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OpenSMFS / FRETBursts

Burst analysis software for single and multi-spot single-molecule FRET (smFRET) data.
https://opensmfs.github.io/FRETBursts/
GNU General Public License v2.0
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Lifetime Fitting #6

Open tritemio opened 6 years ago

tritemio commented 6 years ago

From @ncodina on November 15, 2016 16:59

I was wondering if there is already some function implemented to calculate lifetimes from the TCSPC histogram?

Copied from original issue: tritemio/FRETBursts#48

tritemio commented 6 years ago

Not out-of-the-box, but you can use straight lmfit to do the fitting. You can find an example of fitting with IRF deconvolution using least-squares or maximum likelihood in the following notebook (it uses simulated data):

https://github.com/tritemio/notebooks/blob/master/Lifetime_decay_fit.ipynb

Also you can fairly simply compute a per-burst "mean lifetime" with:

http://fretbursts.readthedocs.io/en/latest/plugins.html#fretbursts.burstlib_ext.calc_mean_lifetime

This can be used, for example, to build the plots like mean lifetime vs ratiometric E (see Seidel group MFD analysis).

tritemio commented 6 years ago

The notebooks recently published in this repository show how to do lifetime fitting on multispot data using both tail fitting and IRF reconvolution of the lifetime histogram with different models (1, 2 or 3 exponentials).

The notebooks are pretty long, for the part relative to lifetime fitting see this section:

http://nbviewer.jupyter.org/github/tritemio/polimi_tcspc_16ch/blob/master/16-CH%20POLIMI-TCSPC%20Bursts%20Analysis-2015-09-08_s5_FRET.ipynb#Population-Lifetime-Fit