ScanImage r3.6 README (Beta)

r3.6-beta13

Significant, but self-explanatory, changes to menu layouts in MainControls and PowerControl window
New 'View' menu on MainControls dialog allowing all windows/figures that may have been closed to be redisplayed
Scan Amplitude in Configuration dialog now is intended to be entered in optical degrees of the scanner, using new variable 'opticalDegreesFactor' in INI file to convert this to scanner command units (i.e. volts). This encourages users to think of their scan amplitude in terms of the angle scanned by scanning device.
Several legacy, but not fully vetted/current, features have been eliminated: UncagingMapper, PowerBoxStepper, ROI Cycler
The dialog 'Laser Function Panel' used for selecting which beams are active during various modes has been renamed to 'Beams' and is available directly from the Settings... menu.
Cycle Mode functionality remains apparent in dialog, but is disabled. This is also not supported in r3.6.
scim_install() has been eliminated. Installation is now as it was traditionally done – add unzipped installation contents to ScanImage path using 'Add with subfolders' in Matlab.

Significant performance enhancements to key data processing functions (makeStripe.m and makeFrameByStripes.m). These have allowed frame rates of >60Hz to be sustained (e.g. 512x32 frames at 0.5ms/line)
User is now provided options for how to handle the slow scan dimension flyback. User can select to have the flyback to occur during the final line of the image, in which case Pockels flyback blanking (if selected) will be in effect. Additional option to discard this line is also provided.
Trigger time logged to header file (internal.triggerTime) has improved accuracy. Previous approach using DAQ Toolbox reported version was found to be unreliable.
Handling of countdown timer during LOOP operation has been improved.
Repeat period for acquisition is now stored to header (internal.repeatPeriod)
Negative input voltages are now supported, by selecting appropriate option in Channels dialog.

Bug preventing 4 channel operation fixed
Image display figures now show exactly the lines of image, rather than half of the top and bottom line.
PowerBox boundaries could run off the edge of the image. This is no longer possible.
Long buffered GRAB acquisitions are no longer unnecessarily aborted when sufficient memory exists; if memory error occurs, a helpful error message is provide

Trigger time logging to ScanImage TIF header has been fixed/improved/modified:
- Field previously named 'dioTriggerTime' has been renamed to 'softTriggerTime' and still reports the same value – the time at which the function dioTrigger() is invoked.
- A new header field – 'triggerTime' – has been added which reflects a more accurate record of the acquisition's start time, as discussed further below
- 'triggerTimeInSeconds' header field has been eliminated – this can easily be computed in post-hoc analysis.
Somewhat reorganized 'scim' folder (again)
- @scim_tifStream class is now visible to user in 'scim' folder. Some users may find this useful for their analysis.
- All other files not intended for use are in 'scim_private' subfolder
- As before, the 'scim' folder can be 'installed' on analysis machines and operate standalone from ScanImage, although it also includes utility functions intended for use during ScanImage (e.g. scim_parkLaser)

Improved r2008b compatibility: suppress superfluous warning message
Various improvements reducing execution time of key 'streaming' functions – makeStripe() and makeFrameByStripes()
A new measurement of the trigger time – the 'triggerTime' header field – has been added, which represents a timestamp taken in an AcquisitionStarted callback, rather than the time dioTrigger() is called. This allows (fairly) accurate trigger time logging, including in externally triggered LOOP mode.
Trigger time strings (both 'triggerTime' and 'softTriggerTime') are now reported to header with millisecond precision

BUGFIX: The 'softTriggerTime' (formerly 'dioTriggerTime') header field (as well as the new 'triggerTime' header field) reflects trigger time of present acquisition, rather than trigger time of previous acquisition, which could occur during externally triggered LOOP mode.

Reorganized INI file. The rig configuration section of the INI file has been separated from the 'internal' portion. This will make future upgrades much smoother, as changes to the INI file will not be required.
Accordingly, this is the last time to suggest that you should remake your standard.ini file from scratch based on the standard_model.ini file included with this release
The distribution is also reorganized. Now consists of just two folders: ScanImage and scim. The latter folder contains functions/classes that all begin with the prefix 'scim', and are functions meant to be useful to ScanImage users during and after ScanImage operation.

Support for higher and adjustable AI and AO rates (to 5MHz and 200kHz, respectively), including auto-adjustment with line scan rate. In particular, 1.25MHz AI rate is used at 2ms/line, 2.5MHz at 1ms/line, and 5MHz at 0.5ms/line. Higher speeds improve ability to optimize bidirectional scan images. Auto adjustment of AI rate to corresponding line scan rates eliminates need to adjust the LUT when switching scan speeds.
Among the 'scim' functions is a revamped scim_openTif() function which is a file reader/viewer/processor function. This function can be useful as a standalone 'program', as well as useful within your custom analysis scripts.
(A. Ponti) 'Pseudo-focus' mode now functions for both GRAB and LOOP acquisitions
Among the 'scim' functions is a revamped scim_openTif() function which is a file reader/viewer/processor function. This function can be useful as a standalone 'program', as well as useful within your custom analysis scripts.
Linescan state is now stored as part of a configuration, allowing customized line scan configurations to be stored and recalled (e.g. as a 'fast configuration')

BUGFIX: Frame rate display and variable now correctly updates for all fill fraction changes
BUGFIX: ROI selection now works correctly again for case of non-square aspect ratio

Configuration dialog box is significantly revamped/improved, in support of improved sawtooth and new bidirectional scanning capabilities. See documentation.
'Cusp delay' renamed to 'acquisition delay'; 'line delay' renamed to 'scan delay'

Support for bidirectional scanning to 0.5ms/line
Support for an 'array' of scan parameters applying to various zoom levels. This allows scan parameters to change automatically as zoom is varied.
Sawtooth scans now use a 'cycloid' waveform during flyback.
Support for 4 acquisition channels
Support for user-adjustable voltage range per channel
Access of 'Fast Configurations' via dedicated buttons on the Main Controls dialog
Handle case of 'acquisition delay wraparound' – i.e. case where data is acquired during command of next line – which occurs during some fast scans. (Requires 'image striping' to be disabled).
'Merge' window now allows color for each channel to be user-specified
Improved user interactivity for graphical ROI, linescan, powerbox selection, etc.
Improved ROI and Power Box positioning accuracy