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This documentation is for a legacy ScanImage version. The current documentation is ScanImage 2019.
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Introduction


Stimulus groups are a special kind of ROI group that define a parametric path instead of a 3D volume. A stimulus group is comprised of multiple ROIs that define a continuous sequential laser path. Multiple groups can be defined and stored in the Photostimulation interface. Once the groups are defined, the Triggering Stimulus Patterns article describes how to go about commanding them.

Designing Stimulus Patterns


Stimulus groups allow complete freedom in designing the path for the laser to take. Best practices should be followed to ensure desired results. A stimulus pattern is comprised of a sequence of stimulus functions, each of which can be parameterized with position, size, rotation, laser power, number of repeats, parametric function, and custom parameters for the parametric function. The stimulus function can be chosen from a set of built in or custom stimulus functions.

A typical stimulus pattern begins with the laser at the parking position to minimize exposure of the sample to laser light (even with the pockels cell blanked). Time must be given to allow the laser to travel from the parking position to the first cell (or ROI) to stimulate. A parametric stimulus function can then be chosen for the given cell with parameters such as laser power and duration. Finally the laser should be returned to the parking position. A stimulus group to stimulate one cell would therefore have three ROIs:

  • Pause function
  • Stimulation function (ex: logspiral)
  • Park function

If it is desired to stimulate multiple ROIs in one pattern, a pause should be inserted between stimulations to allow transition time, IE:

  • Pause function
  • Logspiral function
  • Pause function
  • Logspiral function
  • Pause function
  • Logspiral function
  • Park function

The pauses between stimulations are important because the galvo's require time to travel between ROIs. Without the pauses (or if the pauses are too short), the pockels cell will be open while the galvo is still traveling to the desired ROI, causing light exposure to the wrong part of the sample. If too large of a change in position is commanded without adequate transit time, or if the stimulus pattern is too demanding of performance from the galvo's, the galvo controller may reset, causing a momentary loss of galvo position control. It is therefore important to carefully design the stimulus pattern to avoid this and test the pattern to make sure the results are desirable. The best way to test for desired results is using the monitoring and logging feature to verify proper response from the galvos.

Using the Stimulus Editor


To create stimulus groups, launch the Photostimulation Controls window from the main controls window. The list on the left shows all stimulation patterns that have been defined. Click the new button to create a new empty stimulus group. With it selected, click the edit button to launch the stimulus editor.

In the stimulus editor, an image can be copied in to serve as a context for designing the stimulus pattern. If an image acquisition is active or has been completed, the copy buttons can be used to copy the last acquired image. A tiff file can also be loaded as an image context.

To add a stimulus function, first click the "Add" button under current ROI. Next, you will define a stimulus function for this ROI. The "Default Scanfield" panel on the right allows you to set the parameters of the stimulus function that you will then draw. Set the desired parameters, then click the "Add" button under "Current Scanfield." You can then use the cursor to draw the stimulus in the axes on the top left. In this way you can add a series of functions that get executed sequentially. The "Current Scanfield" panel allows you to modify parameters of the selected stimulus function. The "Move Up" and "Move Down" buttons allow you to reorder the sequence of functions.

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