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Three-Dimensional Volume Rendering Microscopy Resources

Section Overview:

In order to obtain the most significant amount of information from the two-dimensional image stacks acquired through confocal microscopy, three-dimensional volume rendering software is necessary. In recent years, a vast array of software programs have been developed to help microscopists meet this critical need, many of which are open-source and freely available. Featured within this selection of three-dimensional volume rendering resources are websites that describe and distribute some of the most powerful software tools available to microscopists.

Web Articles

  • 3-D Doctor - 3D-Doctor, written and distributed by Able Software Corporation, is an advanced 3D image visualization, rendering and measurement software package designed for microscopy and related imaging applications. The software creates 3D surface model and volume rendering from two-dimensional cross-section images using PC platforms.
  • 3D Reconstruction - Established as a service of the National Biocomputation Center at the Stanford University Medical Center, this site provides a basic explanation of reconstruction, a descriptive list of software available for three-dimensional reconstruction, an array of reconstruction images and videos, and an extensive collection of pertinent references and Internet links.
  • 3D Slicer - An ongoing collaboration between the MIT Artificial Intelligence Lab and the Surgical Planning Lab at Brigham and Women's Hospital, the 3D Slicer is a freely available, open-source software program for visualization, registration, segmentation, and quantification of data.
  • Alicona Imaging - In digital microscopy, Alicona Imaging is internationally recognized for its leading three-dimensional reconstruction, visualization, and analysis software and hardware. The company provides solutions in research and development, as well as in production for material development, life sciences, pharmacy, forensic applications, and more.
  • Applied Precision - The Seattle-based Applied Precision offers a wide variety of products and services, but of most interest to scientists with three-dimensional volume rendering needs is the DeltaVision Spectris, an integrated system of illumination, optics, stage mechanics, and software. In addition to product details, the company's website offers FAQs and a gallery of QuickTime videos and still images.
  • AutoQuant Imaging - AutoQuant Imaging concentrates on providing both two- and three- dimensional image restoration software products to meet the needs of life science microscopy. The company's website presents product, sales, and support information, as well as an educational section that offers tips and covers topics such as three-dimensional deconvolution and algorithms.
  • Bitplane Inc. - The goal of Bitplane Inc. is to create software that enables novel investigation while liberating researchers from routine image management housekeeping. In their efforts to achieve this goal, the company has developed a number of three- and four-dimensional visualization tools for microscopic images, such as Imaris and Imaris MeasurementPro.
  • Center for Biomedical Imaging Technology - Based at the University of Connecticut Health Center, the Center for Biomedical Imaging Technology is the home of NRCAM, the National Resource for Cell Analysis and Modeling, which is developing the Virtual Cell Modeling and Simulation framework. In addition to access to this resource, the organization's website features an overview of ongoing research that includes information about three-dimensional visualization and sample images and videos.
  • General Nanotechnology, LLC - General Nanotechnology, LLC created and dispenses Probe 3D, a software system for three-dimensional image rendering, enhancement, and analysis. The company also offers SmartFocus, a program that facilitates programmable computer control of microscope stages and imaging systems. Free demos and an image gallery are included on the website.
  • ImageTool - ImageTool is a free image processing and analysis program for the Microsoft Windows line of operating systems, which is capable of three-dimensional volume rendering. Visitors to the site can download the software and a variety of plug-ins, while a short FAQ addresses basic user concerns.
  • Improvision - A respected international company that designs and develops software systems for scientific imaging, Improvison offers a variety of useful information on their website, including in-depth tips and a searchable application library. One of the company's leading products is Volocity, an interactive volume visualization system that will run on a standard desktop computer.
  • Intelligent Imaging Innovations - The company, more commonly known as 3i, designs and produces high-end, user-friendly digital imaging systems and software that integrate state-of-the-art automated fluorescence microscopes with powerful multi-dimensional data acquisition and analysis.
  • MicroView - An open source, freely distributed three-dimensional volume viewer and analysis software program, the MicroView can be downloaded from this site, which also includes a description and a listing of key features.
  • NIH Image - A public domain image processing and analysis program for the Macintosh, NIH Image can be downloaded from this homepage, which also features a FAQ, an online manual, a mailing list, tutorials, and a helpful section dedicated to fluorescence and confocal microscopy. Image J, a similar program for use with Java, and numerous plug-ins, such as the 3DView, can also be downloaded here. Links to related websites and those with additional plug-ins are provided as well.
  • Scientific Volume Imaging - Scientific Volume Imaging is a company that concentrates in deconvolution and volume rendering software. In addition to product descriptions, the website features a section on topics in deconvolution, a knowledge database that contains answers to frequently and not-so-frequently asked questions regarding an array of relevant topics, and an index of talks on three-dimensional microscopy and similar subjects, which leads visitors to downloadable PDF files.
  • Scientific Volume Imaging: FreeSFP - Based on a physically realistic light propagation model, the SFP renderer allows you to view your raw and deconvolved multi-channel 3D datasets in a very intuitive manner. This freeware is downloadable from SVI's website.
  • VayTek - Specializing in scientific digital imaging and presentation applications, VayTek manufactures and distributes deconvolution, three-dimensional volume rendering, measurement, and presentation software. Also offered are packages that supply digital control for microscope peripherals. Besides product details and free demos, the site includes a well-developed FAQ that addresses basic and complex issues, extensive application notes, a list of recommended books and articles, and sample images and videos.
  • VolPack Volume Rendering Library - Written by Phillip Lacroute, Volpack is a portable software library that facilitates volume rendering, which is freely available for both research and commercial use. The website includes an overview of the software, downloadable files, and access to volume rendering datasets and sample images and videos.

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