Laser-scanning microscopes are indispensable tools for biomedical research. Typically, commercial laser-scanning microscopes are controlled by proprietary, purpose-designed electronic hardware and computer software. It is often difficult if not impossible to adapt these systems to new experimental needs, such as incorporating laser microbeam systems for microsurgery or photoactivation. WiscScan was built to address this difficulty. WiscScan combines nearly all the functionality of a laser-scanning microscope/microbeam apparatus into a single software package. This package controls scan waveform generation, signal conditioning, and microbeam pointing. It runs inside a commercial, general-purpose digital signal processor (DSP) residing on a PCI card inside a desktop PC. This host computer loads programs onto the DSP and provides control for microscope focusing and stage movement through a graphical user interface. This all-software approach has allowed us to develop a powerful and flexible development platform for laser-scanning microscopes and has facilitated the incorporation of new functionality such as fluorescence excitation lifetime imaging.


  • Pockels cell can be fully controlled from WiscScan GUI in all systems.
  • Laser power meter output is shown on WiscScan.
  • New XYZ generator added to WiscScan.
  • Automatic white balance controller for QCam was added to WiscScan.
  • DCC gain controller was added to WiscScan GUI.

This is an accordion element with a series of buttons that open and close related content panels.

Version History

WiscScan: Older Versions

What’s new in WiscScan:

WiscScan 7.1.0 (Beta Build 2869)

OME XML Metadata:
All metadata inconsistencies have been resolved to match the new OME schema, confirmed by successful OME XML validations and FIJI Image Stitching.

Metadata Group Update:
First-time users will now be allowed to choose which research group they’re experimenting with, allowing for a more comprehensive experimenter information collection during imaging.

Updated Hardware Information for ULTRA:
The ULTRA workstation now saves hardware information in metadata pertaining to the settings used for each image acquired.

Flow Cytometry Applications:
The new flow cytometry feature is fully operational, allowing for particle sorting with four different methods. Sorting automation includes syringe pump and valves, allowing for fully automated experiments.

Many more bug fixes!





Support for New ASI firmware:
Can serially control ASI’s MS-2000 motor controller

Support for Olympus Z-motor:
Can serilally control the Olympus BX61WI for Ultra

Support for a Motor Controll interface:
Can add as many new motor controllers as desired

Support For The Sutter Instrument Filter Wheel For SLIM:
Can control the SI filterwheel and save appropriate images and metadata

Metadata Recall:
Can recall the metadata for the previous experiment correctly.
This data is saved only after the first time it is entered at each login

WiscScan 6:

MaiTai laser support:
Can tune to a particular excitation wavelength
Cannot yet automate across multiple wavelengths

NetID login:
Use Wisc NetID to log in to WiscScan
Files automatically uploaded to LOCI’s OME file server

Improved OME-TIFF metadata:
100% validated and working
Works with ImageJ and Fiji using Bio-Formats

Share experiment summaries on UW Forward:
Optional; check a box in WiscScan to enable
See: http://forward.library.wisconsin.edu

Many bug fixes!