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

1. Set up the subject

Procedure

Subject Information

Type your name, the subject name, and any other information that you think will be helpful in the future.

Virtual section settings

Total height of image volume and Distance between image planes are automatically identified.
Set top (bottom) of ROI: Distance between the top (bottom) of the tissue and the top (bottom) of the virtual section.

To set the top or bottom of the region of interest (ROI), scroll the mouse wheel, or press Page Up/Down on the keyboard to focus through the section then click the SET TOP (BOTTOM) button.

Number of virtual sections: Number of desired virtual sections you will count for this subject. The appropriate number of virtual sections depends on your experimental goals, the density or sparsity of objects you will count, and the shape and size of your ROIs.
Virtual section thickness: Automatically calculated virtual section height (the distance between the ROI top and bottom divided by the number of virtual sections).
Sphere radius: Represents the radius of the spherical volume that you are going to count within the virtual section.
Use Hemispheres: Check the box to use the top hemisphere for counting instead of the whole sphere. Uncheck the box to use a sphere. Note: If you use hemispheres, markers that are on the bottom edge of the hemisphere are factored in as half counts in the results. See explanation of marker totals.