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.
• FENNEC — Python toolkit that classifies single-molecule FRET bursts directly from raw photon timestamps using a dilated convolutional neural network, predicting for each burst whether the FRET efficiency was dynamic or static, whether the acceptor photobleached, and whether it blinked. Uses FRETBursts for background estimation and burst search.
• 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.