AngioQuant: quantification of angiogenesis through image analysis

Citation: Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, and Ilya Shmulevich, "Robust quantification of in vitro angiogenesis through image analysis," IEEE Transactions on Medical Imaging, vol. 24, no. 4, pp. 549-553, April 2005.


AngioQuant is an automated image analysis tool for quantification of angiogenesis. It is designed for in vitro angiogenesis assays that are based on co-culturing endothelial cells with fibroblasts. AngioQuant provides quantitative and repeatable measurements of the lengths and sizes of tubule complexes as well as the numbers of junctions (branching points) in the tubule complexes. The resulting quantification data are saved in the comma separated values (CSV) format. The CSV files can be easily opened in a spreadsheet program such as Microsoft Excel®.

AngioQuant requires an installation of the MCR libraries, a MATLAB® runtime component provided by The MathWorks, Inc. The MCR libraries can be downloaded from this site. Alternatively, AngioQuant can be run under MATLAB 6.5 (R13) or higher with the Image Processing Toolbox. Instructions on the installation and use of AngioQuant can be found in the User's manual. Information on the underlying image processing methods can be found in the original manuscript. The set of test images that is used in the manuscript is also available for download on this site. If you would like to receive notifications of future updates, please send us your e-mail address.

[AngioQuant]


Standalone version

The standalone version of AngioQuant is available for Microsoft Windows based systems. The file AngioQuant.zip includes the necessary files. If you have not installed the MCR libraries, you need to also download the file MCRInstaller.exe. The MCR libraries must be installed before installing AngioQuant. Installation instructions for AngioQuant and the MCR libraries can be found in the user's manual and in the README.txt file.

The author's limited rights to the deployment of the standalone version of AngioQuant are governed by a license agreement between the author and the MathWorks. The license agreement can be found at http://www.mathworks.com/license/. AngioQuant is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. The author as well as the MathWorks and its licensors are EXCLUDED FROM ALL LIABILITY for damages or any obligation to provide remedial actions.

Note: there are reports saying that installing the MCR libraries fails on Windows 2000 based systems. Under Windows XP there seems to be no problems. More information on this issue will be posted here when it is available.

MATLAB toolbox

The toolbox version of AngioQuant can be run on any platform for which MATLAB® is available. An installation of MATLAB 6.5 (R13) or higher with the Image Processing Toolbox is required. Installation instructions can be found in the user's manual and the READMETBX.txt file.

The AngioQuant Toolbox is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

The AngioQuant Toolbox is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Further downloads


Supplementary materials


Version history

11 Aug 2005: minor update (v1.33)
6 May 2005: minor update (v1.32)
28 Feb 2005: minor update (v1.31)
24 Feb 2005: major update (v1.30)
05 Jul 2004: major update (v1.20)
12 May 2004: minor update (v1.11)
02 Mar 2004: major update (v1.10)
22 Jan 2004: minor update (v1.01)
14 Jan 2004: original release (v1.00)


Contact

Antti Niemistö
Institute of Signal Processing
Tampere University of Technology
P.O. Box 553
33101 TAMPERE
FINLAND
E-mail: antti.niemisto@tut.fi
Tel: +358-3-3115 4507
Fax: +358-3-3115 4989

Ilya Shmulevich
Associate Professor
Institute for Systems Biology
Seattle, WA 98103
USA
E-mail: is@ieee.org

Wei Zhang
Director
Cancer Genomics Core Laboratory
Department of Pathology
The University of Texas M. D. Anderson Cancer Center
1515 Holcombe Blvd., Unit 85
Houston, TX 77030
USA


antti.niemisto@tut.fi
Last updated: 16th Aug 2005