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software [2018/10/23 08:18] sisamakissoftware [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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 === Complete packages === === 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]]
 +  * **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|]]   * **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|]]
-  * [[http://www.mpc.hhu.de/en/software/software-package.html|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://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]]**   * **[[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]].      * **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]]. 
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   * [[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).   * [[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/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.
  
   *  [[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.   *  [[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.
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 /* * [[software:FCS viewer]] ..This became redundant as its developer released Pycorrfit*/ /* * [[software:FCS viewer]] ..This became redundant as its developer released Pycorrfit*/
  
-  * [[https://github.com/dwaithe/FCS_point_correlator| FCS Point Correlator]] FCS Bulk Correlation Software accepting pt3 and ptu files.+  * [[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]]
  
   * [[software:FLIMFit]]. FLIMfit is an open source package for rapid analysis of large FLIM datasets.    * [[software:FLIMFit]]. FLIMfit is an open source package for rapid analysis of large FLIM datasets. 
 +  
 +  * [[https://github.com/zhengkaiyu/FIMAS]] Fluorescent Imaging Analysis Software
  
   * [[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.]]   * [[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.]]
- + 
 +  * [[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. 
 + 
 +  * [[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. 
 === Libraries/scripts/readers === === Libraries/scripts/readers ===
   * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-Demos| Demo Code for reading PicoQuants PTU File format]]   * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-Demos| Demo Code for reading PicoQuants PTU File format]]
 +
 +  * [[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]]   *  [[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]]
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       * Import Filter for pt3 files: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:picoquant_.pt3_image_reader:start]]       * 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]]       * Import of ptu/pt3 image files (+intensity/average lifetime stacks): [[https://github.com/ekatrukha/PTU_Reader]]
-  *  [[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/s. It can also compute intensity time traces and post select photons based on that." 
  
-  * [[https://github.com/QuantumPhotonicsLab/readPTU]] Probably same as above+ 
 +  * [[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]]   * [[https://github.com/trevhull/ptuT3toT2|ptuT3toT2 - a program that converts ptu files from picoquant from T3 mode to T2 mode]]
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     * [[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]]   * **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   * **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]]    * 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, ...)
 +
 +
  
 ===  Demos about Controlling PicoQuant Devices === ===  Demos about Controlling PicoQuant Devices ===
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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 ===
software.1540282722.txt.gz · Last modified: 2018/10/23 08:18 by sisamakis