ScanImage r3.7 Documentation (Provisional)

New Features in ScanImage 3.7

• Works with latest Matlab (2010b) and DAQmx (9.2.2). Supports X series boards, for the second DAQ board (for Pockels and/or more clock signals)
• No longer uses/requires DAQ Toolbox - 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)
• Automatic power adjustment during stack collection, based on configurable/measurable length constant
• Exports line/frame/pixel clock signals. (This feature is most powerful with new X series boards, where you can get all the clocks)
• Next Triggering feature: allows external trigger (e.g. from behavior apparatus) to stop an acquisition, or to start a new file with advanced number without stopping acquisition
• Continuous file streaming supported for stacks and is now the only mode. A configurable running data buffer is maintained still, for online processing needs.
• Enhanced 'User Functions' capability, with numerous events to which user functions, with optional modulating arguments, can be bound.

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