Qu for MATLAB
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Qu for MATLAB |
Qu is a MATLAB toolbox for the visualization and analysis of N-dimensional datasets targeted to the field of biomedical imaging. It supports several microscopy image formats and offers a plugin mechanism and a consistent API for easy extension. One of its advantages compared to similar tools is that it makes use of the power of MATLAB and can use its innumerable tools and functions.
Qu makes use
and extends MATLAB’s Image Processing Toolbox to address the
needs of scientists in the field of biomedical research. It allows the
visualization and analysis of 4D (XYZT) datasets with any number of
color channels. It allows the loading of several microscopy formats and
offers a consistent API to handle the image data, the metadata, and the
results of the analyses associated to the data. Primary and derived
data are stored in a “Qu project”, a container
class that can be saved to disk and reloaded later to continue the
analysis from where it was left. In the future, I plan to add database
support to (optionally) store Qu projects. Qu implements a plugin mechanism
(still under development), that allows users to develop their own
processing functions and easily add them to the Qu framework without
having to modify the core package. Qu requires MATLAB and the Image
Processing Toolbox to run but can make use of any tool(box) that runs
on the user’s MATLAB installation. Taking advantage of the
capabilities of MATLAB to interface with Java classes and dynamically
linked libraries, the user can easily implement new processing and
analysis tools in the MATLAB programming language, Java, C/C++,
and Fortran, or make use of existing ones. The results can then
easily be stored and visualized in
Qu through the API. Plugins will also be downloadable from
sourceforge.net. An example plugin is contained in the Qu core package.
Moreover, Qu offers a connection to Bitplane’s Imaris through
ImarisXT, allowing the two-way exchange of data between Imaris and Qu.
Qu is a generic image processing package with enhanced processing functions.
Qu supports several microscopy formats.
Qu offers a connection to Bitplane's Imaris through ImarisXT (Windows only).
Qu is easily expandable through API and plugins mechanism (in development).
Qu can be run on Windows 32/64 bit and Linux 32/64 bit.
For all
other platforms supported by MATLAB, only the compilation of a few C++
libraries is
required.
Qu is open source (see License below).
Qu has a good API documentation.
Qu requires MATLAB 7 (R14) or above.
Qu for
MATLAB is distributed under the terms of the Mozilla Public
License Version 1.1.
You may obtain a
copy of the License at http://www.mozilla.org/MPL/.
Software distributed
under the
License is distributed on an "AS IS" basis, WITHOUT WARRANTY
OF
ANY KIND, either express or implied.
See the License for
the specific language governing rights and limitations under the
License.
The Original Code is
"Qu for MATLAB".
The Initial
Developer of the Original Code is Aaron Ponti.
All Rights Reserved.
See also the MPL FAQ.
Qu contains third-party code:
a modified version of tiffread4.m
http://www.cytosim.org/other/index.html
Copyright (c) Francois
Nedelec
Cell Biology and Biophysics, EMBL
Meyerhofstrasse 1; 69117 Heidelberg; Germany
http://www.embl.org
http://www.cytosim.org
Bio-Formats
http://www.loci.wisc.edu/ome/formats.html
Bio-Formats is a standalone Java library for reading and writing
popular microscopy file formats, written by Melissa Linkert,
Curtis Rueden,
Chris Allan
and Eric
Kjellman. It is capable of parsing both pixels
and metadata for a large number of formats as well as writing to
several formats.
Copyright (c) Laboratory for Optical and Computational Instrumentation
http://www.loci.wisc.edu/
MATITK
http://mial.fas.sfu.ca/researchProject.php?s=308
Copyright (c) 2004-2005
Vincent Chu and Ghassan Hamarneh
Medical Image Analysis Lab, Simon Fraser University, Canada
Insight Toolkit
http://www.itk.org/
Copyright (c) 1999-2003 Insight Software Consortium
MatlabBLG (stripped)
http://www.stanford.edu/~dgleich/programs/matlab_bgl/
Copyright (c) 2006
David Gleich
mixturecode
http://www.lx.it.pt/%7Emtf/mixturecode.zip
A software for the unsupervised learning of finite mixture models,
associated to (and described in) the following paper:
M. Figueiredo and A. K. Jain, "Unsupervised learning of finite mixture
models", IEEE Transactions on Pattern Analysis and
Machine Intelligence - PAMI, vol. 24, no. 3, pp. 381-396, March 2002.
Copyright (c) Mario
Figueiredo, (c) 2000-2002
Instituto Superior Tecnico
1049-001 Lisboa, Portugal
So far there are no releases to download (Qu is still in late-alpha stage).
The current development version can be checked out through svn with the following instruction set:
svn co
https://qum.svn.sourceforge.net/svnroot/qum/trunk $MATLABHOME/matlab/qum
where MATLABHOME is an environbment variable pointing to your MATLAB code (see Installation instructions).
If you are not familiar with subversion or version control in general, you can find some information here: https://sourceforge.net/docs/E09 and http://svnbook.red-bean.com/en/1.1/index.html.
For Windows users: I recommend TortoiseSVN.
Download and save startup.m
and cgenpath.m to $matlabroot\toolbox\local.
$matlabroot is the MATLAB Installation directory (something like C:\Program
Files\MATLAB\R2006a\)
Set the environment variable MATLABHOME:
Right-click on My Computer
Select Properties: the System Properties panel appears
Click on the Advanced Tab
Click on the Environment variables button
Click on New under the panel "User variables for _your_user_name_"
Add the following information:
Variable name: MATLABHOME
Variable value: some directory where you want to checkout "Qu for MATLAB"
Create a subdirectory matlab in $MATLABHOME
Checkout "Qu for MATLAB" into $MATLABHOME/matlab/qum
Start MATLAB and type Qu at the command prompt.
Download and save startup.m
and cgenpath.m to $matlabroot/toolbox/local.
$matlabroot is the MATLAB Installation directory (something like /usr/local/matlab/)
Set the environment variable MATLABHOME:
Edit the file .bashrc in your home directory and add following entries
# Here we set MATLABHOME to the user's home directory
# but it can be any directory where you have read/write access
export
MATLABHOME=~/
# Workaround for
MATLAB 7.0.4 64 bit's problem on SuSE Linux 9.3
#
(not necessary for the other platforms and later versions)
LD_ASSUME_KERNEL=2.4.19
export
LD_ASSUME_KERNEL
You will need to logout and login again for the changes to take effect.
Create a subdirectory matlab in $MATLABHOME
Checkout "Qu for MATLAB" into $MATLABHOME/matlab/qum
Start MATLAB and type Qu at the command prompt.
I don't have a Mac :-( If somebody wants to ...
write some installation instructions and
compile the c++ libraries under /lib/mex for PowerPC and send them to me ;-)
... I would really appreciate.
Please use Qu's project page to report bugs.
Aaron Ponti
aarpon@users.sourceforge.net