Jenett Arnim, Schindelin Johannes E, Heisenberg Martin
Lehrstuhl für Genetik und Neurobiologie, Biozentrum, Am Hubland, D-97074 Würzburg, Germany.
BMC Bioinformatics. 2006 Dec 29;7:544. doi: 10.1186/1471-2105-7-544.
In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy.
This paper describes the Virtual Insect Brain (VIB) protocol, a script suite for the quantitative assessment, comparison, and presentation of neuroanatomical data. It is based on the 3D-reconstruction and visualization software Amira, version 3.x (Mercury Inc.) 1. Besides its backbone, a standardization procedure which aligns individual 3D images (series of virtual sections obtained by confocal microscopy) to a common coordinate system and computes average intensities for each voxel (volume pixel) the VIB protocol provides an elaborate data management system for data administration. The VIB protocol facilitates direct comparison of gene expression patterns and describes their interindividual variability. It provides volumetry of brain regions and helps to characterize the phenotypes of brain structure mutants. Using the VIB protocol does not require any programming skills since all operations are carried out at an intuitively usable graphical user interface. Although the VIB protocol has been developed for the standardization of Drosophila neuroanatomy, the program structure can be used for the standardization of other 3D structures as well.
Standardizing brains and gene expression patterns is a new approach to biological shape and its variability. The VIB protocol provides a first set of tools supporting this endeavor in Drosophila. The script suite is freely available at http://www.neurofly.de2.
在果蝇中，用于大脑功能分析的新的遗传学、生理学、分子学和行为学技术正在迅速积累。这些对昆虫大脑功能的多样研究使用了可可视化的基因表达模式，并提供了操纵神经元群体的方法作为共同基础。为了利用这些模式，人们需要了解它们的典型解剖结构。
本文描述了虚拟昆虫大脑（VIB）协议，这是一套用于神经解剖学数据的定量评估、比较和呈现的脚本套件。它基于3D重建和可视化软件Amira 3.x版（Mercury公司）。除了其核心部分，即一种将个体3D图像（通过共聚焦显微镜获得的虚拟切片系列）与共同坐标系对齐并计算每个体素（体积像素）平均强度的标准化程序外，VIB协议还提供了一个用于数据管理的精细数据管理系统。VIB协议有助于直接比较基因表达模式，并描述它们的个体间变异性。它提供脑区的体积测量，并有助于表征脑结构突变体的表型。使用VIB协议不需要任何编程技能，因为所有操作都在直观易用的图形用户界面上进行。虽然VIB协议是为果蝇神经解剖学的标准化而开发的，但程序结构也可用于其他3D结构的标准化。
对大脑和基因表达模式进行标准化是研究生物形态及其变异性的一种新方法。VIB协议提供了第一套支持果蝇这一研究工作的工具。该脚本套件可从http://www.neurofly.de免费获取。
