Example of time-dependent analysis for widefield particle extinction using Extinction Suite v4.1.5 or higher

This dataset was provided by Nicole Slesiona. The label includes "Extinction..." as a requirement of the Suite in order to recognise the folder structure, however the data is not made up of extinction images. Instead it is a time-series of fluorescence data, each image of which can be analysed in a similar way as typical extinction data. The exposure time per frame was \(\tau=3\,\)s. The imaging was performed with an objective of numerical aperture \(\mathrm{NA}=1.4\) and magnification \(M=100\times\). The emission wavelength is \(\lambda\sim650\,\)nm. The data has been post-processed to remove hot pixels and background gradients, though the specific methodology there is not important for the user to understand. The data is ready to analyse as-is and serves only to show how to run the time-dependent analysis and the kinds of results one can expect.

It should be noted that the analysis operates in exactly the same way whether one has time-dependent extinction or fluorescence data. However, time-dependent extinction data can be obtained simply by choosing to save all extinction timepoints when running the "Extinction Analysis" module after having acquired shifted-reference data using the stage-camera synchronous recording method. Note that choosing to save all extinction timepoints results in an additional folder containing the timepoints for each channel and polariser angle in the experiment. In the case of the data above, we have only one such folder, since the fluorescence was detected in only one filter range (centered at \(\lambda=650\,\)nm. Here, the folder containing the fluorescence data has been titled to mimic how the folder would be titled if the suite was used to create timepoints from extinction data.

1. Run ExtinctionSuite v4.1.5+

2. Mode Selection

3. Module Selection

4. Choose Base Folder

5. AnalysisPrimary
          analysis options

Created by Lukas Payne, 18/09/2021, edited 19/09/2021 WL.