On startup of a system with motorized stage and/or focus a request will appear asking if the components should be driven to the end switches and calibrated. This ensures that you begin working with absolute coordinates in this session with the microscope. If the microscope power is cycled, then this process should be repeated. This function is of particular use if you continually work with a sample carrier e.g. 96 well plate, of the same format mounted in the same manner repeatedly with a given experiment template. If you perform a carrier calibration once with a calibrated stage, then the carrier calibration is essentially always valid. This is done in the Sample Carrier section of the Tiles tool. Note these features are only available if you have a license.

The request to calibrate stage and focus on startup can be activated/deactivated under Tools > Options > Startup/Shutdown > Stage/Focus Calibration.

 

  1. You have licensed this functionality and activated it under Tools > Toolkit Manager.
  1. Put your Sample Carrier on the stage.
  2. Go to the Acquisition tab.
  3. Select a low magnification objective (e.g. 10x) from the Microscope tool in the Right Tool Area.
  4. Click Live and find your focus area either using transmitted or fluorescence light.
  5. In the Stage tool of the Right Tool Area, activate the Show all mode and then click Calibrate.
  6. Check if the alignment and orientation of your camera and joystick is correct by dragging the software joystick up, down, left and right and observe whether the movement of your image corresponds to movement of the circle.
    The alignment of the camera is correct if the movement of a given stage axis is congruent to the corresponding axis of the image. An offset in the alignment will be seen as a saw tooth pattern along the edge of a tiled image (e.g. 4x4 tile region).
    In addition, check whether the image movement also corresponds accordingly when you move the hardware joystick of the stage.
  7. If the orientation of the camera to the software joystick (stage tool, right tool area) is incorrect, go to the Camera tool, activate the Show all mode, and click Model Specific. The orientation of the camera (image) can be adjusted by flipping, rotating, or mirroring.
  8. Alternatively, you can and may also need to invert the x- and y-axis of your stage in the MTB in order to align the hardware joystick and the software-controlled stage movement.
  9. Ensure that all the prerequisites (e.g. channel and camera settings) for a Tiles & Positions experiment on your sample are fulfilled. If necessary, use the Smart Setup for the setup.
  10. After you have defined at least one channel (e.g. EGFP), activate the Tiles checkbox.
  11. If you wish to work with a sample carrier, complete the following steps.
  12. Open the Tiles tool and activate the Show all mode.
  13. In the Tiles tool, open the Sample Carrier section.
  14. Click Select....
  15. Select a sample carrier template and click OK.