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PYCORRFIT(1) PyCorrFit PYCORRFIT(1)

NAME

PyCorrFit - PyCorrFit Documentation [image]





Welcome to the documentation of PyCorrFit (version 1.3.1+nopack),
    a data analysis software for fluorescence correlation spectroscopy
  (FCS).






ABOUT PYCORRFIT


In current biomedical research, fluorescence correlation
    spectroscopy (FCS) is applied to characterize molecular dynamic processes in
    vitro and in living cells. Commercial FCS setups only permit data analysis
    that is limited to a specific instrument by the use of in-house file formats
    or a finite number of implemented correlation model functions. PyCorrFit is
    a general-purpose FCS evaluation software that, amongst other formats,
    supports the established Zeiss ConfoCor3 ~.fcs file format. PyCorrFit comes
    with several built-in model functions, covering a wide range of applications
    in standard confocal FCS. In addition, it contains equations dealing with
    different excitation geometries like total internal reflection (TIR).




Supported operating systems




    
  
  • Windows 7 and higher
    • 
  
  • Linux (Debian-based)
    • 
  
  • Any other operating system with a Python 3.6 installation (via pip)
    • 











Supported filetypes




    
  
  • ALV correlators (~.ASC)
    • 
  
  • Correlator.com (Flex) correlators (~.SIN)
    • 
  
  • Zeiss ConfoCor3 (~.fcs)
    • 
  
  • PicoQuant (~.pt3) as implemented by Dominic Waithe
      (<https://github.com/dwaithe/FCS_point_correlator>)
    • 
  
  • PyCorrFit (~.csv)
    • 
  
  • PyCorrFit session (~.pcfs)
    • 











Fitting




    
  
  • Pre-defined model functions (confocal FCS, TIR-FCS, triplet blinking,
      multiple components)
    • 
  
  • Import of user-defined model functions
    • 
  
  • Global fitting across multiple model functions or data sets
    • 
  
  • Least squares fit using Levenberg-Marquard, Simplex, and more
    • 
  
  • Weighted fitting with standard deviation
    • 











Tools and Features




    
  
  • Averaging of curves
    • 
  
  • Background correction
    • 
  
  • Batch processing
    • 
  
  • Overlay tool to identify outliers
    • 
  
  • Fast simulation of model parameter behavior
    • 
  
  • Session management
    • 
  
  • High quality plot export using LaTeX (bitmap or vector graphics)
    • 











How to cite


Müller, P., Schwille, P., and Weidemann, T. PyCorrFit -
    generic data evaluation for fluorescence correlation spectroscopy.
    Bioinformatics 30(17):2532-2533 (2014). doi:10.1093/bioinformatics/btu328
    <http://dx.doi.org/10.1093/bioinformatics/btu328>








GALLERY


[image]
  

   <_images/Screenshot_Trace_view.png>[image]
  

   <_images/Screenshot_Select_curves.png>[image]
  

   <_images/Screenshot_Main.png>[image]
  

   <_images/Screenshot_Graphics_output.png>[image]
  

   <_images/Screenshot_Desktop_Win.png>[image]
  

   <_images/Screenshot_Desktop_Raspbian_Jessie.png>[image]
  

   <_images/Screenshot_Desktop_Mac.png>[image]
  

   <_images/Screenshot_Desktop.png>.SH GETTING STARTED




Installation




    
  
  • Windows installers for PyCorrFit are available at the release page
      <https://github.com/FCS-analysis/PyCorrFit/releases>.
    • 
  
  • On Debian-based systems, install via apt-get install
    pycorrfit.
    • 
  
  • If you have Python 3.6 installed, you may install PyCorrFit via pip
      install pycorrfit[GUI]. After the installation, type pycorrfit
      in a command shell to start PyCorrFit.
    • 











Documentation


The documentation is in the process of being transferred entirely
    to readthedocs.org. Currently, it is scattered across several places and it
    is most-likely outdated:















CONTRIBUTE




General remarks


PyCorrFit has no funding and a vanishingly small developer
    community. My personal objective is to keep PyCorrFit operational on Linux
    and Windows which is currently limited by the free time I have
  available.


An active community is very important for an open source project
    such as PyCorrFit. You can help this community grow (and thus help improve
    PyCorrFit) in numerous ways:





  
1.

  
Tell your colleagues and peers about PyCorrFit. One of them might be able
      to contribute to the project.

  
2.

  
If you need a new feature in PyCorrFit, publicly announce a bounty for its
      implementation.

  
3.

  
If your research heavily relies on FCS, please consider diverting some of
      your resources to the development of PyCorrFit.

  
4.

  
You don't have to be a Python programmer to contribute. If you are
      familiar with reStrucuredText or LaTeX, you might be able to help out with
      the online documentation.

  
5.

  
Please cite: Müller et al. Bioinformatics 30(17): 2532–2533,
      2014, DOI:10.1093/bioinformatics/btu328
      <https://dx.doi.org/10.1093/bioinformatics/btu328>

  
6.

  
Sponsor me on GitHub <https://github.com/sponsors/paulmueller> or
      donate via Liberapay <https://liberapay.com/paulmueller>.








If you are planning to contribute to PyCorrFit, please contact me
    via the PyCorrFit issue page on GitHub such that we may coordinate a pull
    request.






For documentation writers


To build this documentation, fork PyCorrFit, navigate to the
    docs (not doc) directory and run.




    
  
  • pip install -r requirements.txt followed by
    • 
  
  • sphinx-build . _build.
    • 







This will create the html documentation on your computer. Syntax
    warnings and errors will be displayed during the build (there should be
    none). After making your changes to your forked branch, create a pull
    request on GitHub.


If you only found a typo or wish to make text-only changes, you
    can also use the GitHub interface to edit the files (without testing the
    build step on your computer).






For developers






Running from source


It is recommended to work with virtual environments
    <https://docs.python.org/3/tutorial/venv.html>.






Windows


The easiest way to run PyCorrFit from source on Windows is
    Anaconda <http://continuum.io/downloads>.




    
  
  • conda install matplotlib numpy pip scipy wxpython
    • 
  
  • pip install cython wheel simplejson sympy lmfit
    • 
  
  • pip install -e . # in the root directory of the repository
    • 











Ubuntu Linux


PyCorrFit requires wxPython >= 4.0.1 which is not available as
    a binary wheel on PyPI. However, the wxPython people have wheels specific to
    certain Ubuntu versions
  (<https://www.wxpython.org/pages/downloads/>):













Testing


PyCorrFit is tested using pytest. If you have the time, please
    write test methods for your code and put them in the tests directory.
    You may run all tests by issuing:








pip install -r tests/requirements
pytest tests















Pull request guidelines


Please fork PyCorrFit and create a pull request (PR) introducing
    your changes.















CHANGELOG


List of changes in-between PyCorrFit releases.




version 1.3.1









  
•

  
maintenance release




















version 1.3.0

























version 1.2.1









  
•

  
fix: compatibility with newer versions of scipy (#211
      <https://github.com/FCS-analysis/PyCorrFit/issues/211>)




















version 1.2.0








    
  
  • enh: add support for PicoQuant cor file format
    • 
  
  • ref: code cleanup
    • 
  
  • setup: modernize build pipeline
    • 
  
  • tests: remove deprecated pytest-runner
    • 
  
  • setup: require Python 3.10
    • 



















version 1.1.8









  
•

  
docs: fix typo in legacy PDF (#195
      <https://github.com/FCS-analysis/PyCorrFit/issues/195>)




















version 1.1.7








    
  
  • docs: add sponsor links to contribute section
    • 
  
  • docs: add gallery with all images in docs/gallery
    • 



















version 1.1.6








    
  
  • fix: improve support for Confocor FCS file format (see discussion in
    #37)
    • 
  
  • ref: make pathlib.Path a standard in readfiles
    • 
  
  • code cleanup
    • 
  
  • drop support for Python<3.6
    • 



















version 1.1.5









  
•

  
docs: fix build with recent version of latex (#191
      <https://github.com/FCS-analysis/PyCorrFit/issues/191>)




















version 1.1.4









  
•

  
maintenance release




















version 1.1.3









  
•

  
maintenance release




















version 1.1.2








    
  
  • ci: Automated release to PyPI with appveyor and travis-ci
    • 
  
  • fix: support lmfit >= 0.9.11
    • 



















version 1.1.1

























version 1.1.0











    
  
  • Add option in Preferences to automatically close tools after usage
    • 
  
  • Add keyboard shortcuts (thanks @toubol)
    • 
























version 1.0.1











    
  
  • Fetch latest available version from GitHub releases
    • 
  
  • New dependency for "simplejson" Python package
    • 
  
  • Move appveyor recipe to separate folder
    • 























version 1.0.0

























version 0.9.9

























version 0.9.8









  
•

  
Bugfixes:



























version 0.9.7








    
  
  • Second triplet time is now larger than first triplet time by default
    • 
  
  • Remove a hack that causes a run through all pages e.g. when an average is
      created
    • 
  
  • Bugfixes:
    • 





    
  
  • Opening sessions with user-defined models
    • 
  
  • Saving sessions with comments containing non-ASCII characters
    • 
  
  • Windows build: Graphical plot export was misconfigured (added matplotlibrc
      patch in .spec file)
    • 























version 0.9.6









  
•

  
Bugfixes:






    
  
  • Fixed minor wx sizer problems for the tools
    • 
  
  • Fixed 'AttributeError' in page.py if no weights are present
    • 








  
•

  
New confocal fitting models (#111
      <https://github.com/FCS-analysis/PyCorrFit/issues/111>):






    
  
  • 3D+3D, 2D+2D, 3D+2D; no triplet
    • 
  
  • T+T+2D+2D, T+T+3D+2D; double triplet
    • 
  
  • T+3D+3D+3D, T+3D+3D+2D (#40, #59)
    • 








  
•

  
Under the hood:






    
  
  • Separation of core and GUI modules
    • 
  
  • Include tests in distributions for PyPI
    • 
  
  • Improve automated testing on Windows and Mac OS
    • 
  
  • More constraint options for fitting
    • 























version 0.9.5









  
•

  
Bugfixes



























version 0.9.4
































version 0.9.3









  
•

  
Fitting: migrate to lmfit






    
  
  • This introduces a new dependency for building PyCorrFit. (e.g. in Debian,
      the package "python-lmfit" is required)
    • 
  
  • Improved fitting behavior at parameter boundaries
    • 
  
  • Removed "Polak-Ribiere" fitting algorithm
    • 
  
  • Added "Sequential Linear Squares Programming" algorithm
    • 








  
•

  
Heuristic fit (#109
      <https://github.com/FCS-analysis/PyCorrFit/issues/109>):






    
  
  • Detect parameters that are stuck during fitting
    • 
  
  • Fit each curve five times or less and check whether the fit
    converges.
    • 
  
  • If two diffusion time parameter exist in a model, always make sure that
      one parameter is the larger one. This feature can currently not be
      disabled (#110
      <https://github.com/FCS-analysis/PyCorrFit/issues/110>).
    • 







    
  
  • Allow infinity ("inf" and "-inf") parameters for
      models and boundaries.
    • 
  
  • New model: confocal T+T+3D+3D
    • 
  
  • Bugfixes:
    • 


























version 0.9.2









  
•

  
Bugfixes:











    
  
  • Update .pt3 reader to version 8399ff7401
    • 
  
  • Import traces of .pt3 files (experimental, #118) Warning: Absolute values
      for intensity might be wrong
    • 



















version 0.9.1
































version 0.9.0

























version 0.8.9

















  
•

  
Under the hood:






    
  
  • Introduce new classes: Correlation, Fit, Trace
    • 
  
  • Code cleanup and rewrite to support planned features
    • 
  
  • In some cases support older versions of NumPy
    • 























version 0.8.8








    
  
  • Improved support for "ALV-7004" files
    • 
  
  • If you install the GUI with pip, you now need to include the 'GUI'
      requirement: 'pip install pycorrfit[GUI]'. The GUI depends on matplotlib
      and wxPython which is not required for scripting with the pycorrfit
      module.
    • 
  
  • Bugfix: missing version string on SuSe linux (#101
      <https://github.com/FCS-analysis/PyCorrFit/issues/101>)
    • 
  
  • Under the hood:
    • 





    
  
  • Python entry point script replaces "bin/" script
    • 
  
  • Windows build system hosted by appveyor.com
    • 
  
  • MacOS X build system hosted by travis-ci.org
    • 
  
  • New builds use wxPython3 (#85
      <https://github.com/FCS-analysis/PyCorrFit/issues/85>)
    • 
  
  • Unicode support without 'reload(sys)'
    • 
  
  • Error messages are more verbose
    • 























version 0.8.7








    
  
  • Removed unused fitting parameter d_eva from model 6022 and secured
      backwards compatibility.
    • 
  
  • Improved support for ALV700X (#92
      <https://github.com/FCS-analysis/PyCorrFit/issues/92>)
    • 
  
  • Bugfix: Corrected false display of Unicode characters on Windows
    • 
  
  • Under the hood:
    • 


























version 0.8.6

























version 0.8.5











    
  
  • Pythonic repository structure
    • 
  
  • Relative imports
    • 
  
  • Windows build machine is now Windows 7
    • 
  
  • Removed strict dependency on matplotlib
    • 























version 0.8.4








    
  
  • Support for PicoQuant data file format Many thanks to Dominic Waithe
      (@dwaithe)
    • 
  
  • Improved compatibility with Zeiss .fcs file format
    • 
  
  • PyCorrFit is now dependent on Cython
    • 
  
  • The module 'openfile' is now available from within Python
    • 
  
  • Installer for Windows
    • 



















version 0.8.3











    
  
  • Massive speed-up when working with large data sets (#77
      <https://github.com/FCS-analysis/PyCorrFit/issues/77>)
    • 
  
  • Plot export: legend position and displayed parameters (#54
      <https://github.com/FCS-analysis/PyCorrFit/issues/54>)
    • 
  
  • Average tool: traces may now start at time points != 0
    • 
  
  • Statistics tool: display on smaller screens
    • 
  
  • ALV data files: updated parser to identify curve types and segment
    traces
    • 
  
  • Zeiss ConfoCor3 data files: some files could not be opened due to dummy AC
      curves
    • 
  
  • Models: default parameters were changed to prevent unstable fits
    • 
  
  • Software: notification dialogs for missing modules or other software
    • 








  
•

  
Bugfixes



























version 0.8.2








    
  
  • The documentation has been thoroughly reworked
    • 
  
  • The user is now warned if he does not have a TeX distribution
    installed
    • 
  
  • Improvements:
    • 











  
•

  
Bugfix: TeX did not work on Ubuntu due to missing imports




















version 0.8.1








    
  
  • Thanks to Alex Mestiashvili for providing initial setup.py files and for
      debianizing PyCorrFit (@mestia)
    • 
  
  • Thanks to Thomas Weidemann for his contributions to the documentation
      (@weidemann)
    • 
  
  • Bugfixes
    • 











  
•

  
Improvements of the user interface



























version 0.8.0

























version 0.7.9








    
  
  • Support for Mac OSx
    • 
  
  • Enhancements:
    • 





    
  
  • Export file format (.csv) layout improved
    • 
  
  • Model function info text in UTF-8
    • 
  
  • Improved waring message when opening sessions from future versions
    • 
  
  • New feature lets user set the range for the fitting parameters
    • 








  
•

  
Bugfixes:






    
  
  • Cleaned minor tracebacks and exceptions created by the frontend
    • 
  
  • Mac version now works as expected, but .app bundling failed
    • 
  
  • Latex plotting features now support more characters such as
      "[]{}^"
    • 























version 0.7.8









  
•

  
Enhancements:






    
  
  • Averages can now be calculated from user-selected pages
    • 
  
  • Pages selected in the Overlay tool are now automatically set for
      computation of average and for global fitting
    • 
  
  • Source pages are now displayed in average title
    • 
  
  • Graph normalization with particle numbers is now possible
    • 








  
•

  
Bugfixes:






    
  
  • Errors during fitting with weights equal to zero
    • 
  
  • Overlay tool displayed last curve after all pages have been removed
    • 
  
  • Global fit did not work with weights
    • 







    
  
  • Session saving now uses 20 digits accuracy
    • 
  
  • CSV export is now using tab-delimited data for easier Excel-import
    • 
  
  • Added version checking for session management
    • 



















version 0.7.7








    
  
  • Fixed: Tools windows could not be closed (or moved on MS Windows)
    • 
  
  • Fixed: .csv export failed in some cases where no weights were used
    • 
  
  • Enhancement: The user is now asked before a page is closed
    • 
  
  • Enhancement: Tool "Page Info" and in exported .csv files,
      variables and values are now separated by a tab stop instead of a
      "="
    • 
  
  • Fixed: Opening a session with an empty page failed in some cases
    • 
  
  • Fixed: Tool "Statistics" missed to output the column
      "filename/title" if that key value is empty - replaced empty
      strings with "NoName"
    • 
  
  • Enhancement: Tool "Overlay" now asks the user to check kept
      curves instead of showing the curves to be removed
    • 
  
  • Enhancement: Tool "Overlay" now has a "Cancel"
    button
    • 



















version 0.7.6









  
•

  
Improved handling












  
•

  
Improved tool "Statistics" (#21
      <https://github.com/FCS-analysis/PyCorrFit/issues/21>)






    
  
  • Fixed the case where "useless" data was produced - instead we
      write "NaN" data, removed warning message accordingly
    • 
  
  • Row-wise ordering according to page numbers (#22
      <https://github.com/FCS-analysis/PyCorrFit/issues/22>)
    • 
  
  • Column-wise ordering is now more intuitive (Fitted parameters with errors
      first)
    • 
  
  • Some columns are now checked by default
    • 
  
  • PyCorrFit remembers checked parameters for a page (not saved in
    session)
    • 








  
•

  
Improved tool "Overlay" (#23
      <https://github.com/FCS-analysis/PyCorrFit/issues/23>)






    
  
  • New feature: Overlay shows run number of each file (upon import), the run
      (or index) of an experimental file is unique to PyCorrFit
    • 
  
  • Upon import, filenames and runs are displayed
    • 
  
  • In a session, the filename/title is displayed
    • 







    
  
  • Web address of PyCorrFit changed from
      "fcstools.dyndns.org/pycorrfit" to
      "pycorrfit.craban.de"
    • 
  
  • Minor bugfixes: Batch control, Global fitting, import dialog
    • 



















version 0.7.5








    
  
  • Added model functions to documentation.
    • 
  
  • Weights from fitting are now exported in .csv files.
    • 
  
  • Rework of info panel for fitting
    • 
  
  • Cleared unintuitive behavior of session saving: The fitting parameters
      were read from the frontend. This could have led to saving false fit meta
      data.
    • 
  
  • During fitting, units are now displayed as "human readable" (#17
      <https://github.com/FCS-analysis/PyCorrFit/issues/17>).
    • 
  
  • Slider simulation now also uses human readable units (#17
      <https://github.com/FCS-analysis/PyCorrFit/issues/17>).
    • 
  
  • Secured support for Ubuntu 12.10 and 13.04
    • 
  
  • Fixed: new line (n) characters for LaTeX plotting on Windows
    • 



















version 0.7.4








    
  
  • New tool: Colorful curve selection
    • 
  
  • Import data: Curve selection possible
    • 
  
  • Average: Crop average according to current page.
    • 
  
  • Fixed: Page now displays Chi-squared of global fit.
    • 
  
  • Fixed: Chi-squared and parameters of global fitting are now stored in
      sessions.
    • 



















version 0.7.3

























version 0.7.2








    
  
  • Bugfix: Issue #10; we now have a goodness of the fit, if weighted fitting
      is performed
    • 
  
  • Bugfix: Weights for fitting not properly calculated (sqrt(std)).
    • 
  
  • Bugfix: Batch control IndexError with Info window opened
    • 
  
  • Tool Statistics: Sort values according to page numbers
    • 
  
  • Tool global: Added weighted fitting
    • 
  
  • Residuals: According to weighted fitting, weighted residuals are
    plotted
    • 
  
  • Average: Variances from averaging can be used for weighted fitting
    • 



















version 0.7.1








    
  
  • Feature: Added Python shell
    • 
  
  • Bugfix: Saving image was not performed using WXAgg
    • 
  
  • Bugfix: Notebook pages were drag'n'dropable
    • 
  
  • Update function now works in its own thread
    • 
  
  • Code cleanup: documentation of model functions
    • 
  
  • Added program icon
    • 



















version 0.7.0









  
•

  
File import dialog was enhanced (#4, #5 - subsequently #7, #8):






    
  
  • Now there is only one "load data" dialog in the file menu
    • 
  
  • The model function is chosen for each type of data that is to be imported
      (AC, CC, etc.)
    • 
























version 0.6.9









  
•

  
Initital GitHub commit


















    
  
  • Index <>
    • 
  
  • Module Index <>
    • 
  
  • Search Page <>
    • 













Author


Paul Müller






Copyright


2014, Paul Müller







  

    April 30, 2026