Image Volume Spaceballs workflow >

Available with the Stereo Investigator Cleared Tissue module only. Click here for more information.

6. Count objects

Procedure

The workflow displays a list of the sections and contours that were drawn for each section.

  1. Click the name of a section to select it. All contours within the section are listed below it.

  2. Click the name of a contour from the list to select it for counting.

  3. Click Start Counting. The workflow displays new options for counting and the first counting site is displayed.

  4. Focus and mark objects of interest as follows:

    1. Focus down until a small circle is visible in the center of the field of view; if the grid spacing is small, multiple circles may be visible.

      1. Select a marker from the Use marker drop-down menu.

      2. Place a marker at each location where a fiber crosses the currently visible circle.

    2. Focus through the section, marking each intersection between a fiber and the sphere, until all intersections have been counted; the circle will appear larger in each subsequent focal plane to represent the sphere or hemisphere.

      If you are using hemispheres and the current focal plane is the closest to the equator of a hemisphere, the marker is counted as 1/2 (see Markers counted as half counts under Sampling results).

  5. Once you've marked all the transections in the site, click next to move to the next counting site.

  6. Repeat steps 3-4 for all sites in a section.

  7. Once all the sites have been visited, clickBegin next section. If no contour has been traced in this section, the workflow redirects you to the Trace your regions of interest step for your next section.

  8. Follow the workflow to the Count Objects step again.

  9. Continue marking each section until you have completed all the sections in the subject.

  10. When complete, click I've finished counting.

Edge cases

For vessels that appear on the edge of the spaceball, use the “center line” rule:

  • If the center line enters and then leaves the probe, mark it twice (at the entrance point and at the exit point).

  • If the center line weaves in and out, mark the centerline every time it enters or leaves the spaceball.

  • If the center line doesn't enter the spaceball, don’t mark it.