Runtime

This section covers run modes, persistence in the Flow Plot, tank/block naming prompts, and log files.

Controlling an Experiment

Runtime Modes

The control buttons allow the user to run or halt the experiment. They are enabled or disabled (grayed out) based on the available choices.

Mode	Description
Idle	Devices are not loaded and are not running.
Preview	Data is saved to a temporary block in the tank. Users can examine data in the Flow Plot. This allows users to modify parameter values before starting the experiment. Data is deleted when switching to Idle mode.
Record	Devices are loaded and running and data is saved to the tank. The Experiment and Subject must be configured before the Record button becomes active.
Standby	Disabled by default and enabled in the Synapse Preferences. In this mode devices are loaded and running but signals are not being acquired and saved to disk. Persistence values changed in Standby mode are saved to the database.

Flow Plot

Runtime Window

The Flow Plot window is automatically displayed in Preview and Record modes for fast, easy visualization of data.

The Flow Plot Tab

The primary plot includes a default plot configuration for each type of data being recorded. Users can adjust the plot settings to refine the display. The example plot above shows a subplot labeled LFP1 that displays 16 channels of streamed biological data using the Neural Stream Processor gizmo.

Other Tabs

Many gizmos add a tab to the tabbed window. The added tab contains runtime control features such as threshold and filtering controls.

Working with Tabs

Tabs can be floated, split, and merged back into the tab framework. Click and drag a tab to float and reposition the window. Right-click a tab then select an option on the shortcut menu to split the main window.

PCA Spike Sorting and Neural Stream Processor Interfaces

Persistence

Any changes to the run-time settings are saved with the Experiment and Subject in the Synapse database. This allows you to The Persistence options on the left toolbar determine how these run-time parameters are saved and reloaded.

Mode	Description
Lock	Locks the currently selected persistence. Otherwise the persistence selection always returns to Best when the experiment ends.
Best	Uses the last settings of any runtime controls for the current experiment and user/subject
Last	Use the last settings from the previous recording, regardless of subject or experiment. This is useful if you are using the same subject with a new experiment. For example, if you have PCA space sorting parameters defined for the subject and want to use them in a different experiment.
Fresh	Don't load any persistence, use the default experiment settings instead
User	Launch the History window. Right-click on a previous recording and choose "Use starting state" or "Use ending state", or right-click in the Changes list at the bottom to select a subset of changes from that recording to use for the next recording.
RT Layout	Choose the window layout configuration. See Layout Persistence below.

Layout Persistence

Information about the window layout and Flow Plot settings (scale factors, plot positioning, etc) is specific to the User and is separate from experiment persistence information. Options are accessible in the RT Layout button. You must have a named User for the layout to be saved.

Layout Persistence Dialog

Option	Description
Clear all to Default	Reset everything to the default layout and Flow Plot configuration scaling
Import from Another Experiment	Choose a previous User and Experiment combination from the Synapse database to load the layout from
Import from Old Run	Load the layout from a previous recording. This uses the block folder directly from disk and does not need the Synapse database for this.
Setup Flow Plots	Configure the ordering of the stores for the current experiment within the Flow Plot. This option also lets you split out different stores to entirely different Flow Plot tabs. This is useful for organizing the layout, particularly when doing multi-subject recordings. Right-click + drag a store name to another plot to make a copy.

Multi-Subject Example Layout

During run-time, the RT Layout button turns into an FP Setup button, which allows you to edit the location of the stores within the Flow Plot(s) and to hide them altogether.

A toolbar at the top of the Flow Plot allows the user to control plot animation.

The toolbar contains the following commands:

Icon	Description
	Play
	Pause
	Scroll back by plot window width (e.g. if span is set to 60 seconds, this button will scroll back in 60 second chunks)
	Scroll back (increments of span/10)
	Scroll forward (increments of span/10)
	Scroll forward by plot window width
	Auto Scale all plots
	Data Monitor Setup (launch dialog)
	Refresh

Additional commands for scaling and shifting plots are available from a right- click shortcut menu on the Store name in the plot.

Shortcut	Description
Auto Scale	Scale the display so that it best fits in the available subplot area.
Scale Up/Down	Incrementally scales the display up or down.
No Shift	Resets the y-axis center to 0.
Shift Up/Down	Shifts the display up or down in the subplot window.
Make larger/smaller	Makes the available subplot area larger or smaller. The other plots are resized accordingly.

Plot Display Options

Users can change the plot type, modify the number of channels viewed, and choose to color traces by channel or sort code in the Display Options dialog.

To modify the display options:

Double-click the left side of the desired subplot, where the store name is displayed

Data Monitor Setup

Users can change settings related to the time span and tracking of the plot window in the Data Monitor Setup window.

Click the Data Monitor button on the plot toolbar to view data monitor settings for the plot.

Setting	Description
Time Span Control
Span	Set the time span (sec) of the plot window.
History	Determine how much plot history will be available to view. Note how the memory requirements change as these settings are adjusted.
Tracking Mode
Reference Epoch	If a reference epoch is selected, the left side of the Plot window will always coincide with the start of the reference epoch event.
Time Axis Overlap	Set the amount of the time axis that is repeated when the plot rolls over. For example, if the span is 10 seconds and Time Axis Overlap is set to 50%, the plot will show seconds 0-10, 5-15 etc.
Time Display Mode	Set the display units of the time axis.
More Settings	Press Shift + Ctrl and double-click the dialog box to display additional settings for the plot appearance, such as background color and labels.