1] Allen Institute for Brain Sciences, Seattle, Washington, USA. [2] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
1] Integrated Research Centre, University Campus Bio-Medico of Rome, Rome, Italy. [2] Department of Electrical and Information Engineering, University of Cassino and Southern Lazio, Cassino, Italy.
Nat Protoc. 2014 Jan;9(1):193-208. doi: 10.1038/nprot.2014.011. Epub 2014 Jan 2.
Open-Source 3D Visualization-Assisted Analysis (Vaa3D) is a software platform for the visualization and analysis of large-scale multidimensional images. In this protocol we describe how to use several popular features of Vaa3D, including (i) multidimensional image visualization, (ii) 3D image object generation and quantitative measurement, (iii) 3D image comparison, fusion and management, (iv) visualization of heterogeneous images and respective surface objects and (v) extension of Vaa3D functions using its plug-in interface. We also briefly demonstrate how to integrate these functions for complicated applications of microscopic image visualization and quantitative analysis using three exemplar pipelines, including an automated pipeline for image filtering, segmentation and surface generation; an automated pipeline for 3D image stitching; and an automated pipeline for neuron morphology reconstruction, quantification and comparison. Once a user is familiar with Vaa3D, visualization usually runs in real time and analysis takes less than a few minutes for a simple data set.
开源 3D 可视化辅助分析（Vaa3D）是一个用于可视化和分析大规模多维图像的软件平台。在本方案中，我们将描述如何使用 Vaa3D 的几个流行功能，包括 (i) 多维图像可视化，(ii) 3D 图像对象生成和定量测量，(iii) 3D 图像比较、融合和管理，(iv) 异构图像及其相应表面对象的可视化，以及 (v) 使用其插件接口扩展 Vaa3D 功能。我们还简要演示了如何将这些功能整合在一起，用于微观图像可视化和定量分析的复杂应用，使用三个示例流水线，包括用于图像滤波、分割和表面生成的自动化流水线；用于 3D 图像拼接的自动化流水线；以及用于神经元形态重建、量化和比较的自动化流水线。一旦用户熟悉了 Vaa3D，可视化通常可以实时运行，对于简单数据集的分析只需几分钟。
