User Functions

Note

Review the ScanImage® API to learn more about automating ScanImage.

ScanImage supports calling user-defined functions in response to acquisition events.

Controls

GUI Options	Description
Function Selection	Dropdown to select current function. Select the ‘+’ option to add a new blank function.
Event Name	Select one of several events of interest occurring before or during an acquisition.
User Function	The function to call in response to the event. Note that multiple events can be sent to the same function.
Arguments	A cell array with optional arguments to pass to your user function.
Enable	If this is checked, the user function will be called when the event is triggered.
Delete	Delete the currently selected user function.

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User Function Definition

A user function has the format:

function name(source,event,arguments)

Argument	Description
source	The UserFunction Class.  You can access the root SI object by accessing the source’s hidden property `hSI` (src.hSI).
event	A MATLAB EventData Class
arguments	A cell array with optional parameters.

Example

function myUserFcn(src,evt,varargin)
   % in myUserFcn.m somewhere on the matlab path.

   disp(['Got Event: ' evt.EventName]); % prints the event
   disp(src);                           % prints the source object (UserFunctions)
   disp(src.hSI);                       % each source object has access to the main

   disp(src.hSI.hScan2D)                % ScanImage® imaging system object for
                                        % methods and property access
end

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Events

Acquisition triggers are triggers used for controlling the start and end of aquisitions. An acquisition mode is a noteable event that happens during acquisition.

General Events

These events are generalized to acquisitions (FOCUS, GRAB, or LOOP).

Event	Description
acqModeStart	Called just before the start of a GRAB or LOOP. This may happen before any data is acquired.
acqModeDone	Called just after the last frame at the end of a GRAB or LOOP.
acqStart	Called just after the first frame is acquired.
acqDone	Called just after the last frame gets acquired.
acqAbort	Called just after an acquisition is aborted. This is usually triggered from the Abort button.
sliceDone	Called just after the shutter is closed after acquiring a slice during a acquisition.
focusStart	Called just after the user presses the FOCUS button.
focusDone	Called just after the FOCUS is aborted. Similar to acqAbort, but only in FOCUS mode.
frameAcquired	Called just after a frame is acquired.
overvoltage	Called when the digitizer experiences an overvoltage condition during an acquisition.

Photostimulation-module Events

User functions can also be triggered from doing photostimulation-related events.

Event	Description
onDmdStimStart	Fires when command to perform an On-Demand stim is received, before the trigger is sent.
onDmdStimSingleComplete	Fires when an On-Demand stim completes if multiple outputs are allowed; more stims can be externally triggered.
onDmdStimComplete	Fires when an On-Demand stim completes if multiple outputs are not allowed; no more stims will occur until next On-Demand command.
onDmdStimExtSel	Fires when an external On-Demand stimulus selection occurs.
seqStimStart	Fires when a Sequence stimulation begins.
seqStimAdvance	Fires when a Sequence element is complete and Sequence advances to the next stim.
seqStimSingleComplete	Fires when a single Sequence is complete.
seqStimComplete	Fires when the last Sequence is complete.
photostimAbort	Fires when photostimulation module aborts.