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This is a repo for a Python based application to open SMS .h5 files, and perform the initial analysis and exporting.

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BioPhysicsUP/Full_SMS

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Full SMS

A graphical user interface-based analysis suite developed by the Biophysics Group at the University of Pretoria, South Africa.

Main Features

  • Performs change point analysis to resolve brightness levels of fluorescence measurements.
  • Uses Agglomerative Hierarchical Clustering to group resolved levels.
  • Performs fluorescence decay fitting to measure lifetimes.
  • Allows filtering and export of analysed brightness/lifetime data.
  • Computes second-order correlation functions from time-tagged photon data.
  • Displays raster scan images and fluorescence spectral time traces.

Known limitations/problems

  • Inability to close measurement file once opened.
  • Some systems may encounter missing numxpr module.

Planned Improvements

  • Improved stability.
  • Additional conversion tools.
  • Additional analysis functionality, such as for fluorescence correlation spectroscopy.

Additional Info

An example file can be downloaded here: https://rb.gy/wtzg0z.

The documentation is available here: https://up-biophysics-sms.readthedocs.io/en/latest/index.html.

This software is to be used only if reference is made to the following paper:

Botha, J.L., van Heerden, B., and Krüger, T.P.J., "Advanced analysis of single-molecule spectroscopic data", Biophysical Reports 4(3), September 2024, https://doi.org/10.1016/j.bpr.2024.100173.