biophysicsup / full_sms

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

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., 2024. Advanced analysis of single-molecule spectroscopic data, arXiv:2404.18945 [Preprint], http://arxiv.org/abs/2404.18945.

full_sms's Issues

Exporting once breaks further exporting

After exporting one file of fitting results to a folder it becomes impossible to do so again if the program isn't restarted.
Error message in dialog window:
"QObject::setParent: Cannot set parent, new parent is in a different thread"

Raised by Francios by email

Fitting results not showing

Fitting results for the lifetime of a particle isn't displayed in the box on the right-hand side if more than one exponential
function is used for the fit. A measured IRF was loaded which was successful.
Error message in dialog window:
"unsupported format string passed to numpy.ndarray.__format__"

Raised by Francios by email

Cannot run main.py

Issue trying to run software from source. Windows 10, python 3.9.

Created new environment and installed packages listed in installation instructions
https://up-biophysics-sms.readthedocs.io/en/latest/usage/installation.html

cloned source code from git hub

python main.py in \src directory gives the following error:

Currently used style: QWindowsVistaStyle
Available styles: ['windowsvista', 'Windows', 'Fusion']
2024-05-16 13:11:02,192 -> MainThread -> main -> main: App created
2024-05-16 13:11:02,192 -> MainThread -> main -> __init__: Multi-threading with maximum 8 threads
2024-05-16 13:11:02,192 -> MainThread -> main -> __init__: System -> Windows
Process Process-1:
Traceback (most recent call last):
  File "\miniconda3\envs\fullsms\lib\multiprocessing\process.py", line 315, in _bootstrap
    self.run()
  File "\miniconda3\envs\fullsms\lib\multiprocessing\process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "\Full_SMS\src\main.py", line 1526, in main
    main_window = MainWindow()
  File "\Full_SMS\src\main.py", line 146, in __init__
    self.spectra_controller = SpectraController(main_window=self)
  File "\Full_SMS\src\controllers.py", line 3188, in __init__
    self.main_window.pgSpectra_Image_View = pg.ImageView(view=pg.PlotItem(), roi=myPlotROI(size=(10, 200)))
TypeError: __init__() got an unexpected keyword argument 'roi'

No way to fix IRF value

Typos in HDF Format

Micro Times (s) -> Micro Times (ns)
Discription -> Description

Fits not included in exported file

When exporting the fitting results using the Export tab the Durbin-Watson parameters of the fits aren't included in the exported file.

Raised by Francios by email