lifetimefitting 0.0.29

PicoHarp TCSPC lifetime fitting tool

LifetimeFittingTool

This is a quick tool I wrote to take some of my TCSPC fluorescence lifetime fitting tools from spectraImport.ipynb and make them usable for other people. It can read PicoHarp .phd files thanks to adreasnow/picoharp-phd and also reads the plain .txt output it can save.

The app itself is a basic least squares regression tool but allows you to fit in linear or logarithmic space, supports up to 4 decays, and can export images as well as .csv files of the fitted histograms

Installing

PyPi

The easiest way to get it is to install it directly from pypy, so as too pull all the dependencies:

pip install lifetimefitting

Manually

• Python (I'm not sure how old you could go, but I know it runs on >3.9)
• Matplotlib
• Numpy
• PyQt6
• Scipy

These can be installed pretty easily via pip

pip install matplotlib numpy scipy pyqt6

or conda

conda install matplotlib numpy scipy pyqt6

Then you can clone the module down and install it manually

git clone https://github.com/adreasnow/LifetimeFittingTool.git
cd LifetimeFittingTool
python setup.py install

Usage

To run the app, all you need to do is execute the module in python and a QT window should appear :)

python -m lifetimefitting

The Maths

Uses the form of the function:

$$ fl(t)=I_0 exp\bigg(-\frac{t}{\tau}\bigg) $$

Where:

• $t =$ Time
• $\tau =$ Fluorescence lifetime
• $I_0 =$ Initial photon concentration

For the corrected fitting procedure, the convolved function is calculated as:

$$ fl=fl(t)_{IRF}\otimes fl(t) $$

$$ fl_{fitted}=\sum_{i=1}^{\text{exponents}} C_i\cdot fl(t)_i $$

Where:

• $fl(t)_{IRF} =$ Fitted instrument response function
• $fl(t)_i =$ Fitted function for each decay
• $C_i =$ Linear coefficient for each decay

$\chi^2$ is calculated as per fluortools

$$ \chi^2 = \sum_{j=1}^{n} (c_j-\hat{c_j})^2/\hat{c_j}\ \chi^2_{red}=\frac{\chi^2}{n} $$