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V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.

URL: http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html

Resource ID: nif-0000-32975     Resource Type: Resource     Version: Latest Version


3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, image

Curation Status




Resource Status

Last checked up;




V3D: A Swiss army knife for bioimage visualization & analysis

Parent Organization

Funding Information

Howard hughes medical institute,

Additional Resource Types

image analysis software, d visualization software, d visualization software, segmentation software, data visualization software

Resource PubMed IDs

PMID: 23633943

Original Submitter


Version Status


Submitted On

12:00am September 21, 2010

Originated From


Changes from Previous Version

First Version

Version 1

Created 5 years ago by Anonymous