Preferences: Stereology
Purpose
The Stereology preferences panel provides customization options for the appearance and function of some stereological probes.
Access Stereology preferences from File > Preferences > Stereology.
Automatic movements
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.
Enable movement to top of stack when using a non-exhaustive acquire: Moves to the top of each image stack when counting an SRS image stack series.
Disable the AutoMove box during stereological procedures: See AutoMove
Use this automatic focus scanning rate: Type a number into the box or use the arrows to adjust the scanning rate when using automatic focus.
Cavalieri
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.
Counting frame
See Counting frames and Counting rules for Optical Fractionator
Force counting frame to be square: Creates a square counting frame as you adjust the frame with your mouse.
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.
Hide counting frame when using local probes: Hides the counting frames when local probes such as Nucleator are being performed.
Use "Not In Z limit " color when above or below disector: When you are above or below the disector, the program changes the color of the counting frame from the default colors (typically red and green) to a single color.
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.
Restrict placing markers to range of Optical Disector: Markers can't be placed outside of the disector.
Display
Choose a color that stands out against the background for the probe shape (cross-hair, line, cycloid, etc.).
Choose a color that stands out against the background when placing tick marks on probe shape (cross-hair, line, cycloid, etc.).
Choose a marker type that will help you visualize the tick marks.
Tick mark size: Type a number into the box or use the arrows to change the size of tick marks.
Results
Configure general settings
Expand all calculations when viewing results: Displays all the categories in the left panel of the Sampling Results window. See 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.
Configure coefficient of error
Display Gundersen CE: Check the box to display the Gundersen CE in the results.
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 Scheaffer CE: Check the box to display the Scheaffer CE in the results.
Display Schmitz-Hof CE: Check the box to display the Schmitz-Hof CE in the results.
Display planimetric results: Lists planimetric data in the results.
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.
SRS
Controls Systematic Random Sampling options.
Exclude nested contours from the region of interest: 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.