.. _alligator-lifetime-and-other-parameters-panel: Lifetime & Other Parameters Panel ================================= Introduction ++++++++++++ This panel contains the *Lifetime & Other Parameters* graph which receives plots from several ``Analysis`` main menu functions, *Phasor Graph* right-click menu functions as well as plots sent by *Decay Fit Parameters Map* right-click menu functions. The plots therefore may have different meaning and sizes. To account for this diversity, the graph has two vertical axes. The left axis (*Lifetime (ns)*) corresponds to lifetime (or in general time) values, while the right axis (*Other Parameters*) is typically used to plot NLSF parameters. The horizontal axis might take on a different name depending on context (for instance ``Time (s)`` for a time series analysis, or ``Intensity`` when plotting a *Lifetime vs Intensity* plot). Axes labels can be edited in the *Scale Legend* box (between the *Graph Palette* and *Cursor Legend* in the figure below) and have only a visual aid function. Each plot can be associated to either one of the two vertical axes by right-clicking on the plot icon in the graph legend and navigating down to the ``Y Scale`` menu: .. image:: images/AlliGator-Lifetime-Graph-Y-Axis-Selection.png :align: center and selecting the relevant axis. Plots that "don't look right" might just be associated with the wrong Y axis. The following is a list of possible plots that will be sent to this panel. Average lifetime ---------------- As discussed in the :ref:`Phasor Ratio panel ` manual page, computation of a phasor ratio is generally accompanied by the calculation of the corresponding average lifetime, based on the formulas in the introduction to phasor ratio references in the :ref:`Phasor Graph panel ` manual page. Decay fit parameters -------------------- As discussed in the :ref:`Fluorescence Decay Fitting ` manual page, it is possible to have the different parameters of a series of fits output sent as separate plots (one plot per selected parameter). These plots are sent to the *Lifetime & Other Parameters* graph. Decay shifts ------------ When decays are aligned with respect to a *Reference Decay* as part of a decay preprocessing step, the corresponding computed temporal shifts are stored in memory. The corresponding series of shifts can be represented as a plot using the ``Plot Decay Shifts`` right-click menu item of the *Lifetime & Other Parameters* graph. Lifetime & Other Parameters graph context menu +++++++++++++++++++++++++++++++++++++++++++++++ The *Lifetime & Other Parameters* graph has some specific context menu items described next: .. image:: images/AlliGator-Lifetime-Graph-Menu.png :align: center . - ``Transpose Plot``: the ``Plot Histogram`` menu item described later only works on the vertical coordinate. In order to histogram the horizontal coordinate of a scatterplot, it is therefore necessary to transpose that plot using this function. - ``Pair Selected Plot``: when two plots have the same abscissa array, they can be written :math:`{(x_i, y_i)}_{i = 1,..,n}` and :math:`{(x_i, g_i)}_{i = 1,..,n}`. Pairing these two plots consists in building the following plot: :math:`{(y_i, g_i)}_{i = 1,..,n}`. - ``Merge Selected Plots``: appends several plots to one another to form a larger plot containing all their data. - ``Plot Histogram``: builds an histogram of the selected plot (with user-defined options described next). This opens the **Histogram** window (described in the :ref:`corresponding page ` of the manual, where a number of further analyses can be carried out. The histogram options dialog is shown below: .. image:: images/AlliGator-Lifetime-Graph-Histogram-Options-Dialog.png :align: center . + The histogram is defined by its *Bin Number* or *Bin Size*, depending on the radio button selection on the right. The corresponding parameter needs to be specified on the left. + Optionally, the *Min Value* and/or *Max Value* to be included in the analysis can be specified (by default, these parameters are set to -Inf and +Inf, meaning that all values are histogrammed). + Pathological values can be rejected before building the histogram (*Filter NaN & Infinite Values* option). + The histogram can be normalized to a sum of 1, making in a *Frequency Plot* if that option is selected. + The histogram can be represented *Left*-aligned, *Centered* or *Right*-aligned depending on the selected *Bin Location* option. + The bins can be "aligned" (*Align Bins* checkbox), that is, the bin boundaries are multiples of the *Bin Size* (either the entered one, or the calculated one). + The maximum number of bin can be limited to the *Max Histogram Size* to avoid cases where the Min and Max values and bin size result in a huge number of (mostly empty) bins, letting AlliGator run out of memory. + Values outside the Min and Max Values can be included in the first and last bin of the histogram if the *Project Outside Values* option is selected. + An option to compute *Intensity-Weighted Histogram* can be checked off to fill each bin with the associated pixel/ROI intensity value rather than 1. + In order to compare intensity-weighted histograms with unweighted ones, the option to compute a *Normalized Weighted Histogram* can be checked off. The corresponding histogram is normalized such that the sum of all its bins is equal to that of the unweighted histogram. - ``Compute Sliced Mean, SDV & CV Plots``: this function allows computing the mean, standard deviation (SDV) and coefficient of variation (CV) of a plot by "slice". Slices correspond to subsets of the plot's data defined by fixed ranges of the abscissa values. The function requires input from the user, provided in the **Sliced Mean, SDV & CV Options** window: .. image:: images/AlliGator-Sliced-Mean-SDV-Options-Dialog.png :align: center . - The slices are defined by: + the first and last values of the abscissa considered (*Axis Start* and *Axis Stop*), which can be manually entered or automatically set to the data minimum and maximum values if the *Use Data Min/Max* checkbox is checked off. + the number of slices (*# Steps*), their "width" (*Step Size*) or their content (*# Elements*) depending on the radio button selection. The corresponding parameter to the left needs to be provided by the user. + within the data in each slice, the data *Lower* and *Upper Percentile* retained in the analysis (allowing to reject outliers). Enter *100* and *0* respectively to keep all data. + *Min # Data Points/Slice*: the minimum number of data points in a slice to compute the mean and SDV (a low number results in more statistical uncertainty). + the *Bin Location* (*Left*, *Center*, *Mean*, *Right*) defines each bin's abscissa: either the bin's lower bound, its center, the mean of all data in the bin or the bin's upper bound. + If the *Output Abscissa Statistics Plots* checkbox is unchecked, the only plots created are the *Mean*, *Standard Deviation* and *# Points* plots as a function of the slice *Start* value. If the checkbox is checked off, two additional plots are output: the *Mean* and *Standard Deviation* of the abscissa values in the slice. + If the *Bootstrap CV's SDV* checkbox is checked off, the *# Replicas* parameter is shown, which allows estimating the standard deviation of the CV of each slice by bootstrapping the sliced data. A reasonable number of replicas is the number of bin elements. (last updated: 2024-09-09)