FLUTE

<div id="top"></div> <!-- *** Readme based on the template here: https://github.com/othneildrew/Best-README-Template --> <!-- PROJECT LOGO --> <br /> <div align="center"> <a href="https://github.com/DaleLOB/FLUTE"> <img src="icons/logo_name.png" alt="Logo" width="352" height="88"> </a> <p align="center"> a Python GUI for interactive phasor analysis of Fluorescence Lifetime Microscopy (FLIM) data <br /> <a href="https://www.cambridge.org/core/journals/biological-imaging/article/flute-a-python-gui-for-interactive-phasor-analysis-of-flim-data/862F290EC14187741BDA6B58E9868FA2"><strong>Publication »</strong></a> <br /> </p> </div>

Usermanual and Tutorial

A detailed user manual is available in the supplemental material of the associated publication:

Gottlieb, Asadipour, Kostina, Ung, & Stringari, Biological Imaging (2023) <a href="https://www.cambridge.org/core/journals/biological-imaging/article/flute-a-python-gui-for-interactive-phasor-analysis-of-flim-data/862F290EC14187741BDA6B58E9868FA2"><strong>"FLUTE: A Python GUI for interactive phasor analysis of FLIM data". »</strong></a>
Please cite this article if you found FLUTE helpful with your data analysis.

A presentation of FLUTE software is available here in open access <a href="https://zenodo.org/records/10839310"><strong> GerBi FLIM workshop slides about FLUTE software</strong></a> <br />

An interactive tutorial is available on youtube <a href="https://www.youtube.com/watch?v=q7W1hcb6V_I&t=2005s"><strong> I2K workshop - Interactive phasor analysis of FLIM data using FLUTE</strong></a> <br />

A demonstration of the use of FLUTE is available in the <a href="https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-30/issue-S2/S23901/Consensus-guidelines-for-cellular-label-free-optical-metabolic-imaging/10.1117/1.JBO.30.S2.S23901.full?tab=ArticleLinkFigureTable"><strong> Consensus guidelines for cellular label-free optical metabolic imaging: ensuring accuracy and reproducibility in metabolic profiling</strong></a>

<br /> <!-- ABOUT THE PROJECT -->

About the project

<div align="center"> <img src="icons/MainWindow.PNG" width="700"> </div>

Fluorescence Lifetime Ultimate Explorer (FLUTE) provides a graphical user interface to explore Fluorescence Lifetime Microscopy (FLIM) using phasor analysis. The GUI allows for quick and interactive analysis of experimental FLIM data, and can export results for further processing.

An example of various FLIM data visualisation and analyses can be seen here:

<div align="center"> <img src="icons/Demonstration.PNG" align="center">

Colormaps of the same data with cursor selection, phase lifetime contrast, modulation lifetime contrast and distance from a known molecular species. Scale bar is 150 um.

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The Fluorescence lifetime imaging microscopy (FLIM) data relative to the publications are in our <a href="https://zenodo.org/records/8324901"><strong>Zenodo repository »</strong></a> <br /> Fluorescein.tif stack contains the fluorescence intensity decay of fluorescein solution with a known lifetime of 4ns, used as calibration. Embryo.tif file contains the fluorescence intensity decay of a zebrafish embryo at 3 days post fertilisation. <br /> Both files have been acquired with the following parameters: <br />

• laser repetition rates = 80 MHz
• bin width = 0.223ns
• temporal bin number = 56 <br />

Built with

FLUTE mainly depends on the following packages:

• PyQt
• Scipy
• Numpy

With the exe compiled using auto-py-to-exe

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Getting started

Running the exe

To quickly start using FLUTE, an exe which works on Windows computers without installing Python is available under releases on the github here.

Running the code

To run the code from this github page, run main.py after installing:

pip install PyQt5, numpy, opencv-python, matplotlib, scikit-image

Prerequisites

FLIM data must be saved or exported as a tiff-stack, where each image of the stack represents a temporal bin of the fluorescence decay measurement. Example data is available in the supplemental data of the release publication.

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License

FLUTE is Copyright (C) 2022 FLUTE

FLUTE source code is Free and Open Source Software released under the terms of the 3-Clause BSD License (see file [LICENSE] for details).

The prebuilt FLUTE executable is a combined work that contains both FLUTE and QT library bindings. It is released under the terms of both the 3-Clause BSD License (for the FLUTE part) and the <a href="https://www.gnu.org/licenses/lgpl-3.0.txt"><strong>GNU Lesser General Public License </strong></a> (for the QT part).