Designtime Reference

When you launch Synapse, you see a streamlined user-interface that automates all but the highest level set-up tasks for you. This is the designtime interface where you can make choices about things like what type of data to collect and what threshold, sorting, or other processing tasks to include in your experiment.

The Synapse Designtime Window

The window is divided into three areas:

1. The Command Bar contains the most often used elements of Synapse.

2. The Processing Tree displays a graphical representation of your experiment.

3. The Details Area displays setting and configuration options at designtime or plotting and control windows at runtime.

At each step of the design process, Synapse uses information about your hardware and selections you've already made to show only the relevant choices. Once added, you can review and modify the settings in the details area. Often, you won't need to make any changes at all. While Synapse supports drilling down to every detail of how the system works, it has also been designed to make that unnecessary for most Synapse users.

The Processing Tree

The Processing Tree is both a graphical representation of the processing tasks that make up your experiment and a design tool. The tasks added to the tree along with how they are ordered and connected forms the processing instructions that will be loaded to the hardware at runtime. Each tree can have many parts or branches.

Devices with input/output functionality form the trunk of the tree. They represent the starting point (or potential starting point) for a branch.
RZ devices appear in the Processing Tree to represent their front panel analog or digital inputs.
Acquired biological signals are often input by a PZ amplifier, so it also appears on the trunk of the tree.

Important

If an input/output device does not show up automatically in the Processing Tree, you will need to edit the rig. See The Rig.

Tasks, such as filtering, signal processing, and data storage form the branches of the tree diagram. They are added to the device that will be used to input or output the signals associated with a particular task.

Click the triangle/arrow to expand or collapse a branch.

Biological signals are typically acquired on a PZ amplifier; so neural processes, like spike detection, are added to the PZ in the tree.

Multiple tasks can be added to any branch, in parallel or one after another with tasks ordered logically.

Mouse over a device to see how the hardware devices are connected.

Context Sensitive Hardware Connection Tip

Using the Processing Tree

The Processing Tree is a simplified view of the experiment. The specifics can be more closely examined in the details area. When an item is selected in the tree, the details area is divided into three sub-areas: the Processing Strip, the Gizmos list, and the Options area.

The information displayed in these three subareas is specific to the selected item or branch:

1. The Processing Strip - displays a drilled down look at the corresponding branch of a signal or data path, following the first inputs of each gizmo in the path.

2. The Gizmos list - displays tasks that can be added to the selected item

3. The Options area - displays configuration options for the selected item

Synapse Designtime Window

Selecting a hardware device in the Processing Tree updates the Gizmos list to show only the tasks appropriate for that device and displays configuration information for the device in the Options area. This information is saved as part of the experiment and is also referred to as a HAL (Hardware Abstraction Layer) because it gives Synapse everything it needs to manage the hardware- related low level programming tasks.

Similarly, selecting a gizmo in the tree displays the settings for the gizmo, typically arranged on tabs in the Options area.

Designtime Window with the Neu1 Gizmo Options Displayed

To reset a device or gizmo:

• Right-click the corresponding icon in the Processing Tree and click Reset to Default on the shortcut menu.

To add a previously unused HAL:

• Right-click a related icon in the Processing Tree and click Add HAL on the shortcut menu.

  This option allows you to add a HAL for a device that is present in your Rig, but previously not in use in the experiment. By adding the HAL directly in the Processing Tree, you avoid returning to the Rig Editor which resets all of your device HALs.

The Gizmos List

Only gizmos that can connect to the currently selected object in the Processing Tree are shown. Select a different item in the Processing Tree and different gizmos will be displayed.

The gizmos are grouped by task type, such as storage or signal conditioning. For the full list of categories and descriptions, see the Gizmo Categories Reference.

Double-click a gizmo to add it to the selected item in the Processing Tree.

Gizmos in the list are like menu choices, they can be added to the Processing Tree more than once and for more then one input/output source.

The Options Area

Name/Source/Block Diagram

The top section of the options area differs slightly depending the device or gizmo selected. It typically displays an editable device or gizmo icon and name. It may also display the Primary Source for the device or gizmo and the Block Diagram toggle button.

The Gizmo Name

The gizmo name is generated automatically for you and is based on the type of gizmo selected. If needed, click the Edit icon to modify the name. The name must be at least three letters long and the first three letters are used to form the Storage ID for any related data stores in the data tank. The field turns red if the minimum three letters are not included.

Important

Changing the name of a gizmo that includes data storage will change the name(s) of the storage ID(s) in the data tank. Synapse will display a warning dialog box the first time you attempt to do this. For sanity, changing the store name after you have started collecting data with the experiment is not recommended.

Run-time Persistence

When Run-time Persistence is turned off for a gizmo, the persistence (for that gizmo only) is always 'Fresh', meaning the designtime settings are always loaded when the recording begins. It overrules whatever the global persistence is set to.

If this box is checked, the gizmo follows the global persistence rules.

The Block Diagram Button

The Block Diagram button provides access to source settings and the block diagram. See the Gizmo Reference for more information.

The Feedback Button

Send TDT feedback on Synapse, this gizmo, or anything else you want to let us know about.

The Help Button

Opens the Synapse Manual to the current gizmo to learn more about it. By default it opens the online manual in a web browser. If internet is unavailable it opens the local PDF in C:\TDT\TDTHelp.

Global Options Buttons

Located below the options tabs and applied across all tabs.

1. Delete button - Delete the gizmo from the Processing Tree.

2. Revert button - Return to the last saved or 'committed' state. You can also use Shift + F7 keyboard shortcut to revert.

3. Commit button - Save changes on all tabs. You can also use F7 on the keyboard to force a Commit.

Experiment Changes and the Revision Log

In Synapse, the experiment is saved each time you make or "Commit" a change. If you need to roll back a change in the experiment design, you can do so in the Experiments Revision Log.

Experiment Revisions Log

You can sort the information by clicking a column header. When you find the version you need, select it and click the Revert button. Use the Show Detailed Changes checkbox to add a details column with a description of the changes that were made in that revision.

If you are continually making changes but want to revert back to a specific version, check the Stable checkbox to flag a particular version you often revert back to. This is a visual indicator for your record only.

Opening the Revision Log

If you have the experiment open and it has a revision history, a "Revision Log" command is added to the Experiment Button menu.

If the experiment is not open:

1. Click the Experiment Button and More.

2. In the Experiment Selection Window, right-click the experiment icon and click Revision Log.

   Experiment Selection Window with Experiment Shortcut Menu Shown

The Connections Diagram

The Connections diagram provides a top-level view of experiment design. The diagram is available from the Menu or the Connections button, and can be printed.

Each node shows available inputs and outputs. The color of arrowheads on the connection arrows indicates the data type (such as logic or floating point). The arrows are also labeled with the channel range for any multi-channel signals.

Common data types include:

floating point type

integer type

logical type

The diagram also functions as a debugging tool. You can double-click a node to jump to the selected gizmo or HAL and make changes.

Connections Diagram

In the diagram above, a logic signal from the RZ2 triggers electrical stimulation. A single channel, floating point signal is passed from the stimulation gizmo to an injector gizmo where it becomes a 16 channel data stream routed to the IZ2 HAL. The diagram also shows data acquired from a PZ5 is passed to two different gizmos for parallel processing.

The Gizmo Slides Window

The Gizmo Slides Window provides a top-level view of the currently selected gizmo. The slides window is available by clicking the '?' button above the Processing Tree.

Each gizmo has a set of slides that show common use cases, example connection diagrams, common inputs and outputs, an overview of the user interface, and more.

When you select a new gizmo, the slides for that gizmo are shown. This is helpful when you are getting to know the user interface and what all the gizmos do.

Gizmo Slide Legend

The Processing Strip

The Processing Strip can be shown as part of the Synapse main window using the Preferences dialog (see Synapse Preferences. It displays a branch of the signal or data path, from the signal source to the item selected in the Processing Tree. The primary purpose of the Processing Strip is to provide information about the signal path at a glance.

The Processing Strip

The number of channels in the signal stream are displayed beneath the gray line representing the signal path. The number shown is the number of channels in the signal at the output of the device or gizmo to the left. In the illustration above, the number of channels at the output of the Map1 gizmo is 16. The number of signals fed into the process was 32, so the illustration shows that the number of channels mapped and passed through does not include all channels.

The numbers below a gizmo display the first channel number in the signal and the number of channels in the signal, that is {first channel:number of channels}. Many gizmos allow the user to change the channel range. This makes it possible to split up a multi-channel signal into several different branches so they may be processed differently.

Menu and Command Bar

Main Menu

Click Menu to display.

Command	Description
Preferences	Launch the Preferences dialog
Edit Rig	Auto-detect hardware or configure devices manually
Clear Session	Clear all experiment settings and return to the default state
Log Window	Open the Log window
Connections	Open the Connections dialog
Notes	See the Notes for the currently selected User, Subject, or Experiment
History	Open the History dialog of past recordings
Clean Storage	Clear database records from old Preview recordings or Empty Data Tank folders that have no blocks in them
Help	Launch the software manual (PDF)
About	View version number and copyright, and update Synapse
Licensing	Activate / de-activate gizmo packages
Exit	Close the program; will prompt to save open experiments
Window>Flow Plot Setup	Set up the flow plot
Window>Merge All	Reset all tabs at run-time to default layout
Window>Show/Hide	Show/Hide specific tabs at run-time

Categories

Click corresponding button to display. Menu options are available in IDLE mode only, unless otherwise specified.

Category	Option	Description
	User Names	Select a user name from the list
	New	Launch a User dialog box to add a new user profile
	Logs	Open a memo dialog box
	More....	Launch the User window where you can choose an existing user or launch the User dialog box to create a new one
	Experiment Names	Select an experiment from the list
	Undo	Return to the state before the last change
	Redo	Redo last action that was undone
	Locked	Locks the current experiment so that no accidental changes can be made to it
	Save As	Launch the Experiment dialog box, where you save the experiment with a name, description, and icon
	Import Experiment	Select a *.synexpz experiment file to import and load
	Export Experiment	Export the experiment along with last persistence and supporting files, such as parameter, stimulation, and map files
	Logs	Open a memo dialog box
	New	Launch the Experiment dialog, where you can create a new experiment
	Revision Log	Open an experiment specific history of changes that can also be used to return to an earlier version of the experiment
	More....	Launch the Experiment window where you can choose an existing experiment or launch the Experiment dialog box to create a new one
	Subject Names	Select a subject name from the list
	New	Launch the Subject dialog, where you can create a new subject
	Logs	Open a memo dialog box
	More....	Launch the Subject window where you can choose an existing subject or launch the Subject dialog box to create a new subject
		Displays current tank and block names. Experiment and subject are used to generate the names according to hierarchy set in the Synapse Preferences. Main label is the string appended to the tank name, sub label is the string appended to the block name

Templates

Templates are experiment files that have been created by TDT. Each template is a basic working experiment that can be run as configured, but you will more likely begin with the template and modify it to meet your needs. Templates have been designed to work with rigs suitable for the type of experiment. When opened, Synapse will attempt to adapt the configuration to your hardware rig and alert you to any conflicts it is unable to resolve automatically.

Synapse Preferences

To view the Synapse Preference dialog:

• Click Menu at the top of the bar and then click Preferences.

General

Preferences Dialog, General Tab

Option	Description
User Login	Choose a user tracking method. For Required, a User must be selected to start a recording. For Required with Password, each user must log in with a password. This is only for organizational purposes and is not a secure method of creating privacy.
Experiments	Select check box to make experiments private per user
Subject	Select check box to make subjects private per user
Date Format	Choose a date format: MM/dd/yyyy, dd/MM/yyyy, or yyyy/MM/dd
Time Format	Choose a time format: h:mm:ss a or hh:mm:ss
Standby Mode	Enable Standby option at runtime. This mode loads the circuits and starts them but does not send the global trigger to begin acquisition. This mode is useful if loading memory buffers through SynapseAPI; it gives the system enough time to load the buffers before starting the recording.
Processing Strip	Show in the main Synapse window
Synapse Server	Add Synapse Server button in gizmo options so that SynapseAPI parameters and syntax can be displayed. Requires a Synapse restart. See the SynapseAPI Manual for more information.
Deprecated Gizmos	LFP Processor gizmo has been replaced with Neural Stream Processor. The Electrical Stimulation gizmo had a major upgrade to the Electrical Stim Driver gizmo. Check this box to show the old gizmos in the gizmo list.
Unlicensed Gizmos	After the trial period expires, gizmos that aren't licensed won't be shown in the gizmo list. Check this box to show the unlicensed gizmos in the gizmo list. See Licensing for more information.
New Exp Behavior	When creating a new experiment, choose whether to keep the existing hardware settings (for example, the enabled IO on the RZ processor, or the LUX configuration on the RZ10 processor), use a fresh state, or Prompt the user for this choice.
Python Directory	When using the Pynapse gizmo, this option stores the default location of your Python installation and the default Python environment to use for Pynapse. See Pynapse Manual for more information.

Data Saving

Preferences Dialog, Data Saving Tab

Option	Description
Hierarchy	Choose how tanks and blocks are associated and named. Experiments with Subjects - Experiments are the primary category under which data is stored. Subjects with Experiments - Subjects are the primary category under which data is stored.
Tank Naming	Choose how tanks are named. Auto - Tanks are named automatically based on preferences. New Tank Each Day - A new tank is created automatically each day. When NOT selected, the same tank is used until the user chooses to create or select a new tank. Note: When using New Tank Each Day, instead of including both data and time, Tank names include the date and Block names include the start time.
Path to Tanks	Enter or browse to choose a folder where tanks will be stored.
Block Naming	Choose how blocks are named. Auto - Blocks are named automatically based on preferences. Prompt - User is prompted to name each new block.

Run-time Ops

Preferences, Run-time Ops Tab

Option	Description
Runtime Window Layout	Save a unique window layout for each user
Data Strobe Rate	Choose how often data is saved to the tank and made available for plotting
Data Read Limit	Choose how much of the server resources are allocated to reading/storing data compared to distributing data to user interfaces. Increase this value if you are getting zBus limited readback warnings
Image Strobe Rate	Choose how often plots are visually updated
Scroll Memory Limit	Choose the maximum amount of memory available to the the main data plot time span and history
Smooth Scrolling	Enable Smooth Scrolling to improve the look of the Data Plot. Note that this adds a 1 second delay between when the data occurs and when it is shown in the Data Plot.
Sorting Widgets...	Choose how often the sort settings are logged into the database. Increasing this value reduces the amount of non-event related change data is recorded while setting up the sort codes.
Prune Persistence...	Removes persistence settings associated with gizmos that have been deleted from the Processing Tree. Also removes the persistence for channels in a sorting gizmo that are no longer used, for example when the channel count is reduced.
Keep Persistence...	When a gizmo name changes, you typically don't want to reset the persistence for that gizmo. Keep this set to Yes.

Cluster Ops

Preferences Dialog, Cluster Ops Tab

These settings are only used in Cluster Processing mode and are not available in Synapse Lite. See Cluster Preferences for more information.

Advanced

Preferences Dialog, Advanced Tab

Option	Description
Compiler Passes	Set the number of attempts the compiler makes to compile the experiment. More passes may be required for larger and more complex experiments.
Compiler Optimizer	When checked, Synapse will remove any unused DSP components during compilation. Compilation will take longer, but this may be required for complex experiments to run on the current rig.
Runtime Errors Before Halt	Set the number of reported errors that can occur before Synapse switches to Idle mode. The count is reset each time Synapse is switched to Record mode.
Tank Engine Cache Delay	The size of the temporary memory buffers. Although a higher setting requires more system RAM, it makes data storage errors less likely.
Persistence Load Delay	Choose the amount of time allowed when switching from Standby to Preview. This ensures all the persistence settings are loaded onto the hardware before the experiment starts. Useful for more complex experiments.
Record Start/Stop Synchronization	Waits for all peripheral devices to be ready before beginning acquisition. Particularly useful for synchronizing the iV1/iV2 Video Capture Interface frame acquisition to the onset of the recording.

Corpus

Preferences Dialog, Corpus Tab

Option	Description
Worker Threads	Set the number of CPU threads allocated to Corpus. If you have any issues getting Corpus to run, try setting this to 1 Thread.
Thread Priority	Set the priority for the Corpus application relative to other applications running on your PC, e.g. Synapse, MATLAB
Lab Rat I/O Delay	Determines the duration of the event loop running on Corpus and the round-trip delay between Corpus and the Lab Rat