Stage Control (Galvo)

The XYZ stage controller allows the user to navigate their sample during standard imaging as well as off-axis imaging through the Virtual XYZ feature.

By default only Scientifica stages are supported by SciScan and all three stages must communicate through a single COM port  To set up a third party stage please see the programming guide.

Interface Walkthrough

Aabsolute position (abs pos.)Displays the current absolute motor position
BPosition save moduleLaunches the Position Save Module
CMovement buttonsContains buttons to move the system in X Y and Z. The four button cluster is responsible for X and Y while the separated up and down buttons control Z. Stages will jog in one direction by holding a direction button down. The numbers in the middle of the X and Y buttons and between the two Z buttons are the current step size; if a directional button is clicked once the stage will move this many microns in the given direction.
DEmergency stopThe Emergency stop button allows you to quickly stop any of the stages even if they are in the middle of a pre-programmed movement.
ERelative Position (rel pos.)Displays the current relative position to user defined "0". Can be used to move to a specific point by over-writing the values and pressing enter.
FReverse directionChanges which direction the given arrows move the stage.
GSet stage speedThe set stage speed button will allow you to set a fast and slow speed for the XYZ stages, clicking the button launches a window to set the speeds, detailed in Speed Settings
HLP (Long Press) EnableEnables or disables continuous movement when movement buttons are pressed and held.
IVirtual XYZThe virtual XYZ radio button has been designed specifically to allow a virtual focus axis for use with the Scientifica Tiltable Objective Mount (TOM)
JSet zeroAllow you to zero the relative position of each motor to the current position, either individually or all at once.
KMovement buttons Set custom move in microns, appears in the drop-down menu C


Absolute and Relative motor positions

SciScan uses absolute XYZ motor positions (“abs pos.”) for all internal operations. Absolute positions are set such that 0 is in the centre of the travel range of each axis and can only be reset using the calibrate XYZ (found in the maintenance folder in the main SciScan Project. Note that the main SciScan user interface must be running before executing the calibration program. Please follow on-screen instructions when calibrating the absolute motor positions.).
In addition, SciScan also allows users to set an arbitrary ZERO position and will display relative distances to the user-defined ZERO position (“rel pos.”).

Please note: Within the Position Save Module, the term “relative position” refers to XYZ distances from a user-defined ORIGIN, which may not necessarily be identical to the user-defined ZERO position.

Virtual XYZ

Virtual XYZ Angle Interface
Virtual XYZ Angle Interface

SciScan’s virtual XYZ module is designed for use with Scientifica’s Tiltable Objective Mount, or TOM. The software module uses a combination of the microscope’s Z-Focus motor and the XY stage to create a virtual approach axis along any angle the objective is positioned at.

By ticking the virtual XYZ radio button you can enable or disable the module; when enabled a small dialogue box will pop up and prompt the user for two angles, the vertical rotation angle and the horizontal rotation angle that the objective is positioned at. The angle can be read from the scale on the TOM.

Once the angles are correctly entered you can navigate along the virtual axis by using the XY or Z movement buttons in the motor interface, labelled C in the diagram above.

Z-Stacks can also be carried out off-axis. Simply set up the Z-Stack as normal using the motor controller navigation buttons to set your top and bottom planes.

Please note: When setting up a Z-Stack using the Virtual XYZ system, you must set the start and end positions using the software interface and not any hardware controllers, only through software is the navigation system tilted to the angle of the objective.

Speed Settings

Stage speed settings
Stage speed settings

SciScan allows users to set separate speeds for software control and for hardware control. This allows for easier use of the motor controller in the software and eliminates confusion between software speed settings and the fast/slow switches on the Scientifica hardware controllers.

With Scientifica stages the speed is set in arbitrary units between 0 and 50000, 0 being the slowest and 50000 being the fastest setting.

SciScan uses the software speed to navigate between set points, z-stack planes and while using the jog-move feature of the motor controller. If you feel the speed is too slow for point to point navigation then increase the software speed.

The Hardware speed setting is applied whenever you use the hardware interface to move the microscope in fast mode, the hardware controller also has a slow speed switch that works independently of the software control.

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