Slide scanning: Tracing the regions of interest

Now that your workspace is ready, trace the regions to be scanned according to the procedure below. Then adjust your camera settings.

Are you using fluorescence? Set up the Device Command Sequences before you start tracing.

1. Select the objective that will be used for the acquisition and verify that the matching lens is selected in the software.
2. Adjust the light on the microscope in such a way that it is comfortable to look at the slide through the oculars.
3. Turn on the live image mode (Acquire ribbon>Live Image button).
4. Load the slide onto the stage and bring the slide into focus at a low magnification (2X or 5X).
5. Using the joystick, bring the desired location into view.

   Use Joy Track to maintain registration between stage movements and your contours.

6. To begin tracing, right-click and select End Joystick Mode. Place a reference point.
7. Begin tracing a contour around the first region of interest on the slide, staying close to the tissue (see Tracing contours).

   Keeping the contour close to the tissue will reduce acquisition time and make it easier to place focus points.

8. To finish the contour, right-click and select Close Contour ( the module doesn't recognize open contours as regions of interest that can be scanned).
9. Continue tracing contours around all the sections to be scanned.

   Trace around the entire brain section (or even multiple brain sections) or around a single structure in the brain.

   The slide scanning module creates an image file for each region delineated by a contour. To obtain an individual image for each section, trace a contour around each section.