejemplo, mediante SPM8) de las imágenes experimentales y el espacio anatómico de referencia.…”