XuvTools is developed in a cooperative effort from:
  • Chair of Pattern Recognition and Image Processing [www]
  • Friedrich Miescher Institute for Biomedical Research [www]
  • Center for Biological Systems Analysis [www]
 

The Team Behind XuvTools

XuvTools is a joint development of three institutes, all located around the beautiful region 'Dreiländereck', at the borders of Germany, Switzerland and France. Originally, development started in 2007 at the Chair of Pattern Recognition and Image Processing [LMB] at the University of Freiburg, based on a collaboration with the Imaging Facility (now Life Imaging Center [LIC], located at the Center for Biological Systems Analysis [ZBSA]) of the Department of Biology of that same University. To stem the heavy work of incorporating a user-friendly interface, provide documentation and continued support, the Friedrich Miescher Institute [FMI] in Basel joined in 2008. It has since contributed not only the GUI, but sponsored development and provided countless hours of testing and feedback from real-life biologists that use XuvTools on a daily basis.

Many people helped creating this software: The core development of XuvTools has been done by Mario Emmenlauer (website) based on ideas and code from Olaf Ronneberger (website). The user interface is developed by Aaron Ponti (website) and Mario Emmenlauer. The bleaching correction has been largely rewritten by Benjamin Ummenhofer (website) based on original ideas from Mario Emmenlauer. Countless hours of testing went into XuvTools, most notably by Patrick Schwarb (website), Aaron Ponti, and the biologists of FMI Basel. XuvTools releases are compiled and packaged by Niko Ehrenfeuchter (website). This website and major parts of the documentation, presentations and video tutorials have been created by Mario Emmenlauer with the help of Niko Ehrenfeuchter. XuvTools makes use of a set of libraries that have been developed at the LMB Freiburg by various people, notably by Olaf Ronneberger, Mario Emmenlauer, Janis Fehr, Thorsten Schmidt, Alexandra Teynor and many more.

The following Institutes dedicate (or have dedicated) resources for XuvTools development:

Institutes

Chair of Pattern Recognition and Image Processing
Institute for Computer Science
Albert-Ludwigs-University
Georges-Koehler-Allee 052, room 01-030
D-79110 Freiburg i.Br.

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
CH-4058 Basel
Switzerland

ZBSA (Center for Biological Systems Analysis)
Life Imaging Center
Albert-Ludwigs-University
Habsburgerstr. 49
D-79104 Freiburg i.Br.

Support or Join

We are currently looking for skilled programmers as well as for testers. If you have used the software, you can help us. Contact to development is easiest through email, use mario(a)xuvtools.org (replace (a) with the at-sign).

Programmers wanted

We are looking for more skilled programmers to extend our team. Most positions are voluntary, but we have one limited-time funded position available too! If you meet one or more of the following qualifications then you are very welcome to the team!

  • have experience with C or C++
    • (C is sufficient to participate in our image reader/writer project)
    • (Standard-compliant C++ with templates is required for core algorithms)
  • have an idea about GPU computation with CUDA or other toolkit
  • know Visual Studio, GNU gcc or Mac gcc and/or Eclipse
  • have an interest in huge biological data, high performance computing and/or image processing
  • have a basic understanding of image correlation

Acknowledgements

XuvTools uses the following great open source thirdparty libraries for various functionality:

Qt - A cross-platform application and UI framework

Qt is a cross-platform application development framework, widely used for the development of GUI programs (in which case it is known as a widget toolkit), and also used for developing non-GUI programs such as console tools and servers. Qt is most notably used in KDE, Opera, Google Earth, Skype, Qt Extended, Adobe Photoshop Album, VirtualBox and OPIE. It is produced by Nokia's Qt Software division, which came into being after Nokia's acquisition of the Norwegian company Trolltech, the original producer of Qt, on June 17, 2008.
www.qtsoftware.com/

fftw - the fastest Fourier transform in the west

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. The FFTW package was developed at MIT by Matteo Frigo and Steven G. Johnson.
http://www.fftw.org/

libbioimage - A cross-platform bio image and meta-data library

libbioimage is the library behind the BioImage Convert command line image conversion utility. It can read and write many image formats, extract ROI and meta-data stored in images. Accepted image formats are: BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III, JPEG, PNG, BMP, IBW, OME, RAW and video: QuickTime, AVI, MPEG1/2/4, Flash, etc. libbioimage is developed at the Center for Bio-Image Informatics of the University of California, Santa Barbara, by Dmitry Fedorov Levit and others.
http://www.bioimage.ucsb.edu/downloads/BioImage%20Convert

Bio-Formats - Java-based bio image and meta-data library

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. The primary goal of Bio-Formats is to facilitate the exchange of microscopy data between both different software packages and different organizations. It accomplishes this goal by converting proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.
http://www.loci.wisc.edu/software/bio-formats

HDF5 - A versatile large data set library

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. It includes a versatile data model that can represent very complex data objects and a wide variety of metadata, a completely portable file format with no limit on the number or size of data objects in the collection, a software library that runs on a range of computational platforms, from laptops to massively parallel systems, and implements a high-level API with C, C++, Fortran 90, and Java interfaces, and much more. The HDF5 data model, file format, API, library, and tools are open and distributed without charge.
http://www.hdfgroup.org/

contact.txt · Last modified: 2010/09/18 21:10 by mario
Contact: admin(a)xuvtools.org