5 – Supported Peripherals

SciScan is able to communicate to a wide range of peripheral devices to integrate control into a single interface. SciScan communicates with these devices through either USB interfaces or through TTL control. These control mechanisms are specified and set in the Peripheral.Settings section of the .ini file.


SciScan communicates with the microscope’s XYZ motor through a USB-to-RS232 (COM port) adapter that is built into the rack mountable stage driver. Only Scientifica XYZ stages are supported in SciScan by default – drivers for other stages can be written by users.

Intensity Control

SciScan offers two ways to integrate laser intensity control; either a motorised half-wave plate option or a Pockel’s cell (Galvo, Resonant).

  • Motorised Half-Wave Plate – Also referred to as the Motorised Intensity Controller or MIC, SciScan can be configured to communicate with a MIC motor through a USB-to-RS232 (COM Port) adapter that is built into its rack mountable driver. Only Scientifica MIC modules are supported by default, however, the driver can be modified for different motors if needed.
  • Pockels Cell – The Laser power control interface can be setup to output a 0-2 V signal on an analogue output channel which can be used to drive any suitable EOM through its modulatory range.
    • For multiphoton applications, typically the Conoptics Model 350-80LA modulators are used with the Model 302RM Driver
    • Pockels cells are the modulation system of choice for resonant scanning systems due to their fast response time. SciScan comes with a turn-around blanking module for the resonant scanning system to blank the beam during the non-linear portion of the resonant mirror’s travel.

Piezo Objective Positioners

SciScan will operate several different Piezo objective positioners for fast volume scanning. The analogue channel outputs an analogue 0-10V signal to drive the Piezo through its complete range. This output is scaled depending on the volume specified in the Z Stack settings and the scale factor specified in the .ini file.

  • The P-725 PIFOC® with the E-665 Controller from Physik Instrumente would be suitable for most applications.

Mechanical Shutters

SciScan supports a single mechanical shutter which should be placed in the laser path before the beam enters the scan head but after any intensity control. The digital output channel hat controls the shutter outputs a +5V digital signal via TTL to the shutter controller. The shutter opens with the +5V TTL and closes again with a 0V signal. Any shutter that operates on this logic should be compatible with the software.

  • The SH05 mechanical shutter and SC10 controller are typically used.

Scanning Mirrors

The data acquisition system is capable of outputting a  ±10V command waveform. Please consult the data sheets for your scanning mirrors to confirm the maximum safe input range. Voltages sent to the scanning mirrors can be set in the Analogue Output Tabs (Galvo, Resonant).

  • Standard Galvos – SciScan outputs a ±10V analogue signal as a control voltage to the Galvo drive boards. Any scanning mirror that accepts a similar command waveform should work with SciScan.
    • Typical Scientifica systems make use of MicroMax series 671XX single axis drivers and are used in conjunction with 8315kL mirrors from Cambridge Technology which utilise a maximum ±5V range.


  • Resonant Galvos – SciScan for Resonant makes use of 8kHz CRS series scanning mirrors from Cambridge Technologies
    • These mirrors typically accept a 0-5V voltage that will scale the scan range.

PMTs and Preamplifiers

SciScan constructs the acquired image using either a unipolar positive or unipolar negative analogue signal. the Galvo DAQ system accepts a ±10V signal while the resonant scanning system accepts a ±1V input. Any PMT+Preamp combination that produces an appropriate output should work with SciScan. Please choose pre-amplifiers appropriately.

In the case of HyperScope that can image as a resonant or galvo system, Scientifica provides variable pre-amplifiers that are switched remotely when the system is switch between galvo or resonant scanning.

Automated Signal Switcher

SciScan is designed to reconstruct images using signal read out on a NI 5734 digitizer or a PCI-6110 for resonant or galvo system respectively. To direct the detector signals to the correct acquisition card, we are using an Automated Signal Switcher (8×8 Single Matrix BNC switch from LinkBone).


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