Setting up a focus map for slide scanning

Once the scanning settings are defined, you are ready to create a focus map. Follow the procedure below then scan and compile the virtual slide.

 

If you don't need a focus map and the entire scan can be done at the current Z -depth, right-click and select Start scanning slide.
To terminate the focus map setup and return to the tracing window, right-click and select Exit without scanning.

  1. Once the file name and location have been specified, the contour appears inside a grid.

    If no grid is visible, click in the contour to display the grid; if clicking the contour doesn't work, right-click within the tracing window and verify that Show All Scan Sites is checked.

  2. Create a focus map for each region of interest to be scanned using one of three methods:
    • Hold down the Shift key and click several sites to create a triangulation pattern between the selected sites.
    • Right-click and select Random focus sites.
    • Right-click and select Use markers to select sites.

    If the tissue is particularly wavy or uneven, use more sites for a better quality image.

  3. To remove a selected site from the focus map, click it.
  4. Once all the focus sites (i.e., grid cells) have been selected, right-click and select Focus at selected sites.
  5. The stage navigates to each selected site and the Focus Site dialog box opens. Bring the site into focus and click OK .
    • To skip the current site, click Skip this site; that focus site will be removed from the focus map.
    • To exit the focus map, click Cancel.
    • For Device Control options, click More.
  6. When all the focus sites have been set, the focus grid is displayed with a colored interpolated focus map.
    • Yellow represents the focus sites selected at Step 2.
    • Green represents Z where the difference between Green Z and Z from each adjacent site is less than the threshold value you defined.
    • Red represents Z where the difference between Red Z and at least one adjacent site is equal or greater than the threshold value.
  7. To add focus sites, hover the mouse over the desired grid cell, right-click, and select Add to focus site list. Bring the tissue into focus and click OK.
  8. Once the focus map is satisfactory, right-click and select Start scanning slide with pre-focus. The acquisition process begins.