Embedded Files
Basic time trace analysis tools only require emission periods to be defined.
This is done automatically for multispot (non-ALEX) data files, but requires an intermediate action for us-ALEX files (period definition in the us Alternation Period page) or ns-ALEX files (period definition in the Nanotime Display page).
Advanced functionalities (such as background or other corrections, burst identification, etc.) require other analysis steps to be performed before they become available. We will discuss them in a separate section below.
1. Basic functions
1.1 Time Trace Definitions
The time trace analysis tool allows representing different functions of the photon streams as binned time traces. The simplest type of function is an intensity, such as Donor or Acceptor. Functions of interest are added to the Time Trace Definitions array (red box labeled "1." in the Figure below):
In this example, 3 photon stream intensities are visualized, the second one being represented as a negative quantity in order to allow its easy visualization in a kind of mirror view facing the other two time traces.
The time traces resolution is specified with the Time Bin control, whose unit can be changed by the user by typing a valid unit (s, ms, us, etc.).
1.2. Time Trace Playback
The time traces can be computed and displayed step-by-step or continuously in its totality by pressing the Step into Trace (>>) or the Play Time Trace (>) buttons, respectively (green box labeled "2." in the Figure above).
The # Photons/Step control to their left allows the user to define how many photons are read and processed at each step. Use a value of -1 to load all photons at once. This is needed if you want to use the time trace as part of a script.
In the Play Time Trace mode, it is possible to slow down the playback speed by checking the checkbox next to the Playback Delay gauge, and adjusting the value of the delay from 1 ms to 1 s per step. It is also possible to pause the playback by pressing on the Pause Time Trace button (||).
Note that the Stop Playback button (red square to the right) actually stops and clears the time trace, therefore use the Pause Time Trace button instead if your purpose is to temporarily pause playback.
Pressing on the Pause Time Trace button resumes playback.
During playback, or step-by-step computation, a progress bar appears below the playback controls, indicating the fraction of data file processed at a given time.
The Window Width control (below the time axis, indicating 100 ms in the Figure above) can be used to set the size of the time trace window represented within the graph's bounds. It is also possible to zoom (graph control tools at the bottom left of the graph) or define the window bounds directly by entering their values on the time axis. The scrollbar allows moving back and forth through the time trace.
An important fact to keep in mind is that the graph is limited to 10^6 data points per time trace.
If the duration of the file is larger than 10^6 times the Time Bin, the beginning of the time trace will be lost.
1.3. Time Trace Display Styles
Once the time traces start to be displayed, their style can be modified in the graph legend. As for other histograms, time trace bin abscissa represents the lower (left) bound of each bin. Therefore, the only appropriate time trace style is that shown in the Figure below:
1.4. Time Trace Histograms
It is possible to build an histogram of a given time trace by right-clicking on its name and selecting on of the options in the Histogram.submenu:
The first option will result in an histogram encompassing all bins in the time trace, while the other two categories will only keep bins which correspond to (i) bursts or selected bursts and (ii) remaining bins after the previous two selections. For instance, NOT Burst Bins Histogram will build the histogram of bin values corresponding to every bin in the time trace that does not overlap with a burst.
A dialog window pops-up, asking the user to specify the bin size. The resulting histogram is displayed in the Histogram Window (which is opened if it wasn't already). Note that the data can be rebinned and inverted later on in this latter window.
1.5. Other Functionalities
The Align with us ALEX Period checkbox forces time trace bins to start at multiples of the us ALEX period. This is useful mostly for Time Bin values which are comparable to (and multiple of) the alternation period.
The ALEX Corrections checkbox applies ALEX corrections to the photon statistics used to compute the different time traces.
2. Advanced Functions
A number of functionality of the time trace analysis tools require some additional processing to be performed.
2.1. Background corrections
When background rates have been computed in the Background Analysis page, checking the Background Corrections checkbox applies this correction to the time trace quantities. Note that currently, time-dependent background correction is not supported in time traces.
2.2. Bursts Time Traces
Once a burst search has been performed, the Bursts time trace provides information on the location of detected bursts as shown below (vertical gray bars across the graph). The Bursts time trace is binned with the specified resolution (which might be larger than most burst duration) and counts the number of detected bursts during each time bin. The vertical axis used to represent this time trace is fixed to [0, 1], which means that, as long as the number of bursts within a bin is larger or equal to 1, a gray bar appears. However, there could be a very short burst, or many short bursts, or this bin could be part of a long burst covering successive bins in the time trace. The # Bursts indicator at the bottom right of the Graph indicate how many bursts are located in the bin pointed at with the mouse (i.e. at Cursor Location (s)).
If some Burst Analysis has been performed in the Burst Analysis page, "constrained bursts" (i.e. bursts meeting a set of specified constraints) will be defined. Checking the Constrained Bursts checkbox shown above will specify the Selected Bursts time trace to display (in black in the example shown above) the time bins in which one or more such bursts are present. Like for the Bursts time trace, the Selected Bursts time trace counts bursts but is represented between 0 and 1, resulting in a vertical bar crossing the graph wherever there are bursts meeting the specified constraints.
If ALEX Analysis has been performed in the ALEX Analysis page and a set of bursts have been selected in the ALEX Histogram, checking the ALEX-selected Bursts checkbox will specify the Selected Bursts time trace to display the time bins in which one or more such bursts are present. The two previous checkboxes can be combined with obvious results.
2.3. Additional Time Traces
to be added
3. Burst Inspector
When burst time traces are available, opening the Burst Inspector window (see the corresponding manual page in the ALiX Windows section) allows obtaining information on individual burst statistics.
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