Analyzing in MatLab

Trace_D1_210_v*_turbo.m is used to extract all traces. Run this m-file for each data file in your directory, before proceeding to Analysis.

You need to use the correct exposure time (most likely 100 ms, check your lab journal). You might want to choose a maximum display value of 600.

Analysis_D1_210_turbo_less is used to select traces and calculate the dwelltime of the full trace. Run it after all traces for all data files in that folder are extracted.

More details are found below.

Analyzing with ‘Analysis*.m’

In analysis you are going to select good or bad traces. Let's first look at how to select this.

Ideally only one of the ends (Cy3 and Cy5) transmits light. So the trace should be anti-correlated over time.

Below is an example with a trace that shows an anti-correlated signal.

Figure 2: This is an example of a good trace. You can clearly see it is anti-correlated. For further analyzing this trace, you need to press ‘s’ and enter.

All traces are automatically saved and can be later on discarded by Analysis_D1_210_turbo_less.

Here will be some examples of unclear traces.

Figure 3: Here you can clearly see that the one is switching, but the other one is not. Here is probably only the donor (Cy3) active in the graph. The acceptor is not active in this graph. It is not recommended to use this for further analysis of the signal.

Figure 4: In this graph it might look like only the donor is active. But if you look closely these are correlated. Most probably there was some ‘junk’ floating around.

Figure 5: In this trace there is no clear sign of anti-correlation. This seems to be mostly noise. This trace is not useable.

Execute the script ‘Analysis_D1_210_turbo_less_v*.m’ and follow the instructions.

• • Press p+enter to do dwelltime analysis and continue to the next trace.

  • Press only enter to discard the trace and not use it for dwelltime analysis.

This will produce three files: “dwelltime_down.dat” , “dwelltime_up.dat” and "selected.dat."

Note: if you get multiple traces with lots of noise & low signal, you might want to focus on the traces with higher intensity, and by default discard the lower intensity traces: