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2. Trace your region(s) of interest

Procedure

Serial Section

Working on: Select the section from the drop-down menu.

  • Add new section: Click the button to add a new section.

    The newly created section becomes the active section in the Working on drop-down menu, and it appears in the Virtual Section Manager.

  • Edit section: Click to edit information about the section selected in the Working on drop-down menu.

If you have one section per slide, follow the entire workflow for one section at a time up to the Count Objects step. When you're done counting for that section, click the Add New Section button in the Count objects step and follow the prompts for the next section.

If you have multiple sections on a single slide, tracing the regions of interest for all the sections in this step may be more efficient.

Trace your Region(s) of Interest on the Current Slide

  1. Select a contour type from Contour drop-down menu.

    To adjust contour settings, such as name and color, click the cog icon to open the Contour Settings window (equivalent to opening contour preferences from the File menu).

    You may want to name contours for the area(s) of interest in which you are counting and change colors to maximize visibility.

  2. Focus through the section as needed. The current section is indicated in green in the Z-meter.

  3. Trace a contour to delineate a region of interest (use the same contour type for the same region of interest in subsequent sections). Right-click and choose Close contour to complete your contour(s). Do not use open contours.

    You can trace more than one contour if you plan to count different regions of a structure, different structures, or have material from more than one test subject on a slide.

    Example: You are counting the Substantia Nigra (SN) and you want to delineate left SN counts separate from the right SN counts. Use a different contour for each side (making sure you use the same contour choices for subsequent sections). The data can then be easily viewed per side or across the entire structure, provided that both sides were counted with the same sampling parameters.

    1. Click Select Objects from the Trace ribbon.
    2. Click the contour you want to edit; Stereo Investigator Cleared Tissue Edition displays small white squares over contour points.
    3. Once the white squares are visible, right-click to access contour editing tools.
    4. Right-click and select Exit the Selection Tool when you finish editing.

Tracing Options

You can change the size of the AutoMove box by clicking the cog icon in the Tools section of the Move ribbon to open movement preferences.

Tracing methods: Choose your preferred contour tracing method. Note that you can change the method while you are tracing by right clicking and selecting a different method from the right-click menu:

  • Simple click: Click to place a point, move the cursor to a new position then click again to draw a line segment between the two points. Continue to place points that delineate the region of interest.
  • Rubber line: Similar to simple click tracing; as you move the cursor to a new position, a "rubber line" is drawn from the last point you placed to your current cursor position.
  • Continuous Line: Trace by clicking and dragging the mouse.