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software [2018/09/11 09:46] adminsoftware [2023/11/15 14:22] (current) admin
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 {{tag> software acquisition analysis}} {{tag> software acquisition analysis}}
  
-~~TOC~~ +~~TOC~~ 
 ====== Software ====== ====== Software ======
  
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 ==== Data Analysis ==== ==== Data Analysis ====
  
 +  
 +=== Complete packages ===
  
-  +  * **snAPI**  is a powerful Python wrapper which enables seamless communication and configuration with PicoQuant Time Correlated Single Photon Counting Instruments (TCSPC devices). It harnesses the advantages of C++ for optimal speed and performance and bridges the gap between the high-speed capabilities of your PicoQuant TCSPC device and the ease of use and versatility of Python. [[https://github.com/PicoQuant/snAPI]] 
-  * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-DemosDemo Code for reading PicoQuants PTU File format]]+  * **FLUTE** is a Python GUI for interactive phasor analysis of Fluorescence Lifetime Microscopy (FLIM) data [[https://github.com/LaboratoryOpticsBiosciences/FLUTE]]. 
 +  * **PAM** is a software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with a focus on experiments using pulsed interleaved excitation.[[http://pam.readthedocs.io|]] 
 +  * [[https://www.mpc.hhu.de/software/3-software-package-for-mfd-fcs-and-mfis|Software Package for Multiparameter Fluorescence Spectroscopy and Imaging by research group Seidel, HHU]]: A collection of independent sotftware packages which enable the user to perfrom the analysis workflow put forward by the group.Please note that a trial version is available. 
 +  * **[[https://github.com/OpenSMFS|Open Tools for Solution-Based Single-Molecule Fluorescence Spectroscopy]]** 
 +    * **FRETBursts**: software for burst analysis of freely-diffusing single-molecule FRET (smFRET) measurements including μs-ALEX.  [[http://tritemio.github.io/FRETBursts/|FRETBursts Homepage]] and [[http://dx.doi.org/10.1101/039198|paper]].  
 +    *  **PyBroMo** [[https://github.com/tritemio/PyBroMo|simulator for single molecule FRET experiments of freely diffusing particles.]]    
 +    * [[https://www.researchgate.net/project/Open-Computational-Tools-for-Single-Molecule-Spectroscopy|Researchgate group Open Computational Tools for Single-Molecule Spectroscopy]] 
 +   
 +  * [[software: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).
  
-  * [[https://github.com/qpl-public/readPTU|A Python library to read PTU files]] \\ From the authors: "The main purpose of the library is to compute g<sup>2</sup> from the photon arrival times as fast as possible, as our files often go into multi GB sizes. With a good SSD we can parse >3GB/sIt can also compute intensity time traces and post select photons based on that."+  *[[https://github.com/khemmen/katcorr/|Katherinas correlator]] is a collection of scripts and correlators that are inspired by the paper Ries...Schwille 2010 Optics Express "Automated suppression of sample-related artifacts in FCS"
 +These scripts have different scopes and use the library [[https://github.com/Fluorescence-Tools/tttrlib|tttrlib]] to read and correlate time-tagged time resolved (TTTR) files.
  
-  * [[https://github.com/QuantumPhotonicsLab/readPTU]] Probably same as above+  *  [[http://flim-analyzer.ip-korea.org/|FLIM-FRET analyzer]]: open source software for automation of lifetime-based FRET analysis. This is a Microsoft Windows application originally developed in C#. The main goal of this application is to provide the FLIM community a user-friendly application.
  
-  * [[https://github.com/trevhull/ptuT3toT2|ptuT3toT2 a program that converts ptu files from picoquant from T3 mode to T2 mode]]+/* * [[https://www.tu-ilmenau.de/bmti/forschung/ophthalmologische-technik/flimx/|FLIMX]]:A Software Package to */ /*Determine and Analyze the Fluorescence Lifetime in Time-Resolved Fluorescence Data from the Human Eye*/
  
-  * [[https://timetag.github.io|Extensible Time-tag Analyzer]] +  * [[http://www.fluortools.com/software|Fluortools]].Fluorescence Decay and Anisotropy Analysis.
- +
-  * [[https://github.com/hammer-wang/exciton_diffusion|exciton diffusion (Matlab)]]+
    
- / * [[https://github.com/PicoQuant/Notebooks]] Jupyter Notebooks reading the tiff files exported by SymPhoTime */ 
  
-  * [[https://de.mathworks.com/matlabcentral/fileexchange/61789-ptu-to-matlab-converter?focused=7307670&tab=function|Reading PicoQuants PTU File formats to MatLab 100x faster than the Demo Code]]+  * [[http://pycorrelate.readthedocs.io/en/latest| PyCorrelate]]:Pycorrelate computes fast and accurate cross-correlation over arbitrary time lags. Cross-correlations can be calculated on “uniformly-sampled” signals or on “point-processes”, such as photon timestamps. Pycorrelate allows computing cross-correlation at log-spaced lags covering several orders of magnitude. This type of cross-correlation is commonly used in physics or biophysics for techniques such as fluorescence correlation spectroscopy (FCS) or dynamic light scattering (DLS).
  
-  *  [[https://www.researchgate.net/project/Open-Computational-Tools-for-Single-Molecule-Spectroscopy|Researchgate group Open Computational Tools for Single-Molecule Spectroscopy]]+  *  [[http://www.dkfz.de/Macromol/quickfit|QuickFit 3.0]]: 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. 
  
-  * PAM is a software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with a focus on experiments using pulsed interleaved excitation.[[http://pam.readthedocs.io|]] 
  
-  ImageJ Import Filter for pt3 files: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:picoquant_.pt3_image_reader:start]]+/* * [[software:FCS viewer]] ..This became redundant as its developer released Pycorrfit*/
  
-  * ImageJ import of ptu/pt3 image files (+intensity/average lifetime stacks): [[https://github.com/ekatrukha/PTU_Reader]]+  * [[https://github.com/dwaithe/FCS_point_correlator| FCS Point Correlator]] FCS Bulk Correlation Software accepting pt3 and ptu files. for fitting see https://dwaithe.github.io/FCSfitJS/ 
 +[[https://dwaithe.github.io/FCSfitJS/| FCS fit JS]]
  
-  * **DecayFit - Fluorescence Decay Analysis** [[http://www.fluortools.com/software/decayfit]] +  * [[software:FLIMFit]]. FLIMfit is an open source package for rapid analysis of large FLIM datasets
-  * **AniFit - Anisotropy Decay Analysis** [[http://www.fluortools.com/software/anifit]]+
      
-  * [[software:PyCorrFit]]+  * [[https://github.com/zhengkaiyu/FIMAS]] Fluorescent Imaging Analysis Software
  
-  * [[http://pycorrelate.readthedocs.io/en/latest/PyCorrelate]] +  * [[https://timetag.github.io|Extensible Time-tag Analyzer]]. ETA, the extensible time tag analyzer, is an event driven programming language with graphical user interface for analyzing, plotting, and fitting of time tagged data.[[https://eta.readthedocs.io/en/latest/intro.html|More info.]]
  
-  * QuickFit 3.0: http://www.dkfz.de/Macromol/quickfit/+  * [[https://pals3d.readthedocs.io/en/latest/|Pals3D]] is a graphical application to support the use of a Time-Correlated Single Photon Counting system for application to Positron Annihilation Lifetime Spectroscopy. [[https://github.com/avancra/Pals3D]]. 
  
 +  * [[https://github.com/SarthakJariwala/Python_GUI_apps]] Graphical User Interface (GUI) Python apps written in python using qt and pyqtgrpah for quick analysis of scientific data. It also includes the ability to convert data to H5 if needed.
  
-  * [[software:FCS viewer]]+  * [[https://lifefit.readthedocs.io/en/latest/]] LifeFit is a Python package to analyze time-correlated single-photon counting (TCSPC) data sets, namely fluorescence lifetime and time-resolve anisotropy decays. 
 +  * [[https://github.com/ryoheiyasuda/FLIMage_public]] FLIMage allows for controlling TCSPC hardware and generate fluorescence lifetime images in real time. The main part of the source code is free for academic and educational uses. It is used and tested in the Yasuda lab (Max Planck Florida Institute for Neuroscience) on Windows 10 and NationalInstruments DAQmx 18.6. The software is updated frequently.
  
-  * FCS Bulk Correlation Software accepting pt3 and ptu files \\  [[https://github.com/dwaithe/FCS_point_correlatorFCS Point Correlator]]+=== Libraries/scripts/readers === 
 +  [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-DemosDemo Code for reading PicoQuants PTU File format]]
  
-  * [[software:FLIMFit]] +  * [[https://github.com/Brinkslab/ptu_flim_tools/]] Tools for reading, converting and analysing ptu flim data. 
 + 
 +  * [[https://github.com/ChrisHal/PTU2BIN]] Tool to convert PicoQuant PTU filesto BIN files or IgorPro binary wave files (IBW) 
 + 
 +  *  [[https://de.mathworks.com/matlabcentral/fileexchange/61789-ptu-to-matlab-converter?focused=7307670&tab=function|Reading PicoQuants PTU File formats to MatLab - 100x faster than the Demo Code]] 
 +  *  **libpicoquant:**  Tools for reading PicoQuant file formats: [[https://github.com/tsbischof/libpicoquant]] 
 + 
 + 
 +  * **Open Microscopy's BioFormat** supports PicoQuant bin files ([[glossary:pre-histogrammed_image|pre-histogrammed Image Data File]]) [[https://www.openmicroscopy.org/site/support/bio-formats5/formats/picoquant-bin.html]] 
 +   
 +  * **ImageJ data readers**- 
 +      * Import Filter for pt3 files: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:picoquant_.pt3_image_reader:start]] 
 +      * Import of ptu/pt3 image files (+intensity/average lifetime stacks): [[https://github.com/ekatrukha/PTU_Reader]] 
 + 
 + 
 +  * [[https://github.com/QuantumPhotonicsLab/readPTU]] readPTU: a Python Library to Analyse Time Tagged Time Resolved Data [[http://qpl.eps.hw.ac.uk/]], [[https://arxiv.org/pdf/1903.07112.pdf]] 
 + 
 + 
 + 
 +  * [[https://github.com/trevhull/ptuT3toT2|ptuT3toT2 - a program that converts ptu files from picoquant from T3 mode to T2 mode]]
      
   * **Photon-Tools** Python utilities for working with photon timestamp data from fluorescence spectroscopy experiments [[https://github.com/bgamari/photon-tools]]   * **Photon-Tools** Python utilities for working with photon timestamp data from fluorescence spectroscopy experiments [[https://github.com/bgamari/photon-tools]]
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-  * **libpicoquant:**  Tools for reading PicoQuant file formats: [[https://github.com/tsbischof/libpicoquant]] 
  
- 
-  * **Open Microscopy's BioFormat** supports PicoQuant bin files ([[glossary:pre-histogrammed_image|pre-histogrammed Image Data File]]) [[https://www.openmicroscopy.org/site/support/bio-formats5/formats/picoquant-bin.html]] 
  
  
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-  * **FRETBursts**: software for burst analysis of freely-diffusing single-molecule FRET (smFRET) measurements including μs-ALEX.  [[http://tritemio.github.io/FRETBursts/|FRETBursts Homepage]] and [[http://dx.doi.org/10.1101/039198|paper]]. Have a look also at the **PyBroMo** [[https://github.com/tritemio/PyBroMo|simulator for single molecule FRET experiments of freely diffusing particles.]]   +  * [[https://github.com/hammer-wang/exciton_diffusion|exciton diffusion (Matlab)]] 
 +  
 + /*  * [[https://github.com/PicoQuant/Notebooks]] Jupyter Notebooks reading the tiff files exported by SymPhoTime */ 
 + 
 + 
 +  
 + 
 + 
 + 
          
     *  **FoCuS-point**: FoCuS-point utilises advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualisation.   [[https://github.com/dwaithe/FCS_point_correlator | FoCuS Homepage]] and  [[http://dx.doi.org/10.1093/bioinformatics/btv687 | paper ]]      *  **FoCuS-point**: FoCuS-point utilises advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualisation.   [[https://github.com/dwaithe/FCS_point_correlator | FoCuS Homepage]] and  [[http://dx.doi.org/10.1093/bioinformatics/btv687 | paper ]] 
  
     * [[https://github.com/skyjur/picoharp300-curvefit-ui|TCSPC curve fitting for phd files (Python)]]      * [[https://github.com/skyjur/picoharp300-curvefit-ui|TCSPC curve fitting for phd files (Python)]] 
 +
 +    * [[ https://github.com/SumeetRohilla/readPTU_FLIM | readPTU_FLIM]] Library for reading PTU files (works for MultiHarp, HydraHarp, PicoHarp, TimeHarp acquisition) as well as converting raw TTTR data to FLIM image data stack.
 +
 +    * [[https://github.com/RobertMolenaar-UT/PicoQuant-multi_channel_screen]] The main purpose of the MultiChannel script is one can proccess multiple PTU files or a folder with PTU files and get a series Fluorescent multicolor images with minimal user input. Usefull for screening results during imaging and to be used in presentations.
 +
 +    * [[https://github.com/Fluorescence-Tools/tttrlib| tttrlib]] tttrlib is a low level, high performance API to read and process time-tagged-time resolved (TTTR) data
 +    
 +    * [[https://github.com/GCBallesteros/trattoria| Trattoria]]  Trattoria delivers you the fastest streaming algorithms to analyze your TTTR data
 +
 +    * [[https://picoquantio.readthedocs.io/en/latest/| picoquantio]] is a Python library for reading file formats generated by PicoQuant hardware.
 +
 +
 ==== Data Acquisition ==== ==== Data Acquisition ====
 +  * **snAPI**  is a powerful Python wrapper which enables seamless communication and configuration with PicoQuant Time Correlated Single Photon Counting Instruments (TCSPC devices). It harnesses the advantages of C++ for optimal speed and performance and bridges the gap between the high-speed capabilities of your PicoQuant TCSPC device and the ease of use and versatility of Python. [[https://github.com/PicoQuant/snAPI]]
 +
 +  * **qudi**: A modular laboratory experiment management suite which supports PicoHarp300. [[https://github.com/Ulm-IQO/qudi]]
 +  * **pyPL**: wxpython integration of software and hardware for micro-photoluminescence measurements: WinSpec, PicoHarp, and Thorlabs/APT piezos and stepper motors. \\  https://github.com/kaseyrussell/pyPL
 +  * PicoHarp Multiscan with Prior Stage: [[https://bitbucket.org/ywsong2/uky_ptu_convert]] 
 +  * **Python** interface to communicate with TimeHarp 260: [[https://github.com/impact27/th260]]
 +  * LabView based **Fluorescence lifetime activated droplet sorting** software[[https://github.com/SadatHasan/EasyFlux]]
 +  * [[https://github.com/scopefoundry/]] A Python platform for controlling custom laboratory experiments and visualizing scientific data
 +
 +
 +  * [[https://github.com/CEMES-CNRS/pymodaq_plugins_picoquant]] [[http://pymodaq.cnrs.fr/en/latest/index.html|PyMoDAQ]] plugin for Picoquant instruments (TimeHarp260, ...)
 +
  
-  * qudi: A modular laboratory experiment management suite which supports PicoHarp300. [[https://github.com/Ulm-IQO/qudi]] 
  
-=== Controlling PicoQuant Devices ===+===  Demos about Controlling PicoQuant Devices ===
 == Sepia II and Solea == == Sepia II and Solea ==
  
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   * https://github.com/PicoQuant/PH300-v2.x-Demos   * https://github.com/PicoQuant/PH300-v2.x-Demos
   * https://github.com/PicoQuant/PH300-v3.x-Demos   * https://github.com/PicoQuant/PH300-v3.x-Demos
 +
  
 == HydraHarp 400 == == HydraHarp 400 ==
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   * https://github.com/PicoQuant/HH400-v1.x-Demos   * https://github.com/PicoQuant/HH400-v1.x-Demos
   * https://github.com/PicoQuant/HH400-v3.x-Demos   * https://github.com/PicoQuant/HH400-v3.x-Demos
 +
 +== MultiHarp 150 ==
 +  * [[https://github.com/PicoQuant/MH150-Demos]]
  
 === Other === === Other ===
  
-  * **pyPL** wxpython integration of software and hardware for micro-photoluminescence measurements: WinSpec, PicoHarp, and Thorlabs/APT piezos and stepper motors. \\  https://github.com/kaseyrussell/pyPL 
   * PicoHarp Library in Python \\  https://github.com/srgblnch/PicoHarp300   * PicoHarp Library in Python \\  https://github.com/srgblnch/PicoHarp300
  
software.1536659182.txt.gz · Last modified: 2018/09/11 09:46 by admin