Differences

This shows you the differences between two versions of the page.

--- software [2018/10/22 15:00] – sisamakis
+++ software [2019/05/14 08:13] – admin
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 {{tag> software acquisition analysis}}
+~~TOC~~
-~~TOC~~
 ====== Software ======
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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|]]
+  * [[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]]
-  * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-Demos| Demo Code for reading PicoQuants PTU File format]]
+  * [[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/s. It can also compute intensity time traces and post select photons based on that."
+  *  [[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/QuantumPhotonicsLab/readPTU]] Probably same as above
+/* * [[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/trevhull/ptuT3toT2|ptuT3toT2 - a program that converts ptu files from picoquant from T3 mode to T2 mode]]
+  * [[http://www.fluortools.com/software|Fluortools]].Fluorescence Decay and Anisotropy Analysis.
-  * [[https://timetag.github.io|Extensible Time-tag Analyzer]]
+  * [[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://github.com/hammer-wang/exciton_diffusion|exciton diffusion (Matlab)]]
+  *  [[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.
- /*  * [[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]]
-  *
+/* * [[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.
+  * [[software:FLIMFit]]. FLIMfit is an open source package for rapid analysis of large FLIM datasets.
-  * ImageJ Import Filter for pt3 files: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:picoquant_.pt3_image_reader:start]]
+  * [[https://github.com/zhengkaiyu/FIMAS]] Fluorescent Imaging Analysis Software
-  * ImageJ import of ptu/pt3 image files (+intensity/average lifetime stacks): [[https://github.com/ekatrukha/PTU_Reader]]
+  * [[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.]]
-  * **DecayFit - Fluorescence Decay Analysis** [[http://www.fluortools.com/software/decayfit]]
+  * [[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]]
-  * **AniFit - Anisotropy Decay Analysis** [[http://www.fluortools.com/software/anifit]]
-  * [[software:PyCorrFit]]
-  * [[http://pycorrelate.readthedocs.io/en/latest/ | PyCorrelate]]
-  * QuickFit 3.0: http://www.dkfz.de/Macromol/quickfit/
+=== Libraries/scripts/readers ===
+  * [[https://github.com/PicoQuant/PicoQuant-Time-Tagged-File-Format-Demos| Demo Code for reading PicoQuants PTU File format]]
-  * [[software:FCS viewer]]
+  *  [[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]]
-  * FCS Bulk Correlation Software accepting pt3 and ptu files \\  [[https://github.com/dwaithe/FCS_point_correlator| FCS Point Correlator]]
-  * [[software:FLIMFit]]
+  * **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 \\
+  "readPTU is a python package designed to analyze time-correlated single-photon counting data. The use of the library promotes the storage of the complete time arrival information of the photons and full flexibility in post-processing data for analysis. The library supports the computation of time resolved signal with external triggers and second order autocorrelation function analysis can be performed using multiple algorithms that provide the user with different trade-offs with regards to speed and accuracy. Additionally, a thresholding algorithm to perform time post-selection is also available. The library has been designed with performance and extensibility in mind to allow future users to implement support for additional file extensions and algorithms without having to deal with low level details. We demonstrate the performance of readPTU by analyzing the second-order autocorrelation function of the resonance fluorescence from a single quantum dot in a two-dimensional semiconductor." [[http://qpl.eps.hw.ac.uk/]]
+  * [[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]]
@@ Line 89: / Line 96: @@
-  * **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]]
   * **dspFRET**: Matlab code for analyzing TTTR data from PicoQuant. Typical application is analysis of single pair FRET measurements with pulsed interleaved excitation (PIE-FRET). \\  https://github.com/RobinsonLab/dspFRET
+  * [[https://github.com/hammer-wang/exciton_diffusion|exciton diffusion (Matlab)]]
+ /*  * [[https://github.com/PicoQuant/Notebooks]] Jupyter Notebooks reading the tiff files exported by SymPhoTime */
@@ Line 108: / Line 120: @@
   * **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]]
 ===  Demos about Controlling PicoQuant Devices ===
@@ Line 128: / Line 141: @@
   * https://github.com/PicoQuant/HH400-v1.x-Demos
   * https://github.com/PicoQuant/HH400-v3.x-Demos
+== MultiHarp 150 ==
+  * [[https://github.com/PicoQuant/MH150-Demos]]
 === Other ===