Configuration (r3.8)

• : (Read-Only) Displays the name of the active Configuration (CFG) file – i.e., the most recently loaded CFG file, if any.

• : Launches dialog to select a ScanImage Configuration (CFG) file file to load. Identical to selecting the button or menu item on the Main Controls panel.

• : Launches dialog to save the current ScanImage Configuration to a specified CFG file. Identical to selecting button or menu item on the Main Controls panel.

• : Changes made to controls throughout the Configuration panel do not immediately update the current ScanImage Configuration, i.e. the current ScanImage state. When a change is made, the button becomes active and changes are applied only when pressed.
  Note that the controls in the section Sec C DO take immediate effect IF the changes occur during Focus mode operation

• : Saves the current ScanImage Configuration to the active Configuration (CFG) file. Identical to selecting from the Main Controls panel menubar.
  This control only appears active if a change to one of the controls in the Configuration panel has occurred (and been applied) since the active Configuration (CFG) file was last loaded.
  If a change to the current ScanImage Configuration is made outside of the Configuration panel, then use the button or menu item on the Main Controls panel in order to save the changes (if desired).

The controls in this section pertain to the concepts described in Scan Configuration Basics.

• : Specifies the number of input sample bins to use during the Acquisition Period of each scanned line. This value becomes the number of horizontal pixels in the displayed image and the stored image.

• : Specifies the number of lines to scan with the Fast dimension scanner during each Frame of acquisition, while simultaneously adjusting the Slow dimension position (except during a Line Scan). This value becomes the number of vertical pixels in the displayed image and the stored image.

• : Specifies the time (in ms) to spend during each line scanned by the Fast dimension scanner, including both the Acquisition Period as well as non-acquiring time for flyback and/or turnaround.
  The value can differ somewhat from the value, based on the setting (as described in Fast Dimension Optimization)
  The Acquisition Period = 0.8192 * (as described in Fast Dimension Optimization)
  At this time, ScanImage supports values down to 0.5 ms/line with enabled and 1ms/line otherwise

• : Enables, when selected, Bidirectional scanning. When not selected, Sawtooth scanning is used.

The parameters in this section relate to the Fast Dimension command signal. The full meanings/effects of the parameters in this section, as well as procedures to set their values optimally, are described in Fast Dimension Optimization.

Unlike other parameters on the Configuration panel, changes to these parameters are immediately applied during a live acquisition (only in FOCUS mode), allowing their effect on the acquired image to be readily visualized. When these parameters are varied while not live imaging, then must be pressed for the changes to update the current ScanImage Configuration.

The parameters set in this section apply to the currently configured value (in the Main Controls panel). When changes are applied, the values are updated accordingly.

• : Adjusts the Acquisition Delay value required by ScanImage during processing the input data. To produce the optimal/correct image from the scanned data, this value must match the actual delay between the Acquisition Period of the Fast command signal and the corresponding period in the physical scanner's position response.
  Adjusting this value while Sawtooth scanning will shift the displayed image; adjusting it while Bidirectional scanning will adjust the alignment of every-other-line in the image.

• : Selecting this enables adjustment of the in fine increments
  The fine increment for the is the sampling period determined by the value

• : Value represents time (in microseconds) by which to extend the linear ramp at the beginning of each Acquisition Period in the Fast command signal.
  This value is read-only when Bidirectional () scanning is enabled, as the ramp extension is determined (implied) by the value.

• : (Read-only) Value displays the duration of each period of the Fast command signal, each of which corresponds to the scan of a single Line. This value may differ somewhat from the user-specified ) value, according to the currently specified .

• : Value represents the fraction of the occupied by the Acquisition Period – the portion of each period of the Fast command signal during which the input signal data is processed. Adjusting this value actually sets the value (because the Acquisition Period is fixed for a given ).
  The value of 0.8192 corresponds to case where the matches the value
  (Reducing/increasing) the (below/above) 0.8192 (increases/decreases) the value

• 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 ='BehaviorExpt' and =1, specified in the Main Controls panel, there will be six files named 'BehaviorExpt1_001' through 'BehaviorExpt1_006.

• : Lock to always match the # Frames value set on the Main Controls panel (right-hand control).
  Selecting results in one file per slice, during stack acquisitions

• : This checkbox determines whether disk logging functionality is enabled for GRAB/LOOP mode, causing image data to be automatically saved to disk during the acquisition
  A running buffer of the most recently acquired frames is maintained in the variable. The size of the running data buffer is specified by the values in the User Settings panel. Distinct values are used depending on whether is selected or not.
  Control is linked to checkbox on Main Controls panel

As described in Fast Dimension Optimization, optimal settings for the Fast command signal can be amplitude-dependent and therefore vary with the value. To address this, ScanImage allows distinct sets of the discussed in the last section to be stored for different levels as part of the ScanImage Configuration. These sets of variables correspond to the entries in the Scan Parameter Array – which is 'indexed' by the level.

• : This value stores the minimum zoom level to allow for the current ScanImage Configuration. This value constrains the value set in the Main Controls panel.
  This is useful when preparing a ScanImage CFG File which employs a fast (small) value that may stretch the physical scanner limits (e.g. current drive, servo control, or thermal limits)

• Constant @ Zoom >=: This value determines the length of the Scan Parameter Array. levels above this level use the same values as those configured at this level.

• : This determines the zoom level to set and/or display in the Fill Fraction, Acq Delay, and Scan Delay text controls within the section.
  This value can range from 1 to Constant @ Zoom >= (values can be stored for zoom levels below the value, although they have no effect).
  Scrolling through the values allows one to scroll through the Fill Fraction, Acq Delay, and Scan Delay values stored for each level

• : These correspond to the parameters described in the section, specifying the parameters to use at each level.

Further background on these parameters can be found in Pockels Flyback Blanking.

• : Enabling this option implies –
  • The Pockels Cell command signal(s) generated by ScanImage for the (active) Beams are 'blanked' outside of the Acquisition Period of the Fast command signal
  • If is selected, the Pockels Cell command signal(s) generated by ScanImage for the (active) Beams are 'blanked' during the the final line of each Frame to allow for flyback of the Slow dimension scan

• : Specifies a time (in microseconds) by which the Acquisition Period value used to determine the Pockels Cell command signal(s) is extended (increased) relative to the actual value for the Fast command signal.
  This parameter specifies extra 'cushion' to use in the Pockels command signal(s), ensuring the signal is not 'blanked' during the actual Acquisition Period.
  This cushion 1) accounts for light modulator response time and 2) provides tolerance for errors in the .

This section determines the sample rates used by the Analog Input and Analog Output channels used by ScanImage.

• : Specifies the sample rate (in MHz) of the Analog Input channels used by ScanImage to digitize the PMT (or other photodetector) input signals

• : Specifies the sample rate (in kHz) of the Analog Output channels used by ScanImage to generate the Fast and Slow scanner command signals, as well as the Pockels (or other light modulator) command signal(s) generated for each Beam
  Increasing this value can improve the positioning accuracy of scan regions selected for the Power Box feature and with the tool (in the Main Controls panel).
  At this time, the Analog Output sample rate for the channels used for the scanner and Pockels cell command signals are required to be equal

• : This option (available for both the and controls) causes the sample rate to be automatically determined by the current value
  For the , selecting causes the to remain constant for common values of – this allows the ScanImage image displays to appear consistent as the scan speed is varied, with fixed levels (set on the Image Controls panel)

The full meaning/effects of the parameters in this section are described in Slow Scan Dimension Settings.

• : Specifies that the Slow command signal should be a staircase – i.e. should step to a discrete level for each line in the Frame – rather than a continuous ramp.

• : Specifies that beginning of flyback for Slow command signal will coincide with start of final line in the Frame; also, if is selected, then the Pockels (or other light modulator) command signal will be 'blanked' during this (entire) final line
  If this option is disabled, then the Slow command signal flyback begins at the end of the Frame meaning, practically, that it occurs during the first line of the succeeding frame
  This option is valuable for fast scan speeds (low values) as the flyback may take nearly as long as a single line scan; hence the Pockels 'blanking' is appropriate

• : Specifies that the final line of acquired data during the Frame is discarded and does not appear in the image display figures and is not recorded to the stored image files.
  This option is disabled and inactive if is disabled
  This option is often used with an odd value for specified, so that the stored/displayed number of lines is even (e.g. 257 can be specified to store/display a 256 line image)

• : ScanImage generates Fast and Slow command signals on the 2 analog output channels of the DAQ board specified by in the INI File. This value specifies for which scanner, X or Y, the Fast command signal is generated; the Slow command signal is generated for the other scanner.
  The INI variables specify the mapping of the X and Y physical scanners to the 2 DAQ output channels.
  Adjusting allows one to rotate the image by 90 degrees.

• : Specifies the time (in ms) following the start (trigger) of a GRAB acquisition or LOOP Repeat, or an Image Stack Slice, that the optional shutter signal generated by ScanImage should switch to Open state.
  See Shutter Control for more information.

• : In many circumstances, ScanImage processes the input data in evenly-subdivided segments of each Frame termed Stripes, allowing the update of image display figures to appear more 'real-time'. Selecting prevents this from occurring, forcing ScanImage to display images one Frame at a time.

This section displays read-only parameters determined by the other values specified in the Configuration panel.

• : Specifies the number of samples acquired on the Analog Input channels used for the PMT (or other photodetector) input signal during the Acquisition Period occurring during each Line Period () of the Fast dimension scan. This value depends on:
  • 
  • 

• : Specifies the number of Analog Input samples from the input signal(s) which are generally summed together to compute the value for each horizontal pixel that is computed by ScanImage to assemble an image for each Frame of acquisition to display and/or store) . This value depends on:
  • ( and )
  • The samples can be averaged, rather than summed, if is selected in the Image Controls panel.

• : Specifies the total time spent during the acquisition of samples for each horizontal pixel computed by ScanImage.
  This value is computed simply as: = *

• : Specifies the total time spent for each Frame of acquisition.
  This value is computed simply as: = 1 / ( * )
  The total time for a ScanImage acquisition is determined exactly by the number of frames acquired times the Frame Period (= 1 / ) – i.e. there are no gaps between Frames