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Virtual Tissue (slide scanning): Setting up a focus map

Now that the acquisition settings are defined, you are ready to create a focus map. Follow the procedure below.

 

If no focus map is required, and the entire scan can be acquired at the current Z -depth, right-click and select Start Virtual Tissue Scan.
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 does not work, right-click within the tracing window and verify that Show All Scan Sites is checked.
    ClosedMultiple contours
    • For multiple contours, click the contour of interest to create a focus map for that contour.
    •  To select multiple contours, click each of them.
    • The selection order determines order and naming for acquisition. The contour you clicked first is acquired first and its file name is base name-1, the contour you clicked second is then acquired and its file name is base name-2, and so on.
  2. Create a focus map for each region of interest to be acquired.
    • Hold down the Shift key and click several grid cells to create a triangulation pattern between the selected cells.
      • To remove a selected cell from the focus map, click it.
      • If the tissue is particularly wavy or uneven, use more cells for a better quality image.
  3. Once all the focus sites (i.e., grid cells) have been selected, right-click and select Focus at selected sites.
  4. 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.
  5. When all the focus sites have been set, the focus grid is displayed with an interpolated focus map .
  6. 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.
  7. Once the focus map is satisfactory, right-click and select Start Virtual Tissue Scan with Pre-Focus. The acquisition process begins.

 

Acquiring and compiling Virtual Tissue images

 

See Virtual Tissue Overview

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