Introduction

Starting the application

The goal of this program is analysing intensity measurements obtained from time series of fusion events. Data should be collected in a single Excel file for easy importing of multiple cells. Starting the aplication can be done by running the main_FA2.m file. Please make sure that the main application folder is added to the Matlab path, as well as the dependencies folder. See the quick start page for a quick introduction on how to import, process and export the data.

Main interface

After starting the main interface it will show the interface with some controls inactivated and ready for loading data. After loading the data and performing the detection, all controls are active and allow for reviewing parameters and detection.

Main dialog (empty)
Figure 1: Main dialog after loading and detection

Highlighted are the menu and tool bar, the condition and cell navigation, the plot type, the results table and plots.

Menu bar

The menu has many functions that allow for reviewing the data and generating plots. The File menu allows you to load data, and save a session file after importing data, as well as exporting data to different output formats (see the output documentation). The Edit menu allows you to remove all data, the current cell or the current site. If data is loaded, you can add non-releasing cells or relabel cell conditions. There is also an option to relabel outliers, which will move them to a new group. You can also adjust the detection and classification settings via the preferences option (see the preferences documentation). The Analysis menu allows for exploring the detection settings, as well as performing the detection and classification (see the algorithms documentation). The Plots menu is available after detection has been completed, and allows you to plot several parameters in different plot styles (see the plotting documentation). The Help menu shows this documentation, as well as an about dialog with the version information of the software and data container. It also has the template creator function, which allows the creation of a suitable Excel file for data import (see the protocol information).

Tool bar

The tool bar contains controls for viewing and navigating the sites, as well as viewing the plots.

Tool bar buttons
Figure 2: The tool bar buttons, with buttons for loading, viewing, navigation, plotting and help

It contains buttons in 5 groups, separated by dividers. The first group contains buttons for (from left to right): loading data, Save and Save As. The second group contains buttons to activate tools specific for plots: zooming in and out, panning, data tip and switching the legend on and off. The third group contains the controls for moving to the first, previous, next and last site within a cell. Navigation of events can also be done by using the left and right arrow keys on the keyboard. Switching between cells within a group can be accomplished by using page down (PgDn) and page up (PgUp) to go to the next or previous cell, respectively. The keyboard navigation does not loop around: if the last event is displayed, pressing the right arrow key will have no effect. The same holds for the cell navigation using the page up and down keys. The fourth group contains the buttons for showing the explore detection interface, and buttons for exporting data. Finally, the fifth group contains a button for the settings, the log viewer and the documentation (this file).


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Condition and cell navigation

When data is loaded, it is grouped according to the condition in the sheetname. Please note that the condition label is case-sensitive, meaning that WT and Wt are different conditions. The condition popup allows the user to select the current condition, with the associated cells that belong to that condition. If you wish to modify the condition label in order to correct typos, select Edit | Relabel conditions from the menu. The cell popup menu in the main interface allows the user to select a sheet containing the data from that cell. Doing so will update the plots and the table.

Main plots

The 2 plots show the traces selected in the plot type panel; for single color data, the pHluorin option is the only available option. For dual color data, the default option is both channels, with the pHluorin channel in green and the mCherry channel in red. The title of the plot indicates the site number and name (in brackets), and the localization after the colon. Fusion events are indicated in the pHluorin channel using colored traingles: a right-pointing one for the onset and a left-pointing one for the end of an event. For dual color data, the loss of cargo in the mCherry signal is indicated by an open circle. If field stimulation was used, then the stimulation period is indicated by blue bars, while the ammonium period is indicated by a green patch. The bottom plot shows a detail of the currently selected fusion event, and can be used to manually adjust the start and end point of the event.

Results table

The results table shows a quick overview of the results from the current cell. The first 4 rows contain summary data for this cell. when clicking on a row in the table that belongs to a specific site, the plots for that site will be shown. It is also possible to remove an event from a cell by unchecking the box in the Keep? column. To add the event back into the data set, check the box for that event to re-enable it. To hide all deselected events, uncheck the Show all events? checkbox. The Sort Event button on the top of the table will cluster the traces in three blocks: the undetected ones on top, the slow detected ones as second and the standard detected ones as last block.

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