title: Extensible visualization and analysis for multidimensional images using Vaa3D.
abstract: 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.
authors.affiliation: 1] Allen Institute for Brain Sciences, Seattle, Washington, USA. [2] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
authors.forename: Hanchuan
authors.identifier: 0000000234783942
authors.initials: H
authors.lastname: Peng
authors.affiliation: 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.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bria
authors.affiliation: Allen Institute for Brain Sciences, Seattle, Washington, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Integrated Research Centre, University Campus Bio-Medico of Rome, Rome, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Iannello
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA. [2] BioImage, LLC, Bellevue, Washington, USA.
authors.forename: Fuhui
authors.initials: F
authors.lastname: Long
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology; D003198:Computer Simulation; D004330:Drosophila / Q000033:anatomy & histology; D021621:Imaging, Three-Dimensional / Q000379:methods*; D009474:Neurons / Q000648:ultrastructure; D012984:Software; D014584:User-Computer Interface