Introduction

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.

Publications

  1. Extensible visualization and analysis for multidimensional images using Vaa3D.
    Cite this
    Peng H, Bria A, Zhou Z, Iannello G, Long F, 2014-01-01 - Nature protocols
  2. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.
    Cite this
    Peng H, Ruan Z, Long F, Simpson JH, Myers EW, 2010-04-01 - Nature biotechnology

Credits

  1. Hanchuan Peng
    Developer

    1] Allen Institute for Brain Sciences, Seattle, United States of America

  2. Alessandro Bria
    Developer

    1] Integrated Research Centre, University Campus Bio-Medico of Rome, Italy

  3. Zhi Zhou
    Developer

    Allen Institute for Brain Sciences, Seattle, United States of America

  4. Giulio Iannello
    Developer

    Integrated Research Centre, University Campus Bio-Medico of Rome, Italy

  5. Fuhui Long
    Investigator

    1] Janelia Farm Research Campus, Howard Hughes Medical Institute, United States of America

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Summary
AccessionBT000240
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByFuhui Long