ScanImage r3.7 Documentation (Provisional)

New Features in ScanImage 3.7

• Compatibility with latest Matlab (2010b) and DAQmx (9.2.2).
• Compatibility with X series boards, for the second DAQ board (for Pockels and/or more clock signals)
• DAQ Toolbox no longer required
• Automatic power adjustment during stack collection
• Exports line/frame/pixel clock signals
• Next Triggering feature
• Continuous file streaming supported for stacks
• Enhanced User Functions capability
• Enhanced Fast Configurations

Upgrading from ScanImage 3.5 or 3.6

• 3.7 has a new model INI file , which is quite thoroughly documented. You should make a new standard.INI file based on this model, following the comments.
  It is recommended to create a separate folder(s) for your INI/CFG/USR files under 3.7, to keep them separate from data files for any older version you may also maintain installed.

• The Shift and Scan Amplitude values that previously referred to X/Y now refer to Fast/Slow. A new control in Configuration dialog indicates mapping from X/Y to Fast/Slow axes. Adjusting this allows you to rotate the image 90 degrees.
  The INI file contains the separate mapping of X/Y to DA Channels 0 & 1, which is fixed on initialization.

• The Scan Amplitude values are replaced by Scan Angular Range values, in the Configuration dialog. It now represents the full (peak-peak) angle of the scan range, specified in optical degrees, rather than half angle as in 3.6 (and earlier verisions). Therefore new values will generally be twice the Scan Amplitude values in ScanImage 3.6/3.5.
  The model INI file has improved/expanded the explanation of the voltsPerOpticalDegree variable. Please read carefully, and provide feedback if this is not clear!
  If the voltsPerOpticalDegree value in 3.7 differs compared to your setting in 3.6 (i.e. because it's clearer now and therefore set correctly), you will need to further adjust your Scan Angular Range values compared to previous Scan Amplitude values.
  In general, the new default Scan Angular Range value of 15 should not often require modification by most users. If you see the field-of-view is different (smaller) than you're used to, look closely at the voltsPerOpticalDegree value/notes in the INI file.

• It is recommended to copy your old CFG files to a separate folder for 3.7, and then load and re-save each of them individually. This will make your CFG files 3.7 compatible.
  Note the ScanAmplitude values will not be applied in 3.7. The Scan Angular Range values should be adjusted before saving each CFG file.

• 3.7 requires the clock synchronization between boards (main board and Pockels) be on RTSI 7, not RTSI 6 as with ScanImage 3.6.
  If running both 3.6 & 3.7, you should connect both RTSI 6 and RTSI 7(or connect all, with a ribbon cable).
  If running both 3.5 & 3.7, no change is required

• You can run 3.7 on same machine that is running 3.6 or older version
  Typically, your newer Matlab will set path to 3.7 and older Matlab will set path to older version
  If running both 3.5/3.6 & 3.7 on same machine, DAQmx 8.8 is required. This is earliest version of DAQmx supported by 3.7, while 3.5/3.6 doesn't run on 8.9 or higher.
  Note that X series boards are only supported from 9.0 forward.

Guide to New Features

Frame/Line/Pixel Clock Export

• Each clock output requires a National Instruments counter/timer channel. These must be specified in the INI file – frameClockBoardID, frameClockCtrID, lineClockBoardID, etc.
  Note that Ctr0 on the primary board (acquisitionBoardID) is reserved by ScanImage, and not available for frame/line/pixel clocks
  X series boards have 4 counter/timer channels, while other board families have only 2 counter/timer channels

• Finite clock generation is only possible with X series boards. When using a non-X series board, additional clock 'ticks' may appear after acquisition is finished, because the counter output is actually stopped in software.

• Consequently, pixel clock generation – which requires finite clock generation – is only possible with X series boards at this time.

• For Frame/Line clocks, the edge not specified by Polarity signifies the end of Frame/Line. For Pixel clock, the edge not specified by Polarity is controlled by Pixel Fraction.
  The 'end' of Frame/Line indicates that acquisition has ended for current line/frame, and acquisition for new line/frame has not begun. This occurs at the scanner flyback or turnaround time at end of line, or end of last line in frame.
  The Pixel clock handling is different because there are no gaps between pixel periods; thus the location of the 'stop' edge must be user specified (via Pixel Fraction).

• Enable: Each clock can be enabled/disabled. (CFG setting)
• Phase Shift (us): Each clock signal can be phase shifted relative to the true start of frame/line/pixel. Only a positive phase shift (delay) is supported at this time. (CFG setting)
• Polarity: Specifies if rising or falling edge signals the start of frame/line/pixel.
• Pixel Fraction: Specifies at what fraction of the pixel period to generate the edge not specified by the Polarity. Value must be < 1, to allow edge specified by Polarity at start of subsequent pixel period. (CFG setting)

• Export Clocks on FOCUS: If false, the clock signals are only generated during GRAB/LOOP acquisitions, not FOCUS acquisitions. (USR setting)

Settings labeled as CFG settings are saved as part of ScanImage Configuration. Different configuration files can save different values of this setting. This is useful, for instance, if you want the frame clock to be exported only for certain experiments, but not others.

• The pixel clock capability is only available with X series boards support finite output

Next Triggering Feature

*& Next Triggering allows external trigger (e.g. from behavior apparatus) to stop an acquisition, or to start a new file with advanced number without stopping acquisition

Power Adjustment During Stacks

• based on configurable/measurable length constant

Continuous File Streaming Improvements

• Continuous file streaming is now supported for stacks
• Continuous file streaming is now the only mode. A configurable running data buffer is maintained still, for online processing needs.

Enhanced User Functions capability

• Numerous events to which user functions, with optional modulating arguments, can be bound.

DAQ Toolbox No Longer Required

• - instead uses a Matlab class which wraps the NI DAQmx library. This approach is faster and more comprehensive (e.g. allows access to counter/timer features)