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.

Introduction

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 at a glance

• Qu is a generic image processing package with enhanced processing functions.
• Qu supports several microscopy formats:
  • Metamorph STK
  • Zeiss LSM
  • Deltavision DV, R3D
  • Image Cytometry Standard ICS/IDS
  • Bitplane Imaris 5.5
  • multi-page TIFFs
• Qu offers a connection to Bitplane's Imaris through ImarisXT (commercial, 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 and MacOSX (Update: Jonas Dorn contributed compiled libraries for MacOSX)
  For all other platforms supported by MATLAB, only the compilation of a few C++ libraries is required.
• Qu is open source (see License).
• Qu has a good API documentation
• Qu requires MATLAB 7 (R14) or above.

License

Qu is copyright (c) 2005-2009 Aaron Ponti
All rights reserved

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 heavily 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

• 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

Download

Current stable release

So far there are no releases to download (Qu is still in late-alpha stage).

Current development version (requires a Subversion client)

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 environment 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.

Installation instructions

The following instructions seem a bit complicated, but cleanly handle adding qum and all relevant subdirectories to the MATLAB path ignoring the subversion .svn subfolders and the various MATLAB class subdirectories and adding java classes properly.

Windows

• Save startup.m and cgenpath.m to $matlabroot\toolbox\local.
  $matlabroot is the MATLAB Installation directory (something like C:\Program Files\MATLAB\R2008b\)

• 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.

Linux

• 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=~/

  • 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.

Mac OS X

I don't have a Mac :-( If somebody wants to write some installation instructions and contribute them I would really appreciate.

Bug reports

Please use Qu's project page to report bugs.