USER SETTINGS Dialog
All settings in the USER SETTINGS... dialog are (unsurprisingly!) User Settings, i.e. saved to USR files.
: When external start triggering is enabled, via
button on
, this specifies length of time to wait for external trigger to arrive following start of GRAB acquisition or LOOP Repeat before generating a timeout error.
Saving/Memory
Root Save Path Settings
ScanImage typically requires that user specify a save path, via File >> Set Save Path... on the
menu, before the first GRAB/LOOP acquisition in a ScanImage session.
: Specifies root folder to display when selecting File >> Set Save Path... to specify path for file-saving. By selecting a folder at root of hierarchy where user stores data files, the selection of the save path is made much faster.
For example, the folder C:\Data or C:\Data\MyName might be specified, so one can readily select/create subfolder identifying date or other grouping folder immediately below this root in the system folder hierarchy
: Specifies that
is the default save path if none other has been specified. Selecting this option allows user to avoid requirement of specifying a save path (File >> Set Save Path...) for each ScanImage session.
This option works best when user employs a flat file hierarchy, e.g. if the
values specified in
will contain date information and/or other prefix information to allow files and file groups to be identified.
Running Frame Buffer Settings
Although ScanImage normally saves each frame to disk as it is acquired, it is often useful to maintain recently acquired frames in RAM, e.g. for online processing by User Functions.
ScanImage therefore maintains a circular running buffer of the most recently acquired frames in the
state variable (in the Matlab global workspace).
This variable is a nested cell array of 2-D images (frames), indexed as follows:
>> state.acq.acquiredData{<FrameIndex>}{<ChannelIndex>}(<lineIndex>,<pixelIndex>)
where <FrameIndex> counts from the most recent frame.
In previous ScanImage versions, this variable was structured as a cell array of 3D arrays
:
These values specify the number of the most recent frames to store in RAM, in the
state variable, when
is ON/OFF on the
panel.
Value of Inf indicates to buffer the entire acquisition. This is default value when
is OFF, so that entire acquisition can be saved after it completes, manually using File >> Save Last Acquisition As...
When
is ON panel, ScanImage saves each frame of data to open filestream during acquisition
Other Settings
- Unknown macro: {blue}Some users may prefer to separate ('chunk') data from very long acquisitions into several smaller files. This value specifies the number of Frames to log to each file during the acquisition. As further data is collected, a new data file is automatically created.
To disable such 'chunking', this value should be set to Inf (infinite), causing all data to be logged to a single file.
File chunking can be used to avoid the 2GB file size limit in 32-bit Windows
When chunking is enabled, a three-digit number (e.g. 001, 002, etc) is appended to the filename, following an underscore. The number is auto-incremented as each new file ('chunk') is added. For example, if 3000 frames are collected with 500 frames/file, with
Unknown macro: {blue}='BehaviorExpt' andUnknown macro: {blue}=1, specified in theUnknown macro: {report-info}panel, there will be six files named 'BehaviorExpt1_001' through 'BehaviorExpt1_006.
Focus Options
Snapshot Options
ROI Options
Power Control
- Unknown macro: {blue}This option causes the actual power level to be measured using the photodiode (or other power detector), as configured in the INI File for each Beam, following any change to the ScanImage Configuration. The measured value is referenced to the current Pockels Calibration for each Beam, and theUnknown macro: {blue}level value is updated to match the measured level.
A change in the user-specified
Unknown macro: {blue}level is a change to the Configuration, so a measurement will occur.