4 Starting Sciscan and GUI walkthrough

Please note: Before running SciScan for the first time, it is best practice to set up the .ini file correctly to avoid errors on start-up. The best way to do so is using the confirmINIsettings.vi.

Starting the main user-interface “SciScan HYPERSCOPE.vi”

The new main user-interface replaces the old choice to be made between “SciScan GALVO.vi” and “SciScan RESONANT.vi” (still available for stand-alone GG or RG systems, but even they can be started from the new main user-interface). Just double-click on “SciScan HYPERSCOPE.vi” in the SciScan project folder and run the VI:

1) Double click on “SciScan HYPERSCOPE.vi 2) Press the “Run” button (arrow symbol) 3) Main user-interface for SciScan
   

Depending on your current DAQ-Package, there will be up to three light path configurations available, to start up the required SciScan user-interface:

Imaging Path Reso

 
  • When choosing “Imaging Path Reso“, SciScan will be initialized for resonant imaging only
  • This option is available for RGG+GG, RG+GG, RGG and RG systems only (RG starts automatically)
    • Galvo imaging won’t be available whilst this option is selected
    • Simultaneous photostimulation will still be available for dual path systems (RGG+GG, RG+GG)
    • Photostimulation without parallel imaging will be available for RGG systems
  • To switch the current light path configuration, click on one of the other available options
  • Use the “QUIT” button to shut down the software completely

Imaging Path Galvo

  • When choosing “Imaging Path Galvo“, SciScan will be initialized for Galvo imaging only
  • This option is available for RGG+GG, GG+GG, RGG and GG systems only (GG starts automatically)
    • Resonant imaging won’t be available whilst this option is selected
    • Simultaneous photostimulation will be available for dual path systems (RGG+GG, GG+GG)
    • Photostimulation without parallel imaging will be available for RGG and GG systems
  • To switch the current light path configuration, click on one of the other available options
  • Use the “QUIT” button to shut down the software completely

Stimulation Path Galvo

  • When choosing “Stimulation Path Galvo“, SciScan will be initialized for Galvo imaging only
  • This option is available for RGG+GG, RG+GG and GG+GG systems only
    • Resonant imaging won’t be available whilst this option is selected
    • Simultaneous photostimulation is not available, as imaging is carried out on the stimulation (reflective) light path
    • Photostimulation without parallel imaging will be available for RGG+GG, RG+GG and GG+GG systems
  • To switch the current light path configuration, click on one of the other available options
  • Use the “QUIT” button to shut down the software completely

Graphical user-interface overview

There are some changes to the GUI in SciScan 1.3, but the introductory videos are still a good starting point for familiarising yourself with the SciScan GUI. Please refer to the change log, for an overview of all major changes. Here you can find a description of the current Galvo and Resonant GUI:

SciScan 1.2 Galvo GUI SciScan 1.2 Reso GUI

 

Galvo

Resonant

 
Label Name Function
A Menu Shortcut Menu – See Below
B Grid Overlay Slider Adjusts number of cells in grid overlay and displays sizes of each cell
C Reset Zoom Resets the digital zoom to fill the available image area
D Image display area Displays image based on selected tab (F)
E Grid Overlay Grid overlay
F Channel Select Switches between available channels and other display panes
G Frame Counter Counts progress through current acquisition (based on number of frames to acquire)
H Image Display control Displays channel histogram and allows for display averaging or lookup tables
I Notebook Saves notes to text file alongside recorded data
J QUIT Closes SciScan (Hidden in HyperScope – only visible, when the main menu gets stuck / waiting on user action)
K Motor Controller Controls XYZ Motors
L Laser Power Used for either Pockels Cell or Half-Wave plate based attenuation systems to modulate laser power
M Shutter Indicates state of imaging path shutter, open or closed, state can be manually changed or locked
N Open Settings Opens or closes all settings tabs
O PMT Gain Control Control the gain on Scientifica MDU-8000-10 controller
P Focus Starts an acquisition to display a live image (does not save the data)
Q Record Starts an acquisition and displays a live image – data is saved
R Cancel Stops current “Focus” or “Record” action (data up until point of press is saved if in “Record” mode)
S Piezo.Active Enables or disables the use of a Piezo objective positioner (see Piezo Tab pages for more information)
T Basic Settings Contains tabs for basic control of scan
U Advanced Settings Contains tabs for advanced scan control

Menu item Function
Load Allows users to load a previously saved scan configuration
Save Allows users to save current scan configuration to a configuration file
Plugins Provides a list of loaded plugins for quick access
QUIT Quits the software, functions identically to the QUIT button on the GUI (only visible in the stand-alone version – GG or RG)
Help Launches the SciScan Knowledgebase (requires internet access)

 

Was this article helpful?

Related Articles