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
- External triggering enhancements, including Next Triggering
- 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
Power Adjustment During Stacks
When collecting image stacks in scattering tissue, the power level required at each slice in the stack generally increases with depth in order to maintain a fixed signal. ScanImage 3.7 enables this, allowing a simple exponential length constant (Lz) to be specified.
This feature is primarily controlled from the Power Controls window:
P/z Adjust: Checkbox enables/disables automatic 'P vs z' adjustment feature for all beams
Lz: Specifies the exponential length constant for the currently selected beam. Power is increased with depth according to P = P0 * exp^((z-z0)/Lz).
A value of Inf implies no power adjustment should occur for the selected beam.
Value of Lz must be positive
- The zDepthPositive value in the INI file must be set correctly, specifying specify whether larger Z values on the motor controller corresponds to deeper imaging (true by default).
- In general, the user will experiment to identify the Lz value suited for their preparation, which is typically fairly constant from
- The P/z Adjust and Lz controls are User Settings-- i.e. their values are saved to USR files.
Thus during a typical ScanImage session (where USR file is loaded on startup only), the value specified applies to all stack configurations used during session
- Note the power only adjusts in integer increments of the percentage value.
ScanImage 3.7 also provides a facility to measure the Lz value suited for the given preparation, using the Motor Controls window:
When Override Lz is enabled, stack executions initiated via the GRAB button in the Motor Controls dialog (rather than from Main Controls) will use Lz value computed from power levels measured at the endpoints of the stack determined by start and end buttons.
User therefore will typically uses FOCUS mode to adjust power and Z position at both the start and end points of stack, pressing start and end buttons at each point, respectively to record both the Z position and power level(i.e. using a higher power at the deeper endpoint). Then Lz can simply be computed and this value is used instead of that specified in Power Controls window.
If multiple beams are used, a separate Lz value is computed/used for each beam, i.e. power level for each beam is measured at each endpoint.
If value of Lz=Inf in Power Controls window for a beam, then power auto-adjustment is disabled for that beam. Therefore, to use Override Lz feature, some (arbitrary) value (other than Inf) should be entered for each beam for which auto-adjustment is to be used.
When Override Lz is used, the computed Lz value is displayed to Matlab command line, for each beam. Users may find that this is a useful way to measure/determine Lz for their preparation. User can then simply enter this value in the Lz control on the Power Controls window and save value to USR file. Assuming that value is fairly consistent from sample to sample (for given sample type), this avoids need to adjust and record power at both start and end points of each stack.
Frame/Line/Pixel Clock Export
This feature is most powerful with new X series boards. Future ScanImage versions may be able to get more functionality out of other/earlier board families, but this cannot be guaranteed as a development priority.
The Frame/Line/Pixel clock export feature is intended to allow external hardware to be synchronized with start (or end) of each ScanImage Frame, Line, or Pixel.
- Each clock output requires a National Instruments counter/timer channel. These must be specified in the INI file. Both Board and Counter ID values must be specified – i.e. frameClockBoardID & frameClockCtrID must be specified to enable frame clock feature, 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).
The Frame/Line/Pixel clock feature is controlled by the Exported Clocks... dialog (Settings >> Exported Clocks... from the Main Controls menu):
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- 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 considered part of the ScanImage Configuration
and saved to CFG files. 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.
Settings labeled as USR settings are considered part of ScanImage User Settings and saved to USR files.
External triggering enhancements, including Next Triggering
*& 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
Enhanced User Functions capability
- Numerous events to which user functions, with optional modulating arguments, can be bound.
Enhanced Fast Configurations
Continuous File Streaming Improvements
ScanImage 3.5 introduced continuous file streaming as an option for non-stack GRAB/LOOP acquisitions (i.e. acquisitions where # Slices=1)
ScanImage 3.7 adds continuous file streaming for stack acquisitions and removes the ability to enable/disable continuous file streaming mode – this mode is now always used when AutoSave is checked:
- 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.
DAQ Toolbox No Longer Required
ScanImage 3.7 no longer requires use of the DAQ toolbox. Instead, it uses a Matlab class which wraps the NI DAQmx library. This approach has several advantages:
- Faster data read times are achieved (>4x faster), which increases amount of time available for user functions
- More comprehensive coverage of DAQmx features is achieved, compared to DAQ toolbox. For example, the DAQ toolbox does not support counter/timer channels which underlie several of the new features in ScanImage 3.7.