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| software [2018/05/12 07:08] – [Data Analysis] peter | software [2018/10/23 07:47] – sisamakis |
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| EasyTau features a scripting language to automate more complex experiments. Examples of EasyTau scripts can be found on github: https://github.com/PicoQuant/EasyTau-Scripts | EasyTau features a scripting language to automate more complex experiments. Examples of EasyTau scripts can be found on github: https://github.com/PicoQuant/EasyTau-Scripts |
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| [[software:FluoFit]] | [[software:FluoFit]] \\ |
| | Decay curve analysis software |
| ===== Open Source ===== | ===== Open Source ===== |
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| ==== Data Analysis ==== | ==== Data Analysis ==== |
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| | === 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|]] |
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| | * **[[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]] |
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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). |
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| | * [[http://www.fluortools.com/software|Fluortools]].Fluorescence Decay and Anisotropy Analysis. |
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| * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-Demos| Demo Code for reading PicoQuants PTU File format]] | |
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| * [[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. | * [[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). |
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| * [[https://github.com/trevhull/ptuT3toT2|ptuT3toT2 - a program that converts ptu files from picoquant from T3 mode to T2 mode]] | * [[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. |
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| * [[https://timetag.github.io|Extensible Time-tag Analyzer]] | |
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| * [[https://github.com/hammer-wang/exciton_diffusion|exciton diffusion (Matlab)]] | /* * [[software:FCS viewer]] ..This became redundant as its developer released Pycorrfit*/ |
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| /* * [[https://github.com/PicoQuant/Notebooks]] Jupyter Notebooks reading the tiff files exported by SymPhoTime */ | |
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| * [[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://github.com/dwaithe/FCS_point_correlator| FCS Point Correlator]] FCS Bulk Correlation Software accepting pt3 and ptu files. |
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| * [[https://www.researchgate.net/project/Open-Computational-Tools-for-Single-Molecule-Spectroscopy|Researchgate group Open Computational Tools for Single-Molecule Spectroscopy]] | * [[software:FLIMFit]]. FLIMfit is an open source package for rapid analysis of large FLIM datasets. |
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| * PAM is a software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with a focus on experiments using pulsed interleaved excitation.[[http://www.cup.uni-muenchen.de/pc/lamb/software/pam.html|]] | * [[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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| | === Libraries/scripts/readers === |
| | * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-Demos| Demo Code for reading PicoQuants PTU File format]] |
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| * ImageJ Import Filter for pt3 files: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:picoquant_.pt3_image_reader:start]] | * [[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]] |
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| * ImageJ import of ptu/pt3 image files (+intensity/average lifetime stacks): [[https://github.com/ekatrukha/PTU_Reader]] | |
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| * **DecayFit - Fluorescence Decay Analysis** [[http://www.fluortools.com/software/decayfit]] | * **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]] |
| * **AniFit - Anisotropy Decay Analysis** [[http://www.fluortools.com/software/anifit]] | |
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| * [[software:PyCorrFit]] | * **ImageJ data readers**- |
| | * Import Filter for pt3 files: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:picoquant_.pt3_image_reader:start]] |
| * [[http://pycorrelate.readthedocs.io/en/latest/ | PyCorrelate]] | * 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." |
| * QuickFit 3.0: http://www.dkfz.de/Macromol/quickfit/ | |
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| | * [[https://github.com/QuantumPhotonicsLab/readPTU]] Probably same as above |
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| * [[software:FCS viewer]] | * [[https://github.com/trevhull/ptuT3toT2|ptuT3toT2 - a program that converts ptu files from picoquant from T3 mode to T2 mode]] |
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| * FCS Bulk Correlation Software accepting pt3 and ptu files \\ [[https://github.com/dwaithe/FCS_point_correlator| FCS Point Correlator]] | |
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| * [[software:FLIMFit]] | |
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| * **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]] | |
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| * **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)]] |
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| | /* * [[https://github.com/PicoQuant/Notebooks]] Jupyter Notebooks reading the tiff files exported by SymPhoTime */ |
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| * **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 ]] |
| ==== Data Acquisition ==== | ==== Data Acquisition ==== |
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| * 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 |
| | * PicoHarp Multiscan with Prior Stage: [[https://bitbucket.org/ywsong2/uky_ptu_convert]] |
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| === 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 |
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| == HydraHarp 400 == | == HydraHarp 400 == |
| === Other === | === Other === |
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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 | |
| * PicoHarp Library in Python \\ https://github.com/srgblnch/PicoHarp300 | * PicoHarp Library in Python \\ https://github.com/srgblnch/PicoHarp300 |
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