If you want to acquire a topography image in ZEN, you need to start the topography measurement wizard.

  1. You are on the Applications tab.
  1. In the Topography tool, click on Start.
  2. The wizard starts. In the left tool area you see the Step 1/2 Setup, in which you can adjust the acquisition parameters for the topography image. In the center screen area you see the live image from your sample in continuous mode.
    As a default the system is set up to acquire only one single z-stack. In case your region of interest (ROI) is all within your field of view (FoV) continue with step 5 of this guide. If your ROI is bigger than your FoV, you can setup a tiles acquisition in the Tiles tool:
  3. In the Tiles tool, enter the number of desired tiles in the X and/or Y direction input fields, e.g. 3 x 3. This will create a 3 x 3 tiles image with 9 single tiles.
  4. Click on Set stage position to define the anchor point of your tile scan at the current stage position.
  5. In the Navigation (must be expanded first) section click on the arrow buttons to navigate through the single tile images. This can help to check if the tiles cover the full ROI.
  6. In the Acquisition Mode tool, adjust the settings for Objective, Frame Size, and Bits per Pixel according to your requirements.

  7. Note that you can not change the parameters Frame size and Bits per Pixel (Bit Depth) while Continuous mode (Live image) is active. To stop it click on the Stop button in the upper left corner.

  8. Focus on the surface. The default pinhole setting is Max. This allows you to easily focus on the surface just like with a widefield microscope. Of cause focusing via the eyepieces is also possible.
  9. In the Channel tool, adjust the pinhole to the required diameter. For best performance of the system we recommend setting the pinhole size to 1 Airy Unit (1AU button). Since the depth of field is reduced in confocal images you most probably need to slightly adjust the focus position.
  10. Adjust the intensity of the laser. To do so, focus on the brightest section of the z-stack. Then adjust the laser either via the 405 nm slider or the Master Gain slider. Adjust the intensity so that you do not see any overexposed pixels (shown in red).
  11. In the Z-Stack tool, set up the Z-Stack by adjusting the z-range (upper and lower limit of your z-stack). We recommend using First/Last mode for that.
  12. Make sure the whole surface, you want to measure, is within these limits. In case of a tile scan you can use the navigation arrows in the Tiles tool to jump to the different tiles to check.
  13. Click on Next.
  14. The wizard moves to Step 2/2 Z-Stack Acquisition and starts the image acquisition.
  15. After image acquisition the topography image (height map) will be automatically generated. You will see the image in the center screen area after the acquisition and the processing is finished.
  16. Adjust the thresholds by using the Noise Cut slider, if necessary. Note that pixels below the lower threshold are displayed in blue color and pixels above the upper threshold in red color.

  17. In case you have activated Automatic Noise Cut in the Topography tool, this step will be skipped and the topography image will be exported to ConfoMap automatically.

  18. Finish your work in ZEN by choosing the following options:
    - If you click on Export to ConfoMap, the topography image will be directly opened in the ConfoMap analysis software.
    - If you click on Save Topography, you can save the topography image to the file system.
    - If you click on Save Z-Stack, you can save the raw data of the z-stack.
  1. You have successfully acquired a topography image. As the image analysis is performed with ConfoMap software read the ConfoMap documentation for further information.