Extensible visualization and analysis for multidimensional images using Vaa3D

被引：219

作者：

Peng, Hanchuan ^{[1
,2
]}

Bria, Alessandro ^{[3
,4
]}

Zhou, Zhi ^{[1
]}

Iannello, Giulio ^{[3
]}

Long, Fuhui ^{[2
,5
]}

机构：

[1] Allen Inst Brain Sci, Seattle, WA 98103 USA

[2] Howard Hughes Med Inst, Ashburn, VA USA

[3] Univ Campus Biomed Rome, Integrated Res Ctr, Rome, Italy

[4] Univ Cassino & Southern Lazio, Elect & Informat Engn Dept, Cassino, Italy

[5] BioImage LLC, Bellevue, WA USA

来源：

NATURE PROTOCOLS | 2014年 / 9卷 / 01期

关键词：

BIOIMAGE INFORMATICS; QUANTITATIVE-ANALYSIS; PLATFORM; NEUROANATOMY; TOOL;

D O I：

10.1038/nprot.2014.011

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：193 / 208

页数：16

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