Precise three-dimensional (3D) mapping of a large number of gene expression patterns, neuronal types and connections to an anatomical reference helps us to understand the vertebrate brain and its development. We developed the Virtual Brain Explorer (ViBE-Z), a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern; here we demonstrate its utility for mapping neurons of the dopaminergic system. The ViBE-Z database, atlas and software are provided via a web interface.

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SUMMARYTo achieve a detailed understanding of processes in biological systems, cellular features must be quantified in the three-dimensional (3D) context of cells and organs. We described use of the intrinsic root coordinate system (iRoCS) as a reference model for the root apical meristem of plants. iRoCS enables direct and quantitative comparison between the root tips of plant populations at single-cell resolution. The iRoCS Toolbox automatically fits standardized coordinates to raw 3D image data. It detects nuclei or segments cells, automatically fits the coordinate system, and groups the nuclei/cells into the root's tissue layers. The division status of each nucleus may also be determined. The only manual step required is to mark the quiescent centre. All intermediate outputs may be refined if necessary. The ability to learn the visual appearance of nuclei by example allows the iRoCS Toolbox to be easily adapted to various phenotypes. The iRoCS Toolbox is provided as an open-source software package, licensed under the GNU General Public License, to make it accessible to a broad community. To demonstrate the power of the technique, we measured subtle changes in cell division patterns caused by modified auxin flux within the Arabidopsis thaliana root apical meristem.

Silicon nanocrystals were synthesized by CO(2) laser pyrolysis of SiH(4). The fresh silicon nanopowder was oxidized in water to obtain SiO(2) nanoparticles (NPs) exhibiting strong red-orange photoluminescence. Samples of SiO(2) NPs embedded in low concentration in a thin polymer layer were prepared by spin-coating a dedicated solution on quartz cover slides. Using an argon ion laser at 488 nm with higher-order laser modes (azimuthally and radially polarized doughnut modes) for excitation, the three-dimensional orientation of the nanoparticles' transition dipole moment was investigated in a confocal microscope. The linear transition dipole moment was found to be rather stable and randomly oriented. However, dynamical effects such as fluorescence intermittency and transition dipole moment flipping could also be observed. The spectral analysis of single SiO(2) NPs revealed double-peak spectra consisting of a narrow zero-phonon line and a broader phonon band being associated with the excitation of longitudinal optical phonons in the SiO(2) NP.