Probe Run List

Use this command to view and work with the results of probes. displays a list of all the previous stereological runs associated with the current data set.

Viewing the results

  1. Select Probes>Probe Run List (or click the Display  probe Run List button in a workflow) to display the Previous Stereological Runs window.
  2. Select a probe (or several probes) from the list.
  3. Click View Results to open the Sampling Results window.

 

Understanding the results in the Sampling Results window

Result name Description
Marker X Typically, each marker represents one cell type.
Counts by Site Raw data for each counting frame visited in each of the runs.
CE Scheaffer See Coefficients of Error
CE Schmitz-Hof
Z Depth Histogram Z depth location for markers placed in each section.
Planimetry How area and volume are calculated based on the area contained within the traced contour. NOT an unbiased estimate.
Data File Name File name associated with this data set, if the data was already saved.
Date and Time When the probe was completed.
Region Name of the contour type that defines the region of interest. If this is a composite of several runs, displays the contour name used for the first run is shown.
Number of Sampling Sites Number of sampling sites visited on all selected sections.
Counting Frame Area Area of a single counting frame.
Counting Frame Thickness Thickness of the counting frames along the Z-axis.
Counting Frame Volume Volume of a single counting frame.
Counting Frame Width X-axis width of each counting frame.
Counting Frame Height Y-axis height of each counting frame.
Sampling Grid Width Distance between counting frames (sampling sites) along the X-axis.
Sampling Grid Height Distance between counting frames (sampling sites) along the Y-axis.
Sampling Grid Area Area of the region associated with each sampling step.
Section Thickness Value used for section thickness across all sections that were sampled. This should be the minimum actual section thickness as measured by .
Number Weighted Mean Section Thickness Mean of all sections measured by focusing at the top and bottom of the section. This value should be relatively close to the Section Thickness value.
Estimated Population using Number Weighted Section Thickness Report this estimate when thickness was measured at every sampling site and when the section thickness varies dramatically across the sections that include the region of interest. Calculated using only the section thickness measurements from counting sites that contain markers. These measured thickness values are then weighted by the number of objects associated with them to produce a weighted average. The number weighted mean section thickness is reported in the Parameters section and is used to calculate the height sampling fraction.
Total Markers Counted Actual number of markers of this type counted during the probe run.

Sampling Results buttons

Print All Results Prints all the results for the selected probe run.
Copy All Results to the Clipboard Copies all the selected probe run results to the Windows Clipboard.
Edit Shape Factor Displays the Shape Factor dialog box (see Shape Factor). To obtain as accurate an estimate of the Coefficient of Error as possible, use the slider to edit the Shape Factor which describes the shape of the region of interest.
Edit Mounted Thickness Use to adjust the section thickness.
Equations Displays the equations used for the probe run.

 

Export directly to Excel (2003 or later) or copy the results to the clipboard and paste them into a Word document, PowerPoint presentation, Microsoft Excel spreadsheet, etc.

If you modify the results outside of Stereo Investigator Whole Slide Edition, they are not updated in the software.

  1. Click Probes>Display Probe Run List to display the Previous Stereological Runs window.
  2. Select a probe (or several probes) from the list.
  3. Click View Results to open the Sampling Results window.
  4. Click Export to Excel.

 

 

Summary tab Estimates and CEs for each individual marker.
Parameters tab Information to be added to the Methods section of a publication to enable other researchers to test the reproducibility of the results.
Counts by Site tab Information about the measured thickness and number of markers at each site. This information can be used to calculate your own CE or to compare thicknesses/number of cells within a section or between sections
Coefficient of Error tab Several CEs.
CE Variance Details tab Information related to the calculation of the Gundersen and Shaeffer CEs.
Section Details tab Marker counts by section.
All Markers Z Histogram and Individual Markers Z Histogram tabs

Distribution of cells within the tissue.

  • Ideally, with no sectioning artifact from the microtome blade, there is an equal number of markers placed at each “bin” from the top of the site.
  • In practice, there are fewer markers at the bottom/top of each site; set your guard zones so that they cover these regions.
  • A spike of cells at the top of the histogram could be caused by focusing through the tissue or counting cell bottoms at the top of the tissue as though they were cell tops (assuming that cell tops are the unique point you're trying to count).
  • A lower number of cells marked in the middle of the histogram is probably due to an incomplete staining penetration.
Z Depth tab Raw data necessary for your Z depth histogram.
Z Depth Details tab Actual Z values for each marker (rather than markers per bin).
Smoothness tab Distribution of markers within your ROI.
Planimetry tab

Area of each section and volume calculated from this area. Note that this information is biased; for an unbiased estimate of area/volume, use the Cavalieri Estimator.
Z Order tab Z value of the sections and the actual Z at which the contour were drawn in each section.
Raw Report tab Number of markers and tissue thickness per site.

Open Probe: Restarts the probe and lets you revisit each scan site for that probe.

Useful for second reviewers or to resume work for a probe run that couldn't be completed in one session (in this case, the probe is restarted at the scan site that was visited last).

  • If the markers placed during the first run are turned off, a second run can be executed without the visual bias of previous markers.
  • If the second run occurs after the synchronization between the tracing and a given section has been lost (e.g., the slide is removed from the microscope), realign the tracing with the slide to review the original run accurately. See

Delete:Deletes the selected probe run results.

Draw Sites: Use to view the counting frames used for the probe run.

Configure: Displays the Configure Probe Run List dialog .

Use to add, remove, and configure the results.