SciScan Screenshot

Get scanning: Download SciScan 1.2

The latest version of Scientifica’s control and acquisition software for laser scanning microscopes, including the Scientifica multiphoton microscope range, is now available to download from the SciScan Knowledge Base.

This update includes a number of new features that add a variety of new functionality to SciScan as well as some bug fixes to improve performance and stability.

Uncaging Module

SciScan’s uncaging module is designed to allow users to carry out multiphoton, single-point, uncaging or photo activation experiments while recording the result using electrophysiology equipment.

The module allows you to select multiple points within your field of view and use a fast laser attenuator, e.g. a Pockels cell, to flash these points with precise spatial and temporal resolution.

Tiling Pre-set for SciScript

A pre-set has been added to SciScript, SciScan’s add-on scripting feature to automate repetitive tasks, to allow systematic image capture for regions larger than the maximum FOV of the objective. Tile pre-sets are available for both 2D and 3D acquisitions.

A macro to automatically stitch together 2D acquisitions is provided with any recorded 2D tile. Stitching for 3D acquisitions needs to be carried out manually.

Tiling Types:

  • Single Plane – obtains a series of 2D XY scans to create a large single plane image.
  • Slow Z – obtains a series of Slow Z Stacks across the desired region.

Advanced Trigger Output

SciScan’s trigger interface for Galvanometer based scanning systems has been expanded to output user specifiable pulse patterns to aid in triggering of external devices and synchronising equipment with SciScan.

The trigger tab now provides you with four options for customisable trigger. Pulse parameters can be set either in milliseconds or in the number of frames by flipping a switch in the user interface.

  • The legacy frame pulser was available in previous versions of SciScan and was always active by default. In order to maintain backwards compatibility this frame pulser is still available, but it must now be selected from the dropdown menu. This will output a Frame Clock signal derived from the frame rate that you are scanning with and operates with a 50% duty cycle with the rising edge corresponding to the first pixel acquired in a given frame.
  • The continuous pulses mechanism allows you to specify the parameters of a continuous pulse train which will output during image acquisition. Pulse parameters are adjusted using the controls within the tab in the user interface.
  • The single pulse option allows you to specify a single pulse to be output after a user-specified delay and for a user-specified duration.
  • Trigger off

Zoom and Move to ROI

SciScan provides several tools to aid in monitoring and conducting experiments on specific regions of interest.

The Zoom and Move to ROI function allows you to mark either a point in your FOV and the move it to the centre of the field by moving the XY stage, or allows you to select a rectangular region of interest and zoom to it easily.

Arbitrary Piezo Scale Factor

SciScan integrates control of an external Piezo objective positioner in order to carry out volume scanning. Allowing users to capture fast, functional, data in three dimensions.

Previously, scale factors for either 400 µm or 100 µm travel piezo drives were available. The Scale Factor can now be set manually through the .ini file to provide scaled outputs for other devices.

As always, SciScan remains a free, open-source utility for the use of everyone in the Scientific community. If you aren’t already signed up for the knowledge base you can do so automatically on the website.

View the full release notes and download version 1.2.