Physical Fractionator workflow >

3. Trace your region(s) of interest

Serial Section

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

Use the buttons to add new sections or edit the current section as needed.

  • 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 Serial Section Manager.

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

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.

  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.

    1. Click Select Objects from the Trace ribbon.
    2. Click the contour you want to edit; Stereo Investigator Whole Slide 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.

If you are using different contours for different anatomical regions within the same animal (e.g., ipsilateral and contralateral striatum), you can always combine these two regions in the analysis if desired, as long as they have been counted with the same sampling parameters.

Tracing Options

Move the stage automatically when tracing outside dashed boundary (AutoMove): Check the box to enable AutoMove that moves the stage when you click outside the dotted AutoMove area box.

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.