AngioQuant Toolbox
Copyright (C) 2004-2005 Antti Niemistö

This program 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.

This program 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.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

-------------------------------------------------------------------------

The AngioQuant Toolbox 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 AngioQuant Toolbox requires MATLAB 6.5 (R13) or higher with the
Image Processing Toolbox. The AngioQuant Toolbox can be run on any
platform for which MATLAB is available. MATLAB is a registered
trademark of The MathWorks, Inc. (http://www.mathworks.com/). A
stand-alone version of AngioQuant is available in the AngioQuant
homepage at http://www.cs.tut.fi/sgn/csb/angioquant/.

For detailed instructions on the use of AngioQuant, refer to the
user's manual (manual.pdf). The user's manual is also available in the
AngioQuant homepage at http://www.cs.tut.fi/sgn/csb/angioquant/.


CURRENT VERSION
---------------

v1.33 (11 Aug 2005)


INSTALLATION
------------

Extract the contents of the zip package that contains AngioQuant into
an empty directory.


STARTING UP
-----------

1) Start MATLAB.
2) Go to the directory in which the AngioQuant Toolbox was installed.
3) Start the m-file "angioquant".


GETTING STARTED
---------------

The following gives simple instructions on how to use AngioQuant.
Refer to the user's manual for more detailed instructions.

Single image operation:

 1) Open an image by choosing File -> Open.
 2) Perform smoothing by pressing the "Smooth" pushbutton (optional).
 3) Perform segmentation by pressing the "Segment" pushbutton.
 4) Perform thinning by pressing the "Skeletonize" pushbutton.
 5) Perform pruning by pressing the "Prune" pushbutton (optional).
 6) Save data by choosing File -> Save data.

or

 1) Open an image by choosing File -> Open.
 2) Perform the three quantification steps 3-5 by pressing the
    "Quantify" pushbutton.
 3) Save data by choosing File -> Save data.

Batch processing:

 1) Open a directory (batch) of images by choosing File -> Process Batch.
 2) Answer the questions concerning the parameters.
 3) When processing is ready, AngioQuant will prompt for a file name
    for saving the data

The data is saved in a comma separated values (CSV) file. CSV-files
can be opened in spreadsheet programs such as Microsoft Excel. The
CSV-files contain the parameters that were used to analyze each image
as well as the quantification results. The quantification results
include the lengths and sizes of each tubule complex in each image as
well as the number of junctions in each tubule complex.


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 

----------------------------------------

http://www.cs.tut.fi/sgn/csb/angioquant/

----------------------------------------
