Slide scanning workflow >

3. Trace

Overview

In this step, you indicate the areas of the specimen to acquire by drawing contours around them. Later, in step 6. Region selection, you will indicate which delineated regions you want to include in the slide scan.

  • If you selected Scan in a grid... in step 1. Setup, the workflow skips this step because it is not necessary.

  • Drawing at least one contour is required if you selected Scan inside contour only or Scan a rectangle around the contour in step 1. Setup.

  • (optional) Add markers if desired. Markers can be used as focus sites in step 9. Define focus map; they can also be used to mark areas/objects of particular interest.

Procedure

Mode

Click the radio button to enable either tracing contours or placing markers

  • Trace contour: Select Trace contour mode, then indicate the areas of the specimen to acquire by drawing contours around them.

    • Choose your Tracing options (at the bottom of the workflow window)

    • Follow the instructions onscreen in the workflow window and described below to trace your region(s) of interest.

  • Place markers: Select Place markers mode, choose a Marker type from the drop-down list at the bottom of the window and click in the image to place markers.

    Markers can be used as focus sites in step 9. Define focus map.

Trace your region(s) of interest on the current slide

  1. Select Trace contour mode. Choose your Tracing options.

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

    • To adjust contour settings, such as name and color, click the cog icon in the Contours section on the Trace ribbon or go to File > Preferences > Tracing > Contours.

    • Note that you can exclude part of a contour by drawing a second contour inside it and selecting Exclude nested contours from scan region in step 6. Region selection.

    • You may want to name contours for the area(s) of interest that you are scanning and change colors to maximize visibility.

  3. Trace a contour to delineate a region of interest (we recommend using the same contour type for equivalent regions 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; Neurolucida displays small white squares over contour points.
    3. Once the white squares are visible, right-click to access various editing tools.
    4. Right-click and select Exit the Selection Tool once you have finished editing.

  4. Repeat these steps to draw additional contours for each region of interest that you want to include in the slide scan.

Tracing options

Automatically move the specimen when tracing: Check the box to turn on AutoMove. AutoMove is very helpful when contours extend beyond the current field of view.

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.

Markers

(Optional) Markers can be used as focus sites in step 9. Define focus map. In addition, you can place markers on or near structures of interest.

  1. Select Place markers mode.
  2. Select a Marker type from the drop-down list.
  3. Click in the image to place markers.