About this Documentation
ScanImage 3.7 is quite similar to 3.6. This documentation 1) describes changes and new features since ScanImage 3.6 and 2) provides an updated reference guide to the various ScanImage windows. The various concepts described in the ScanImage r3.6.x Documentation are, broadly speaking, still applicable. Many links in this documentation therefore refer back to the Scanimage 3.6 documentation.
Version Compatibility
Please note/follow the Matlab and NI version compatability information. Other versions are known or likely not to work! As discussed further below, it is possible to co-install ScanImage 3.7 with earlier ScanImage versions, by installing multiple Matlab versions on a machine. In such cases, DAQmx 8.8 should be used.
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- Getting Started Guide
- Window Reference Guide
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New Features in ScanImage 3.7
Major New Features
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Unknown macro: {multi-excerpt-include}Upgrading from ScanImage 3.5 or 3.6 (Important Changes)
- 3.7 has a new model INI file
, with several changes from r3.6. 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
Unknown macro: {blue}values are replaced byUnknown macro: {blue}values, in theUnknown macro: {report-info}dialog. They now represent the full-angle (peak-peak) of the scan range, specified in optical degrees, rather than half-angle as in 3.6 (and half-voltage of command signal in earlier versions). Therefore new values will generally be twice theUnknown macro: {blue}values in ScanImage 3.6.
In general, the new default
Unknown macro: {blue}values of 15 optical degrees 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 theUnknown macro: {blue}value/notes in the INI file.
- If using two boards (i.e. second board for Pockels and/or new clock export signals), ScanImage 3.7 requires the clock synchronization between boards be on RTSI 7, not RTSI 6 as with ScanImage 3.6.
If running both 3.6 & 3.7 (see below), you should connect both RTSI 6 and RTSI 7(or connect all, with a ribbon cable).
If running both 3.5 & 3.7 (see below), no change is required
- The INI file now contains a
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If the
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- The
Unknown macro: {blue}andUnknown macro: {blue}values that previously were specified as X & Y are now referred to as FAST & SLOW. A new control inUnknown macro: {report-info}dialog indicates mapping from X/Y to FAST/SLOW axes. Adjusting this allows you to rotate the image 90 degrees.
- The INI file now contains the separate mapping of X/Y to DA Channels 0 & 1 (
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- 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
Unknown macro: {blue}values from 3.6 will not be applied in 3.7. The newUnknown macro: {blue}values should be adjusted before saving each CFG file.
Running ScanImage 3.7 together with earlier versions
You can run 3.7 together on same machine that is running 3.6.x or 3.5.x
- 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.
- Note that maintaining multiple Matlab versions on same machine does not require an additional license or count as an additional activation.
Major 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 can make this adjustment automatically, using a simple exponential length constant (Lz).
The
Unknown macro: {report-info}panel allows this capability to be enabled:
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From the
Unknown macro: {report-info}panel, ScanImage 3.7 also provides a facility to measure the Lz value suited for the given preparation:
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Show..."> Show...Frame/Line/Pixel Clock Export
ScanImage 3.7 introduces a Frame/Line/Pixel clock export feature intended to allow external hardware to be synchronized with start (or end) of each Frame, Line, or Pixel during image acquisition.
The
Unknown macro: {report-info}dialog controls the Frame/Line/Pixel clock feature:
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Show..."> Show...External triggering enhancements, including Next Triggering
ScanImage 3.7 has more options for external triggering. There are now two types of external triggers:
- Start Triggers: Trigger signals which initiate GRAB/LOOP acquisitions, when EXT is enabled in the
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- Next Triggers: Trigger signals which stop or advance data file of ongoing GRAB/LOOP acquisition. They may also act as a Start trigger and initiate acquisitions.
External trigger signals to ScanImage are input on one of the PFI (programmable function interface) lines specified in the INI file as
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Unknown macro: {vi-statevar}. These specify the list of available trigger sources on a particular rig/setup.
The
Unknown macro: {report-info}dialog, accessed from Settings >> Triggers... on the
Unknown macro: {report-info}menu, allows selection of which trigger source to use:
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Show..."> Show...Enhanced User Functions capability
ScanImage 3.6 and earlier had some support for User Functions. The original implementation had a few critical limitations, however:
- Only one event – the end of a GRAB acquisition or LOOP repeat – lead to user function execution
- User functions were required to be on the Matlab search path
- No ability to pass arguments to the user functions, i.e. to modulate their function
ScanImage 3.7 completely re-implements the User Functions feature to overcome these limitations. The new implementation makes use of the concept of events
recently added to the Matlab language.The
Unknown macro: {report-info}dialog, accessed from Settings >> User Functions..., allows User Functions to be specified:
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Show..."> Show...Enhanced Fast Configurations
ScanImage 3.7 enhances the interface and capabilities of Fast Configurations – configurations which are configured to be rapidly loaded, at the touch of one key or one button. ScanImage users are encouraged to create several configurations, to represent each of the imaging/experimental modes they use.
The new
Unknown macro: {report-info}window is accessed via Settings >> Fast Configurations... on the
Unknown macro: {report-info}menu:
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Show..."> Show...Continuous File Streaming Improvements
ScanImage 3.5 introduced continuous file streaming
as an option for non-stack GRAB/LOOP acquisitions (i.e. acquisitions where Unknown macro: {blue}=1). This feature saves files to disk as they are acquired, rather than waiting till the end of an acquisition to save the file. This permits unlimited, uninterrupted acquisitions.
ScanImage 3.7 now uses continuous file streaming for all GRAB/LOOP acquisitions (when
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Unknown macro: {blue}option in 3.5.x and 3.6.x has been removed.
As a consequence, ScanImage 3.7 no longer typically maintains a buffer in memory (RAM) of the entire acquisition. Instead, a configurable circular running buffer of the most recently acquired frames is maintained.
The
Unknown macro: {report-info}dialog, accessed via Settings >> User Settings... from the
Unknown macro: {report-info}menu) allows this buffer to be configured:
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Show..."> Show...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.
Other New Features
Finite LOOP acquisitions
In earlier versions, LOOP mode acquisitions were indefinite – the user was required to
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In ScanImage 3.7, the
Unknown macro: {report-info}panel allows user to specify a finite number of Repeats for a LOOP acquisition:
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Show..."> Show...Fractional zoom adjustment
In earlier versions, the
Unknown macro: {blue}control in the
Unknown macro: {report-info}panel allowed the zoom value to be specified in only integer increments. ScanImage r3.7 now allows fractional zoom values, providing greater control over the scan range directly from the
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The
Unknown macro: {blue}value simply represents a division of (both) the
Unknown macro: {blue}values in the
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For most users, the Unknown macro: {blue}values should not require modification – the
Unknown macro: {blue}control, with fractional values, should now provide sufficient adjustment flexibility over the scanned image area.
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Show..."> Show...Slider adjustment of power during FOCUS
In ScanImage 3.7, a new
Unknown macro: {blue}control on the
Unknown macro: {report-info}panel allows the slider to be adjusted during FOCUS, if selected:
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Show..."> Show...Unknown macro: {set-data}More image display colormap options
In ScanImage 3.6.x and earlier, the Image Display windows are always displayed with a grayscale
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ScanImage 3.7 offers a wider range of standard
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The
Unknown macro: {report-info}panel provides the standard
Unknown macro: {report-info}options:
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Show..."> Show...The
Unknown macro: {report-info}dialog provides the capability for a user-defined/configured
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Show..."> Show...Option to average binned samples
To date, ScanImage has summed the input samples obtained at each pixel of the scanned image (see Input Data Processing). The number of samples at each pixel is computed as the
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Unknown macro: {report-info}panel; its value is determined by the
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ScanImage 3.7 adds the option to average, rather than sum, the samples obtained at each pixel. This is available from the
Unknown macro: {report-info}panel:
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Show..."> Show...Support for shutter located before Pockels
The Shutter control signal feature in earlier ScanImage versions assumed that shutter is located after any/all Pockels/modulators in system – i.e. a single shutter is used for all the Beams in use.
ScanImage 3.7 adds option for the Pockels/EOM to be located before the Pockels. This is most commonly used when there is only one beam. To select this option, the
Unknown macro: {vi-statevar}value in the INI file should be set to 1.
The one & only effect of selecting this option is that shutter is opened/closed at start/end of Pockels calibration One effect of the Unknown macro: {vi-statevar}value is that the beam is transmitted through to scope, and potentially specimen, during Pockels calibration. Careful attention should be paid to the
Unknown macro: {vi-statevar}INI file values; the scanner is directed to this angle during Pockels calibration.
Ability to set root save file path
ScanImage 3.7 makes it faster to select the save path, which is typically required at the start of each ScanImage session. The option is available from the
Unknown macro: {report-info}dialog:
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Show..."> Show... - 3.7 has a new model INI file
- Getting Started Guide