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About ViBrism

ViBrism (Virtual Brain with 3D-IDM) -DB is a 3D-map database of endogenous gene expression in a virtual whole mouse brain produced with an original mapping framework Transcriptome Tomography (PLoS One 2012, see a movie on rikenchannel-YouTube “Mapping genes onto brain structures”). We invented a devise system, 3D-ISM (Figure 1A) for material sampling and block-face imaging. The materials are subjected to comprehensive measurement of gene expression and the measured data are 3D-reconstructed by computation using the image data (Figure 1B). BD now contains 36,558 expression maps of the adult mouse brain (C57BL6/J 8-wk male) searchable with gene symbols (“Search by Gene Name”) or expression similarity (“Similarly Expressed Gene Search”) in our Top Page. After the search, 2D/3D expression maps can be browsed and then data files of the maps are downloadable and viewed with a software on your desk-top computer. (visit our “Software” page).

figA
A. Overview of 3D-ISM device system
] : high speed cross-sectioning machine for frozen materials
] : optics system: microscope (MVX:Olympus)
] : camera: CCD (JK-TU52H:TOSHIBA)
ref. Yokota, H. et. al., (2002) Med. Imag. Tech. 20, 660-665.

3D-ISM enables to simultaneously obtain sliced samples for microanalysis and their block-face images.


figB
B. Mapping strategy

Materials are fractionated and subjected to a comprehensive measurement of gene expression and the measured data are 3D-reconstructed by computation using the image data of the fractions.


figC
ref. Y Okamura-Oho et. al., (2012) PLOS One
C. Comparison of 3D Expression maps to ABA maps.

Among the 40 regionally expressed genes, 3D map data of 33 genes were available in ABA. Expression maps in ABA and our maps (ViBrism) were visualized with VCAT. The names of the gene and the area, in which the gene was selectively expressed, are shown at the top and the bottom of panels for ViBrism, respectively.

Figure 1. Transcriptome Tomography (TT)