Creating a Focus Map in LAS X Navigator

Owned by Andrew Vaughan
Last updated: Apr 17, 2023

Some samples are not completely flat (e.g. tissue that is not completely pressed down against a coverslip). A Focus Map will allow you to mark the different heights in the specimen to correct tile scans or Mark & Find experiments so the sample is always in focus. Note that this is for samples that are inherently not flat. It doesn't correct for focus drift that might occur over time.

  1. Open LAS X Navigator.
  2. Make an overview image of the sample (e.g. using Spiral).
  3. Click the Focus Map Point button.
  4. Click on a part of the image where you want to make a focus map point.
  5. Repeat this at various positions.
  6. Click on the Focus Map button.
  7. The dialogue box shows the points you've marked, but the Z is not included.
  8. Click on one of the positions in the Focus Map dialogue to go to that point.
  9. Adjust the focus until it is correct and then click Set Z.
  10. Repeat for each position.