Main Controls (r4.1)

MAIN CONTROLS Panel

: Displays name of currently loaded User Settings (USR) file. If none loaded, field is blank.
- : Launch dialog to select new USR file to load
- : Save current user settings to currently loaded USR file. (Use File >> Save User Settings As... from menubar to save current user settings to a new USR file)

: Displays name of currently loaded Configuration (CFG) file. If none loaded, field is blank.
- : Launch dialog to select new CFG file to load
- : Save current configuration to currently loaded Configuration (CFG) file. (Use File >> Save Configuration As... from menubar to save current configuration to a new CFG file).

/: For GRAB/LOOP acquisitions, number of slices acquired/to-acquire - for the current Repeat (if using LOOP) and for the current volume (if using FastZ imaging).

/: For GRAB/LOOP acquisitions, number of frames acquired/to-acquire at current slice - for the current Repeat (if using LOOP).

/: For LOOP acquisitions, number of times to repeat acquisition of specified & .

: For LOOP acquisitions, specifies time, in seconds, between start (trigger) of each Repeat. Value is ignored when external triggering is used.

: For FOCUS/GRAB acquisitions, displays time, in seconds, since start of acquisition. For LOOP acquisitions self-triggered by ScanImage, displays countdown from specified to start of next Repeat. For LOOP acquisitions with external triggering, displays time since last Repeat was externally triggered.

: Sets stem of filename to be saved for next or ongoing GRAB/LOOP acquisition. The is appended to specified to create the full filename, e.g. test1024_003.tif in example shown.

: Sets number to append to specified to create the full filename. Value is automatically incremented at end of each acquisition (or Repeat) when using LOOP. Value can be manually edited as well. By default, value is incremented

: Increment by 1.

: Launch dialog to select save directory to which files are saved.

: Determines whether disk logging functionality is enabled during GRAB/LOOP acquisitions.

: Specifies # of frames to average together before appending single (averaged) frame to current log file. Value > 1 implies file averaging is enabled. Note this implies data reduction: file size is reduced and raw data is lost. File averaging capability is separate from the display specified in IMAGE CONTROLS.

: Enables/disables external triggering for GRAB/LOOP acquisitions (no effect on FOCUS acquisitions). Button is available when external start trigger is configured in TRIGGERS window.

: Start image acquisition in one of the 3 supported ScanImage modes, described below. Acquisition begins (or is armed to wait for an external trigger) and corresponding button changes to . Pressing stops the ongoing acquisition.
- : Continuous imaging until is pressed (or focusTimeDuration is reached, as specified in USER SETTINGS} without file-saving, external-triggering, etc. Used for searching specimen, panning & focusing, etc.
- : Start (or arm) single acquisition, with file-logging and/or external triggering if enabled, for specified and , and specified in FAST Z CONTROLS if FastZ imaging is enabled.
- : Start (or arm) sequence of GRAB acquisitions, termed Repeats, either for specified if using self-triggering or for each supplied external start trigger until . Also, LOOP mode is used for continuous multi-trigger acquisition modes allowed with next triggering, configured in the TRIGGERS window.

The , , and controls specify the ROI Scan Parameters in ScanImage parlance - they affect the scan generated by ScanImage during acquisition.

Each of these control values are part of the current ScanImage Configuration, i.e. these values are saved/loaded to/from CFG files.

: Specifies factor by which scan angular range is reduced, for both fast & slow dimensions. For SI 4.1 using Thorlabs scanning hardware, values from 1-51 are supported, at specific increments. Adjusting zoom factor will set value to nearest allowed zoom increment.

: Resets value to ROOT ROI value of 1.0 - i.e. to full scan angular range supported by scanning hardware.

: Specifies scan angle offset in specified scan dimension; this effectively shifts scan pattern laterally in the microscope's plane of focus. For SI 4.1 using Thorlabs scanning hardware, value is set in arbitrary units from -127-128. Adjustment is only allowed in slow scan dimension.

: Resets value to ROOT ROI value of 0 - i.e. to center of range supported by scanning hardware.

: Specifies reduction factor (value from 0 to 1) for scan angle (lateral scan extent in microscope focal plane) in specified scan dimension, i.e. allows the aspect ratio of the scanned area to be set.
For SI 4.1 using Thorlabs scanning hardware, is fixed at value 1.
Setting between 0-1 (non-inclusive) specifies a rectangular area scan
Setting = 0 specifies a line scan

: Toggle button switching between 0 (line scan mode) and the current Base ROI value.

: Adjusts the ROI Scan Parameter values to the last saved Base ROI values (using ). By default, the Base ROI scan parameters equal the ROOT ROI values.

: Sets the Base ROI scan parameter values to the currently set values (i.e. of , , and ).

: Sets the scan parameters to ROOT ROI values:
- Zoom = 1
- Shift = 0
- Scan Angle Multiplier Fast/Slow = 1

: Points scanner at center of field-of-view (following specified values). Can be used for scanner alignment purposes. Button renamed to while scanner is pointed to field center. Scanner remains pointed until is pressed.
While scanner is pointed, beam power is adjusted to specified level and shutter is opened (if such hardware is configured in Machine Data File)

The FAST CONFIGURATIONS window, from File >> Settings >> Fast Configurations..., allows specified CFG files to be associated with buttons on MAIN CONTROLS (and keyboard shortcuts) for one click (press) access to frequently-used configurations.

: Load specified Fast Configuration, i.e. settings of CFG file specified in FAST CONFIGURATIONS window.

: Toggle on/off display of the CONFIGURATION window

Child pages

Main Controls (r4.1)