.. _alligator-fluorescence-decay-panel: Fluorescence Decay Panel ======================== The **Fluorescence Decay** panel can be displayed using the pull-down list at the top-right of the main AlliGator window. In the example shown below, a point ROI was selected in the *Tool Palette* on the lefthand side of the *Source Image*, and a ROI decay analysis performed using the ``Analysis:Current ROI Analysis`` menu item (:kbd:`Ctrl+A`). While a Single Gate image is shown in the *Source Image*, the analysis encompasses all gate images, whose intensities at that selected pixels are represented as a decay curve (named ``M9_H00_019: Plot`` [#f1]_). .. image:: images/AlliGator-Fluorescence-Decay-Panel.png :align: center :width: 100% The *Decay Graph* is a feature-rich object which is comprised of different parts, some of which are common to all graph objects and are described in the :ref:`Graph Object Anatomy ` page. In particular, different types of contextual menus are accessible, depending on which area of the graph the user right-clicks: + :ref:`Plot Menu ` + :ref:`Decay Graph Custom Menu ` + :ref:`Cursor Legend Menu ` The first and last ones are similar for all graph objects and are described in detail in the :ref:`Graph Object Anatomy ` page. An overview of the *Decay Graph* custom menu is presented below, specific functionalities being described in other pages of the manual (linked to in the section below). .. _decay-graph-custom-menu: Decay Graph Custom Menu ----------------------- .. image:: images/Decay-Graph-Custom-Menu.png :align: center All items not highlighted in the image above are standard graph object contextual menu items and are described in the :ref:`Graph Object Anatomy ` page (:ref:`Custom Graph Menu ` section). This section will briefly discuss the highlighted submenus, whose functions are described in specific pages. + ``Process Plot(s)``: this menu, shown below, allows various types of plot transformations to be performed. The last category of operations are also available as *pre-processing* operations applied to each decay (before plotting in the *Decay Graph*, or other computations involving decays such as phasor calculation) and are discussed in the :ref:`Decay Preprocessing ` page. .. image:: images/Decay-Graph-Custom-Menu-Process-Plots.png :align: center The remaining ones are: + ``Fit``: this menu currently contains a single item, whose functionality is described in the :ref:`Decay Fitting ` page. .. image:: images/Decay-Graph-Fit-Menu.png :align: center + ``IRF/Reference Plot``: this menu allows defining the reference decay used either for temporal shifting or reconvolution of fit models when using the NLSF analysis features of AlliGator. .. image:: images/Decay-Graph-IRF-Reference-Decay-Menu.png :align: center + ``Export Decay to Phasor Graph``: this menu allows computing the phasor of a pre-computed decay and export the resulting phasor to the *Phasor Graph*. This is for instance useful to export a computed or recorded IRF to the *Phasor Graph* in order to subsequently use it as a calibration phasor. .. image:: images/Decay-Graph-Export-Plot-Phasor.png :align: center + Various Python Plugins: Python plugins menu items and submenus will appear at the bottom of the *Decay Graph* contextual menu. Their names and content will depend on each installation, but typically will contain some examples or default functionalities. .. rubric:: Notes .. [#f1] When the user-selected ROI has a name (that is, when it has been stored in the :ref:`alligator-source-image-roi-manager-window`), this name is appended to the image name, instead of the generic ``Plot`` suffix. A number is autimatically added to the decay name if the same ROI is used several times, or unnamed ROIs are used.