Descriptions / Features

QuickFit 3 is our open-source data evaluation software for FCS and imagingFCS (imFCS) measurement. Actually QuickFit 3 itself is a project manager and all functionality is added as plugins. A set of tested plugins is supplied together with the software. New plugins that provide additional features will be added to this distribution of QuickFit when they become available. Currently these features are supported:

  • Full source code available in parts under GPL3.0 and in parts under LGPL2.1.
  • FCS:
    • dataimport from ALV5000/6000/7000, ISS Alba files, Zeiss Confocor2/3 files, correlator.com .sin-files, PicoQuant ASCII, CSV files
    • correlation of TCSPC files from PicoQuant TimeHarp, PicoHarp, ...
    • model fit with different predefined models (normal/anomalous 1D/2D/3D diffusion, photophysics, TIRF-FCS, SPIM-FCS, DLS ...) and different fit algorithms
    • fit error estimates, using bootstrapping
    • global fitting over several files (e.g. for FCCS analysis)
    • export of fit results as report (PDF/PS), image (PDF/PS/SVG/PNG/JPEG/LaTeX...), data (CSV, SYLK, Excel, Matlab ... also direct copy/paste to Excel/Origin)
    • Maximum Entropy data evaluation for FCS/DLS
    • Extract mean squared displacements (MSD) from FCS measurements (e.g. for polymer physics)
    • calculator for diffusion coefficients of several dyes (included comprehensive database) and particles of different shapes (spheres, ellipsoids, cylinders, ...) in a given solution
  • imaging FCS (imFCS):
    • importing dataset from CSV files
    • correlating any TIFF image series
    • model fit (SPIM/TIR-FCS...)
    • global imaging FCCS fitting (SPIM/TIR-FCCS...)
    • plotting of parameter images, histograms and correlation plots (incl. several robust/normal statistics)
    • export of fit results and parameter images as report (PDF/PS), image (PDF/PS/SVG/PNG/JPEG/LaTeX...), data (CSV, SYLK, Excel, Matlab ... also direct copy/paste to Excel/Origin)
    • multi-threaded fits (~50 fits/second)
    • SPIM-FCS calibration wizard
    • number and brightness analysis
    • PSF determination
    • camera calibration
    • simple colocalization analysis
    • imFCS diffusion laws
  • Microscope Characterization Plugins:
    • PSF from z-stacks of immobilized beads
    • SPIM lightsheet characterization
    • camera calibration
    • simple colocalization analysis
  • spFRET-evaluation of TCSPC data
  • simple and consistent user-interface
  • wizards for many standard tasks (e.g. imaging FCS correlation & calibration)
  • single-particle FRET data evaluation (burst selection)
  • user-defined fit functions
  • image stack 3D volume renderer
  • spreadsheet functionality and advanced plotting in "table" plugin
  • extensive expression parser as part of QuickFit, can also be used inside the table-function for dynamically updated spreadsheets and plots!
  • publication quality plotting
  • export of data (CSV, SYLK, Excel, Matlab ... also direct copy/paste to Excel/Origin) and images (PDF/PS/SVG/PNG/JPEG/LaTeX...) of each plot in the program
  • organization of data and evaluations as a project (.qfp file in XML format, or compressed as .qfpz) to easily save an evaluation
  • online-help system with many references and explanation of the implemented methods (all formulas should be given, so you know what the program does!) and tutorials
  • convenient and customizable user interface
  • spectra viewer with comprehensive set of spectra (including some lamps, filters, detectors and many standard dyes)
  • Linux version can be built from source code
  • we now also release out SPIM hardware control plugins

Please also have a look at the QuickFit screenshots

We will also eventually distribute a SDK that allows you to write your own plugins, using the already provided means in QuickFit (data handling, reporting, project managing, online-help system, ...). If you are already interested in developing your own plugins for QuickFit, please contact Jan Krieger.

Licensing

This software is licensed in parts under the LGPL 2.1 and in parts under the GPL 3.0. In addition, we put it under an informal postcard ware "license": If you find QuickFit usefull and like it, please send us a postcard from your part of the world to


Deutsches Krebsforschungs Zentrum (DKFZ)
Abteilung B040
Im Neuenheimer Feld 580
D-69120 Heidelberg
GERMANY

If you use this software for a publication, you will have to cite QuickFit this in the publication. In the online-help we give examples of how to cite QuickFit. Also have a look at the online-help of the plugins you used to see whether you should cite additional libraries used in these plugins. Here is an example BiBTeX record that can be used to cite QuickFit (update to the version you downloaded or copy an. updated version from the Copyright page of the onine help!):

@misc{quickfit3,
    author={Jan Wolfgang Krieger and Jörg Langowski},
    title={QuickFit 3.0 (status: beta, compiled: ???, SVN: ???): A data evaluation application for biophysics},
    howpublished={[web page] erb+http://www.dkfz.de/Macromol/quickfit/+},
    year={2015},
    note={[Accessed on ???]},
}

A citation may look like this:

JW. Krieger, J. Langowski (2015): QuickFit 3.0 (status: beta, compiled: ???, SVN: ???): A data evaluation application for biophysics, [web page] http://www.dkfz.de/Macromol/quickfit/ [Accessed on ???]

This software is provided as is without any warranties. Use it at your own risk. But: We do our best to make a well tested and good pakage (as it is massively used in our department).

Mailing List

If you want to stay up to date on the development of QuickFit and receive announcements on new versions, we have a mailing list (quickfit@dkfz.de) on the topic.

If you want to subscribe, please open the link below which should send an e-mail to quickfit-request@dkfz.de with the subject "subscribe" (If the link does not work, simply write the e-mail as described yourself, or contact Jan Krieger directly). After a short delay you should receive a welcome message from the mailing list.

SUBSCRIBE to quickfit@dkfz.de

Download

Download the current version (top of the list) of QuickFit 3. The installer will include the SPIM hardware control plugins. Make sure to select this option during install, if you need those plugins:

QuickFit 3.0 (Beta, SVN: 4465, build date: 2015-10-29):

 

Installation: Download the installer for your operating system (32-bit or 64-bit), install QuickFit 3 and start using it. When updating an older installation, please make sure the old version is uninstalled before the new version is installed!

Note: These versions of QuickFit 3 are still beta versions. So error could occur. Please make sure to save your project often (maybe using the autosave option) in order to prevent masisve data loss on crashes. If an error occurs, please send an email with the description to Jan Krieger. You may also send suggestions, wishes, feature requests ... Also testing data is welcome!


The source code of QuickFit 3 and build instructions are now available on GitHub.

Example Data

A large set of different example data sets (especially for imagingFCS/FCCS) is availble on GitHub.

QuickFit 3 source code

The source code of QuickFit 3 and build instructions are now available on GitHub.

SPIM Hardware Control Plugins

These plugins are included in the main installer, so download above and activate the SPIM plugins option during install!

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