easunarunachalam / pytcspc

Time-correlated single photon counting data analysis

pyTCSPC

a Python library for fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS) data analysis:

🚧 Experimental -- there will frequently be breaking changes

FLIM functions

• read Becker & Hickl .sdt files (based on sdtfile) into user-friendly xarray.DataArrays suitable for further analysis
• produce intensity and lifetime images
• fit decay curves

FCS functions

• read Becker & Hickl .spc files into user-friendly xarray.DataArrays suitable for further analysis
• generate FLIM and intensity images and "videos"
• generate kymographs for line-scanning FCS
• calculate correlation functions (based on multipletau)

environments

• generate yaml files by conda env export --no-builds > mmpy.yml

examples

• FCS: fit FCS data for diffusion of Alexa Fluor 488 (to be updated)
• fit_oneexp: fit decay curve for a solution of FAD (to be updated)
• fit_from_image: fit decay curve for NAD(P)H in yeast
• Gibbssampling: to be updated

pytcspc's Issues

Parameter/CI estimation is slow

Fit region, IRF peak/noise regions must be specified manually

Add auto-detection