ScanImage 4.1 is a major release which supports resonant scanning and volume imaging. Resonant scanning allows an order-of-magnitude increase in line scan rate (up to 16kHz supported) compared to scanning with the galvanometer based scanning supported by ScanImage 3.x. Video-rate imaging, e.g. 30Hz for 512x512 pixels, is then readily supported. Resonant scanning may be combined with piezo-sweeps in the axial dimension to achieve volume imaging. For example, it is possible to image from 4 or 8 image planes with an aggregate frame rate of ~8 or 4 Hz, respectively.
ScanImage 4.1 is exclusively for resonant scanning; it complements SI 3.x, which exclusively supports galvanometer scanning. Also, while ScanImage 4.1 has a highly similar user-interface to ScanImage 3.x, it uses an entirely different architecture (fully object-oriented) under the hood.
ScanImage 4.1 requires the use of Thorlabs scanning hardware - the minimum requirement is the Thorlabs MPM-SCAN-64J or MPM-2PKIT Multiphoton Essentials Kit. ScanImage 4.1 supports optional Pockels, motor, and shutter components, similar to ScanImage 3.x. For optional volume imaging, the E-665 controller from Physik Instrumente is supported, which can be used with a variety of suitable piezo actuators (e.g. the P-725 PIFOC). Support for additional piezo controller models could be provided in the future, if demand/need is demonstrated.
ScanImage 4.1 supports (only) a very specific set of Thorlabs scanning hardware/firmware/software. Informing Thorlabs, at time of order, that an MPM system must be ScanImage 4.1 compatible should help guarantee these specifications are met. Users with earlier Thor MPM systems should inquire directly with Thorlabs about updating their system. Note that ScanImage 4.0 (and its associated Thor hardware configurations) is no longer officially supported.
IMPORTANT: Thorlabs is the primary point of contact for ScanImage 4.1 support. They may be contacted at imagingsales@thorlabs.com.
'ScanImage 4.1 Compatible' Thorlabs MPM System Specifications
- Electronics control unit (ECU) with digital (hardware) scan phase adjustment installed
See note about digital scan phase adjustment below - Alazar ATS-9440 digitizer, with firmware version 6.07 and driver version 5.8.7 (or higher)
- Superlogics ScanImage 4.1 workstation:
- Multi-core (>4), 4 or more PCIe slots, 16GB (or higher) RAM, Windows 7/64-bit
- RAID 0 drive pair for data storage, typ. high performance, e.g. 2x Western Digital 10K RPM Velociraptor drive
Computer system is typically included with Thor MPM system - i.e. users need not purchase computer directly!
Digital Scan Phase Adjustment
ScanImage uses scan phase adjustment to select the correct portion of the sinusoidal scan trajectory for imaging. This is required to 'align' the image under bidirectional scanning. New Thor MPM systems include circuitry within the ECU (black box) allowing for digital (hardware) control of scan phase adjustment.
Legacy systems without this circuitry installed can still be operated under ScanImage 4.1. For these systems, only 'software' scan phase adjustment is available. With this degree of freedom alone, it will typically only be possible to achieve bidirectional scan alignment at some zoom levels. Also, unlike hardware scan phase, the optimal software scan phase value at each zoom level changes somewhat with the # pixels and # channels imaged.
Users with legacy systems are encouraged to inquire with Thorlabs about upgrading their system, to overcome these limitations.
Known Issues
ISSUE
WORKAROUND
NIDAQmx error -200479 appears ('Specified operation cannot be performed while Task is running') in some (rare) circumustances.
Type at command line: >>hSI.recover();
Contact developers if issue appears frequently and/or if any pattern leading to issue emerges.
After restarting ScanImage within Matlab session, imaging does not appear to work correctly.
Exit and restart Matlab to restart ScanImage 4.1
Unusually high noise levels, even with no input to digitizer.
Issue has been observed when using external clocking. Disable external clocking by setting Clock Source to '1' in ThorPMTSettings.xml file.
Image Histogram & Image Stats buttons interchanged. Image Stats operation not displaying statistics to command line.
Patch the following files: SI4.m ImageControlsV4.m
Vertical scrolling and/or horizontal jitter in image when software scan phase value falls below some negative-valued threshold
Maximize hardware scan phase value (i.e. use 254) to reduce absolute value of software scan phase if possible, to avoid crossing threshold. In general, maintain software scan phase at 0 and use hardware scan phase exclusively, if possible. Contact developers if, under some scan conditions, it appears impossible to achieve suitable bidirectional scan image alignment without setting software scan phase below negative threshold at which this issue appears.
ScanImage crashes when disk data is logged to becomes full.
No workaround at moment. Ensure sufficient space is available on data logging disk (typically a RAID 0 drive pair) before starting acquisition.
MATLAB becomes partially/fully unresponsive when selecting save directory after a previous acquisition
This issue appears on MATLAB 2012b. There is no known workaround at moment. Users can revert to using to MATLAB 2011b if this issue proves too bothersome.
Error appears on LSM initialization: "Caught unexpected "char*" Exception message is:
fnCall"
National Instruments Measurement and Automation Explorer (MAX) is corrupted. Select 'Reset Configuration Data' and restart computer. NI device name assignments must be re-entered after restart.