Open-source software for PicoQuant data analysis and acquisition

    The following is a curated list of open-source tools that work with PicoQuant data formats or hardware. These are external projects — PicoQuant takes no responsibility for them and provides no support. Please contact the respective authors if you encounter problems. Also note that such projects may not be maintained continuously; check that they support current file format versions and library versions before committing to development work based on them.

    If you maintain a software package that deals with TCSPC data and would like it listed here, please contact PicoQuant support.

    Data Analysis

    General / multi-technique

    • snAPI — A Python wrapper for PicoQuant TCSPC instruments. Uses C++ under the hood for performance and bridges hardware control with Python ease-of-use. Supports histogramming, correlation, heralding, coincidence analysis, and more.
    • PAM (PIE Analysis with MATLAB) — MATLAB-based GUI package originally developed for pulsed interleaved excitation (PIE) and single-molecule FRET. Now covers FCS/FLCS, burst analysis, image correlation spectroscopy, FLIM (phasor), and TCSPC anisotropy. See also: Single-molecule spectroscopy section.
    • Photon Correlation — Command-line tools for performing calculations on photon arrival data from PicoQuant hardware (PicoHarp, HydraHarp).
    • Photon-Tools — Python utilities for working with photon timestamp data from fluorescence spectroscopy.
    • ETA (Extensible Timetag Analyzer) — A graphical event-driven programming language for analyzing, plotting, and fitting time-tagged data. Supports PicoQuant file formats (HydraHarp, PicoHarp, TimeHarp T2/T3) as well as several other vendor formats.
    • FluorTools — Freeware tools for fluorescence decay and anisotropy analysis (DecayFit, AniFit). MATLAB-based with standalone executables available. Note: last updated around 2013–2014.

    FCS / Correlation

    • PyCorrFit — General-purpose FCS evaluation software supporting multiple file formats including Zeiss ConfoCor3. Includes many built-in model functions and handles different excitation geometries (confocal, TIR).
    • FoCuS-point — Python software for TCSPC-based FCS, with support for time-gated filtering (particularly useful for STED-FCS). Accepts PTU and PT3 files directly. Includes batch processing and curve fitting.
    • FCS fit JS — Browser-based FCS fitting tool (companion to FoCuS-point, same author). Runs entirely in the browser with no installation required. Supports multi-component diffusion models and cross-correlation.
    • FRETBursts — Software for burst analysis of freely-diffusing single-molecule FRET (smFRET) measurements including μs-ALEX. See also: Single-molecule spectroscopy section.
    • PyBroMo — Simulator for single-molecule FRET experiments of freely diffusing particles.
    • PyCorrelate — Computes fast, accurate cross-correlations at log-spaced lags over arbitrary time ranges. Suitable for FCS and dynamic light scattering (DLS).
    • QuickFit 3.0 — Open-source data evaluation software for FCS and imaging FCS (imFCS), developed at DKFZ. Plugin-based architecture; supports PicoQuant file formats. Note: last released in 2015, no longer actively maintained.

    FLIM / Phasor analysis

    • PhasorPy — Open-source Python library for analysis of fluorescence lifetime and hyperspectral images using the phasor approach.
    • FLUTE — Python GUI for interactive phasor analysis of FLIM data.
    • FLIMPA — Open-source Python GUI for phasor plot analysis of raw TCSPC FLIM data.
    • FLIMfit — Open-source MATLAB package for rapid analysis of large FLIM datasets, developed at Imperial College London. Supports PicoQuant PTU/BIN file formats via Bio-Formats. Available as a standalone MATLAB app or OMERO client.
    • FLIMage — Controls TCSPC hardware and generates fluorescence lifetime images in real time. Free for academic/educational use.
    • FIMAS — MATLAB-based GUI for analysis of fluorescence microscopy and FLIM data. Imports PicoQuant PTU files (T2/T3), Becker & Hickl SPC/SDT, and several other formats. Actively maintained.
    • napari-flim-phasor-plotter — Napari plugin for interactively loading raw FLIM data and generating phasor plots. Reads PTU files (via ptufile), supports time series, and integrates with the napari ecosystem for downstream analysis.
    • FLOPA (FLIM Open, Process, and Analyze) — Python/napari-based tool for FLIM data opening, processing, and analysis. Supports PTU file import, TCSPC decay histograms, intensity and mean arrival time images, and phasor analysis (pixel-based and object-based).
    • sFLIM — MATLAB library for analysing multi-channel spectrally-resolved FLIM data using a pattern-matching / linear-unmixing algorithm. Developed by PicoQuant.
    • FLIM-FRET Analyzer — Windows application (C#) for automation of lifetime-based FRET analysis, with automated single-cell segmentation and batch processing. Note: developed for Becker & Hickl SPC-830 data; PicoQuant compatibility is not guaranteed.

    Single-molecule spectroscopy

    • PAM (PIE Analysis with MATLAB) — Comprehensive MATLAB package for PIE and single-molecule FRET analysis, including burst analysis (BurstBrowser), photon distribution analysis, and FLCS. Also covers FCS, image correlation, and FLIM. See also: General / multi-technique section.
    • FRETBursts — Python toolkit for burst analysis of freely-diffusing smFRET data, including μs-ALEX. Notebook-based workflow for reproducible analysis. See also: FCS / Correlation section.
    • PIE-smFRET-toolkit — Python toolkit for smFRET experiments using PicoQuant TCSPC data in T3 format, with pulsed interleaved excitation (PIE) and two detection channels.
    • Fretica — User-extendable Mathematica toolbox for analysing single-molecule fluorescence data.

    Lifetime fitting

    • LifeFit — Python package for analysing TCSPC datasets: fluorescence lifetime and time-resolved anisotropy decays.
    • Lifetime_fit — MATLAB scripts for fitting TCSPC lifetime histograms to single, double or triple exponential models with reconvolution (NLLS / MLE-Nelder-Mead).

    Positron annihilation

    • Pals3D — Graphical application for Positron Annihilation Lifetime Spectroscopy (PALS) using a PicoQuant TimeHarp 260 TCSPC system.

    Libraries and File Readers

    • PicoQuant Demo Code — Official demo code for reading PicoQuant PTU file formats in multiple languages.
    • Pre-histogrammed Image Data File — Official example code for reading PicoQuant pre-histogrammed image data files (BIN format). Developed by PicoQuant.
    • tttrlib — File-format-agnostic, high-performance C++ library (Python-wrapped) for reading, processing, and writing TTTR data from PicoQuant and Becker & Hickl devices.
    • Trattoria — Python wrapper around a fast Rust core for streaming analysis of TTTR data. Supports g², g³, intensity traces, lifetime histograms, and more. Currently reads PicoQuant PTU files.
    • ptufile — Python library to read and write PicoQuant PTU and related files (PHU, PCK, PCO, PFS, PUS, PQRES, PQDAT, and more). Actively maintained.
    • pyptu — Python package for loading PicoQuant PTU files. Available on PyPI (pip install pyptu).
    • readPTU — Python library to analyse time-tagged time-resolved data from PTU files.
    • ptu_flim_tools — Tools for reading, converting, and analysing PTU FLIM data.
    • readPTU_FLIM — Python library for reading PTU files (MultiHarp, HydraHarp, PicoHarp, TimeHarp) and converting raw TTTR data to FLIM image stacks.
    • phconvert — Python library for converting Becker & Hickl, PicoQuant PTU, and other TTTR formats to the open Photon-HDF5 format. Actively maintained.
    • PTU2BIN — Converts PicoQuant PTU files to BIN or IgorPro binary wave files (IBW).
    • libpicoquant — C library and command-line tools for reading PicoQuant file formats (PHD, PT2, PT3, and more).
    • picoquantio — Python implementations of PicoQuant data formats for the TimeHarp, PicoHarp, and HydraHarp.
    • Open Microscopy Bio-Formats — Supports PicoQuant BIN files (pre-histogrammed image data).
    • PTU_Reader (ImageJ) — ImageJ import plugin for PTU/PT3 image files, including intensity and average lifetime stacks.
    • PTU_Writer (ImageJ) — Fiji/ImageJ plugin for writing PTU FLIM TTTR files (companion to PTU_Reader, same author). Actively maintained.
    • Python GUI Apps — GUI apps (PyQt / pyqtgraph) for quick analysis of scientific data including PicoQuant files.
    • MultiChannel Screen — Processes multiple PTU files or folders and produces multicolour fluorescence images with minimal user input. Useful for rapid screening during imaging sessions.
    • fastFLIM — Batch converts PicoQuant PTU files to fastFLIM images (same author as MultiChannel Screen and Lifetime_fit).

    Data Acquisition

    • snAPI — Python wrapper for direct communication with PicoQuant TCSPC instruments (see also Data Analysis above).
    • LumiPy — Python interface for controlling and acquiring data from PicoQuant Luminosa microscope systems. Developed by PicoQuant.
    • SymPhoTime Remote Interface — Control SymPhoTime 64 via a network interface for automated or remote acquisition workflows. Developed by PicoQuant.
    • qudi — Modular laboratory experiment management suite supporting PicoHarp 300.
    • ScopeFoundry — Python platform for controlling custom laboratory experiments and visualising scientific data. Includes a PicoHarp 300 hardware plugin.
    • PyMoDAQ plugin for PicoQuant — PyMoDAQ plugin for TimeHarp 260 and other PicoQuant instruments.
    • miniquant-ioc — EPICS Input-Output Controller (IOC) for the PicoQuant HydraHarp 400. Provides a Python interface to the HydraHarp API for integration into EPICS-based beamline or laboratory control systems. Linux only. Available on PyPI (pip install miniquant-ioc).
    • PicoHarp 300 Demos — Official PicoQuant demo code for PicoHarp 300.
    • HydraHarp 400 Demos — Official PicoQuant demo code for HydraHarp 400.
    • TimeHarp 260 Demos — Official PicoQuant demo code for TimeHarp 260.
    • TimeHarp 260 Linux — Library, driver, and demo code for using the TimeHarp 260 on Linux. Developed by PicoQuant.
    • MultiHarp 150 Demos — Official PicoQuant demo code for MultiHarp 150.
    • PicoQuant Sepia2 API Bundle — Drivers and demo code for Sepia II laser control.
    • SepiaWrapper — Experimental Python wrapper for the PicoQuant Sepia II laser control API. Developed by PicoQuant.
    • EasyFlux — LabView-based fluorescence lifetime-activated droplet sorting software.
    Tags
    Open Source ptu Github snAPI
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