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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
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<meta name="description" content="">
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<title>FLIMLib</title>
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<a class="navbar-brand" href="#">FLIMLib</a>
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<ul class="nav navbar-nav">
<li class="active"><a href="#">Home</a></li>
<li><a href="https://github.com/flimlib/flimlib/wiki">Wiki</a></li>
<li><a href="https://github.com/flimlib">Source</a></li>
<li><a href="/pipermail/slim-curve/">Archives</a></li>
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<img src="logo.png" width=210 height=210 class="logo" alt="logo">
<h1>FLIMLib</h1>
<p>An exponential curve fitting library used for Fluorescent Lifetime
Imaging (FLIM).</p>
<p>
<a href="#source" class="btn btn-info btn-lg" role="button">Source »</a>
<a href="#tri2" class="btn btn-primary btn-lg" role="button">TRI2 »</a>
<a href="#imagej" class="btn btn-success btn-lg" role="button">ImageJ »</a>
</p>
</div>
<div class="well">
<p>FLIMLib is developed by Paul Barber and the Advanced Technology
Group at the <a href="https://www.oncology.ox.ac.uk/">Oxford
Institute for Radiation Oncology</a>, University of Oxford, as well
as the <a href="https://loci.wisc.edu/">Laboratory for Optical and
Computational Instrumentation</a> (LOCI) at the University of
Wisconsin-Madison. FLIMLib is used for FLIM functionality in the
<a href="https://www.assembla.com/spaces/ATD_TRI/wiki/Home">Time
Resolved Imaging</a> (TRI2) software, as well as in the
<a href="https://imagej.net/FLIMJ">FLIMJ plugin for ImageJ</a>.</p>
</div>
<div id="source" class="page-header">
<h1>Source</h1>
</div>
<p>
FLIMLib is an open source project licensed under the <a
href="https://www.gnu.org/licenses/gpl.html">GNU General Public
License</a> v3 or later.
</p>
<p>
The FLIMLib library code is written in C89 compatible C and is
thread-safe for fitting multiple pixels concurrently. A Java
interface <code>FLIMLib.java</code> (generated by
<a href="http://swig.org">SWIG</a>) is provided to call the
library from Java code, used by the FLIMJ plugin for ImageJ.
</p>
<a href="https://github.com/flimlib" class="btn btn-default btn-lg" role="button">See the code »</a>
<div id="tri2" class="page-header">
<h1>TRI2</h1>
</div>
<img src="TRI2.png" style="float: right; width: 400px" class="img-thumbnail" alt="TRI2">
<p>
TRI2 is a Windows application that uses FLIMLib to analyze fluorescence
lifetime microscopy (FLIM) data.
<p>
Originally named 'Time Resolved Imaging', TRI2 not only incorporates
processing for time-domain FLIM data but also for RGB spectral unmixing,
foci counting and other batch processing, formatting, printing and export
functions. It's all built on a 'workspace' framework to make it easier to
try out different processing functions on images.
</p>
<p>
The time-resolved image processing functions still remain the core of the
program and Levenberg-Marquardt fitting routines are implemented for
multiple lifetime extraction. Novel Bayesian functions are under
development.
</p>
<p>
The core fitting routines from TRI2 are now open source in the FLIMLib
library. These include RLD, Levenberg-Marquardt, non-negative least
squares and Bayesian.
</p>
<a href="https://www.assembla.com/spaces/ATD_TRI/wiki/Home" class="btn btn-default btn-lg" role="button">Read more »</a>
<div id="imagej" class="page-header" style="clear: right">
<h1>FLIMJ</h1>
</div>
<img src="FLIMJ-plugin.png" style="float: right; width: 400px" class="img-thumbnail" alt="SLIM Curve plugin">
<p>
The FLIMJ plugin for ImageJ provides the ability to analyze FLIM
data within ImageJ, using the FLIMLib library. The plugin can be
installed into the <a href="https://fiji.sc/">Fiji distribution of
ImageJ</a> simply by enabling the FLIMJ <a
href="https://imagej.net/Update_Sites">update site</a>.
Features include:
<p>
<ul>
<li>Fit individual pixels, entire images per-pixel, or do global analysis
on entire images, using FLIMLib's rapid lifetime determination (RLD),
Levenberg-Marquardt (LMA) or global analysis (Global) fitting algorithms</li>
<li>Single, double and triple exponential fits</li>
<li>Gaussian, Poisson and Maximum Likelihood Estimation noise models</li>
<li>Produce one or several fitted images depending which parameters (A,
τ, Z, χ2) are chosen for visualization</li>
<li>Full control over the start and end fit cutoffs known as
"cursors"</li>
<li>Binning options for various kernel sizes to reduce noise and boost
intensity when fitting per-pixel</li>
<li>Support for so-called "excitation" or "prompt" files containing a
recorded system response function to be convolved with the exponential
fit</li>
<li>Batch processing support for analyzing many lifetime images as part
of a scripting workflow</li>
</ul>
</p>
<a href="https://imagej.net/FLIMJ" class="btn btn-default btn-lg" role="button">Read more »</a>
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