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software [2018/09/11 11:46]
admin
software [2018/10/23 10:18] (current)
sisamakis
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 ==== Data Analysis ==== ==== Data Analysis ====
  
 +  ​
 +=== 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|]]
 +  * [[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]]**
 +    * **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).
  
-  +  ​ [[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/​PicoQuant/​PicoQuant-Time-Tagged-File-Format-DemosDemo Code for reading PicoQuants PTU File format]]+
  
-  ​* [[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://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://github.com/​QuantumPhotonicsLab/​readPTU]] Probably same as above +  * [[http://www.fluortools.com/software|Fluortools]].Fluorescence Decay and Anisotropy Analysis.
- +
-  * [[https://​github.com/trevhull/​ptuT3toT2|ptuT3toT2 - a program that converts ptu files from picoquant from T3 mode to T2 mode]] +
- +
-  * [[https://​timetag.github.io|Extensible Time-tag Analyzer]] +
- +
-  * [[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.
  
-  ​* **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]]+
  
-  * [[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.]] 
 +  
 +=== Libraries/​scripts/​readers === 
 +  * [[https://​github.com/​PicoQuant/​PicoQuant-Time-Tagged-File-Format-DemosDemo Code for reading PicoQuants PTU File format]]
  
-  * QuickFit 3.0: http://www.dkfz.de/Macromol/quickfit/+  *  ​[[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]]
  
  
-  * [[software:FCS viewer]]+  * **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/​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."
  
-  * FCS Bulk Correlation Software accepting pt3 and ptu files \\  ​[[https://​github.com/​dwaithe/FCS_point_correlator| FCS Point Correlator]]+  * [[https://​github.com/​QuantumPhotonicsLab/readPTU]] Probably same as above
  
-  * [[software:FLIMFit]] +  * [[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 ]] 
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 ==== Data Acquisition ==== ==== Data Acquisition ====
  
-  * 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]] 
  
-=== 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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 === 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 11:46 by admin