Stereology Preferences

Enable Automatic Moves To Top Of Section	Moves to the top of the section when moving to a new sampling site.
Enable Automatic Moves To Top Of Disector	Moves to the top of the disector (3D counting frame) after the top of the section has been marked.
Disable The AutoMove Box During Stereological Procedures	See AutoMove

Cavalieri

See Cavalieri Estimator Probe

Show Cavalieri Grid In Show Whole File Mode	When the entire file is shown, the Cavalieri grid is superimposed on the tracing.
Display Cavalieri Grid Using Circles	Draws circles around every fourth Cavalieri point.

Colors And Tick Marks

Set Probe Color	Choose a color that stands out against the background for the probe shape (cross-hair, line, cycloid, etc.)
Change Tick Mark Style/Size	Choose a marker type and a size that help you visualize the probe's results better.

Counting Frame

See Counting Frames and Counting rules for the counting frame

Display Counting Frame With Extended Exclusion Lines	Extends the exclusion lines beyond their normal range.
Mark Center Point of Counting Frame	Adds a center point to each counting frame.
Use Not In Z Limit Color When Above or Below Disector	When you are above or below the disector, Stereo Investigatorchanges the color of the counting frame from the default colors (typically red and green) to a single color. These colors can be changed under Counting Frame Colors.
Restrict Placing Markers To Inside of Counting Frame	Markers can't be placed outside of the counting frame.
Restrict Placing Markers To Acceptance Area	Markers can only be placed in the counting frame excluding the guard zones.

Results

Expand All Calculations When Viewing Results	Displays all the categories in the left panel of the Sampling Results window. See Display Probe Run List
Display Partial Calculations of Formulas	Controls the display of the planimetric variance details in an SRS probe; when checked, displays the covariogram values (A, B and C).
Fill Bottom Entries of Columns With Zeroes	If this option is not selected, cells with no recorded values are blank.
Sort Sections In Ascending Order	Applies to the display of probe runs.
Display Planimetric Results	In the Sampling Results window.
CE Selections	See "Coefficients of Error"
Only Display Gundersen CE If 3 or More Runs Exist	Since the Gundersen CE takes into account values from neighboring sections, it is only valid if 3 or more runs have been performed. This option keeps invalid Gundersen CE values from being displayed. It may be helpful to turn this option off during a pilot study to obtain a rough estimate of the CE.
Display Raw Data Report	Includes the number of counts for each sampling site in each probe run.
Display Section Order Report	Lists all sections in order of their actual Z position.

Probes Menu

Only the probes checked appear on the default Probes menu.

SRS

Controls Systematic Random Sampling options.

Exclude nested contours: Nested contours are closed contours contained entirely within another contour. When you select this option, the interior of the nested contours is excluded from the probe layout.