ScanImage r3.5.1 is an incremental release, relative to r3.5. It is being co-released with ScanImage r3.6, primarily as a benefit to legacy users. The most notable change is a restoration of Cycle mode functionality, which had been broken in r3.5. Cycle mode is a feature allowing a sequence of acquisitions to be obtained at a list of pre-defined motor positions.
For users already using Cycle mode or requiring such functionality in their work, ScanImage r3.5.1 should now be used. All other users, both new and old should migrate/adopt ScanImage r3.6 instead.
Find below a listing of all notable enhancements/changes/bugixes in r3.5.1. Refer further below to the ScanImage 3.5.0 README for information on the original r3.5 release.
Enhancements
- Trigger time is now logged with increased accuracy to the TIF header file
- LOOP periods timing now occurs with greater accuracy
- Spine counting analysis software has been added to the distribution, and is accessible as scim_spineAnalysis()
- RepeatPeriod and RepeatsTotal values are now stored to image header
- Double-move during cycle operations when both a cycle and stack home are defined, saving inter-Repeat time
- The number of cycles to execute can now be specified in the Cycle Controls window
Changes
- Distribution has a new directory structure, consisting of 2 directories – ScanImage and scim. The latter directory contains various utility functions beginning with prefix scim that are intended/available for the user. The new directory structure matches that of r3.6.
- The standard_model.INI file now contains only those values which can or need to be edited by user for their rig. The remaining values, not to be user-edited, are now stored in a separate internal.INI file as part of the distribution. This new scheme matches that of r3.6.
Bugfixes
- Cycle mode was completely unoperational in r3.5 with a show-stopper bug.
- The UserFcn GUI was not working properly due to a case-sensitivity bug.
- The option for 'safe' hot-keys in the User Preferences dialog was being ignored
- Saving USR file was not correctly saving the currently active Configuration (CFG File)
- GUI controls would be blanked out when FOCUS mode acquisition ended by timeout, rather than explicit Abort
- High pixel value in LUTs could be below low pixel value
- Resets of merge window following configuration changes had dimensions transposed
ScanImage 3.5.0 README
ScanImage 3.5 has been developed primarily to support ScanImage users who no longer have ready access to the older Matlab version for which earlier ScanImage releases had been developed. ScanImage 3.5 is known to be compatible with Matlab 2007b. In addition, it is now compatible with the newer National Instruments driver (DAQmx), rather than the Traditional NI-DAQ driver required by earlier ScanImage releases.
ScanImage 3.5 is very similar to 3.0 and new users may want to refer to the ScanImage r3.0 Documentation to become familiar with this software.
Changes
However, some important changes have been made. New and returning users should familiarize themselves with the documentation of the Important Changes in ScanImage 3.5. Notably:
- The Selection Dialog no longer appears at startup
- The handling of the INI file, which must be created by the user, has changed somewhat.
- The board wiring required for trigger and clock synchronization has been modified
- The Main Controls window has several modifications
New Features
In addition to these changes, several new features have been added to ScanImage 3.5 to help support ongoing experiments by ScanImage users at HHMI/Janelia Farm Research Campus. These and other Important New Features in ScanImage 3.5 are described fully in the documentation:
- Live RGB channel 'merge' display during Focus mode
- Unlimited & uninterrupted acquisitions via TIF streaming-to-disk
- Ability to accept external trigger, using separate trigger input terminal (e.g. facilitates Ephus-driven acquisitions)
- Enhanced MP-285 interface and configuration
- Improved support for case of 3 'beams' (i.e. 3 Pockels Cells)
- Tools to facilitate beam and scan alignment
- Enhanced 'hot-key' functionality to support rapid program control and configuration switching
Bug Fixes
A handful of bugs identified in ScanImage 3.0 have been addressed in this release.
About Upcoming Releases
Version 3.6 is expected to be released soon after this version, supporting bidirectional and an improved sawtooth scanning user interface.