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software [2018/10/23 07:47] – sisamakis | software [2019/05/21 16:03] – [Data Analysis] admin |
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{{tag> software acquisition analysis}} | {{tag> software acquisition analysis}} |
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====== Software ====== | ====== Software ====== |
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=== Complete packages === | === Complete packages === |
* **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://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). |
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| * [[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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| /* * [[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*/ |
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* [[http://www.fluortools.com/software|Fluortools]].Fluorescence Decay and Anisotropy Analysis. | * [[http://www.fluortools.com/software|Fluortools]].Fluorescence Decay and Anisotropy Analysis. |
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* [[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. |
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| * [[https://github.com/zhengkaiyu/FIMAS]] Fluorescent Imaging Analysis Software |
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* [[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.]] |
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| * [[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]] |
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=== 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]] |
* 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." | |
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* [[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]] |
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* [[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)]] |
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| * [[ 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. |
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| * [[https://tpeulen.github.io/tttrlib/| tttrlib]] tttrlib is a low level, high performance API to read and process time-tagged-time resolved (TTTR) data |
==== Data Acquisition ==== | ==== Data Acquisition ==== |
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* **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]] |
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=== Demos about Controlling PicoQuant Devices === | === Demos about Controlling PicoQuant Devices === |
* 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 |
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| == MultiHarp 150 == |
| * [[https://github.com/PicoQuant/MH150-Demos]] |
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=== Other === | === Other === |