SciScan: Scientifica’s two photon software
My friend Bruno has written some very nice software for Scientifica’s two photon microscope systems. It’s called SciScan.
It’s written in LabVIEW and runs both their conventional galvo and resonant systems. These screenshots are all from the conventional galvo version of the software, but the resonant version looks almost identical (there’s no arbitrary line scan in the resonant version, of course).
In addition to the very basics (frame scans and z-stacks), both galvo and resonant versions can do fast volume scanning using a PIFOC piezo objective mover. Both the slow z-stacks and the fast volume scanning modes can modulate a Pockels cell with imaging depth.
SciScan provides Pockels cell control, PMT control and XYZ motion control and a variety of display features such as color overlay, moving averages, group averages, histograms, normalized or manual display range settings, display palettes to show saturated pixels in red, etc.
For the resonance scanner, the software corrects on-the-fly for the distortion from the sinusoidal mirror velocity profile. They use a National Instrument FPGA in a PXI system for the resonant scanner data acquisition.
For the conventional galvo system, the software provides arbitrary line scans, on-the-fly brightness-vs-time ROI analysis, unidirectional or bidirectional scanning, and arbitrary frames (eg. non-square pixel aspect ratio).
The data acquisition for the galvo system is based on a NI PCI 6110 card with an optional extra card to control Pockels cell and piezo.
For the resonance scanhead, Scientifica have completely redesigned the optical path to overfill the large back apertures of low mag, high NA objectives. This new optical design is also available for the galvo scanhead. Alternatively, they also still have their original galvo system available.
Bruno will be demoing the software at the Scientifica booth at SfN in San Diego.
I like the user interface which is often neglected in this type of program. Minimalist like Biorad’s Lasersharp but contains more information on the screen (like olympus’s software).
I’d love to see support for a console gaming controller (like the old Nintendo 64’s) for control of many of the basic imaging functions (focus, panning, etc.) and perhaps pipette placment too. Rather than constantly moving a mouse to click on small tabs you could sit back to control the imaging session (and avoid RSI).
This looks very nice! Is this open source or compiled code? Since the hardware is pretty much the same on all 2p scopes it should be rather trivial to adapt it to other systems…
Speaking of: Scientifica is running their resonant systems with a 5MS/s card? That seems to be rather slow and would prevent laser pulse lock-in sampling entirely.
Hello ybot,
just to clarify: the resonant scanner runs on a 40MHz FPGA in a PXI system, the galvo system runs on PCI 6110.
Best,
Bruno
I see – my bad (RTFM): I overread it in the post. Thanks a lot for the clarification!
The scientifica systems look more and more promising – I’d love to see one in action once. If I recall correctly that means that they now support your software, Helmchen’s Helios and Janelia Farm’s Scanimage out of the box – is that right? That would be a lot of very much appreciated end-user flexibility.
Best,T
Hello ybot,
if you want to see it in action you can email info@scientifica.uk.com to see whether a demo is scheduled somewhere near you.
Best,
Bruno
Very nice! Can this be used with a AlazarTech digitizer?