Image Volume Spaceballs workflow >

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

7. View the sampling results

Procedure

View the results using one of the following methods:

  • Click a set in the Probe Runs list to select it and click the View Results button. The Sampling Results window is displayed.
  • Click Display Probe Run List (use after running more than one probe if you want results from multiple probe runs). The Previous Stereological Runs window is displayed.

    1. From the list, highlight the probe runs of interest.

      2. To view results for an entire region of interest, Ctrl-click to select all probe runs from the sections containing the region of interest. This will generate results for the entire structure, not just one section of the structure.

    2. Click View Results. The Sampling Results window is displayed.

    3. Click on a category in the left hand panel to display the corresponding results in the right hand panel.

      By default, the Sampling Results window initially displays the estimated population and marker total for the first marker type in the marker bar used for counting. Click on other marker types in the left hand panel to see the corresponding results in the right hand panel.

    4. Optional: Click Export to export all results directly to Excel (2003 or later).

Interpretation

Results are generated for each individual marker type used for counting as well as for all markers combined. By default, the Sampling results window initially displays the estimated length and marker total for the first marker type in the marker bar used for counting. Click on other marker types in the left hand panel of the Sampling results window to see the corresponding results in the right hand panel.

Estimated length by Spaceballs (µm)

The estimated length is calculated based on the total number of markers, the spaceball size, the grid size, and the virtual section height. See Image Volume Spaceballs equation.

Sampling results window

Displays the results of the probes selected in the Previous Stereological Runs window (see Display Probe Run List). Click on a category in the left hand panel to display the corresponding results in the right hand panel.

  • Parameters: File information and parameters associated with the selected probe runs. Descriptions of parameters are listed in the Right panel parameters drop down.
  • Marker X: Length estimate and total number of markers.

    • Adjusted Marker Count: The marker total after adjusting for markers designated as half counts when using hemispheres for the sampling probe. Markers that were placed on the bottom edge of the hemisphere are factored in as half counts. For example, if you place 10 markers total, but 2 of those markers are on the bottom edge of the hemisphere, those 2 markers will be counted as one marker, resulting in an adjusted marker count of 9. The adjusted marker count will be used to calculate the length estimate.

    • Total Markers Counted: Total markers placed. This number includes markers designated as half counts if you are using hemispheres for the sampling probe.

    • Markers Counted as Half Counts: Number of markers that are designated as half counts. If you are using hemispheres (the top half of the sphere as the sampling probe), markers that are on the bottom edge of the hemisphere are factored in as half counts in the results.

  • Counts by Site: Raw data for each site visited in each of the runs.
  • CE Gunderson: See Coefficients of Error. Note: CEs will only be calculated if a minimum of three sections have been analyzed.

  • Variance Details: Raw variance data used in the Gundersen CE calculation. See Coefficients of Error.

  • Planimetry: The area within each traced contour and the volume of the region of interest based on the total area of the contours and the virtual section height.

    Note that planimetry is biased; for an unbiased estimate of area/volume, use the Cavalieri Estimator.

The following results are displayed when Parameters category is selected in the left hand panel of the Sampling Results window:

  • 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.

  • Probe Shape: Displays whether a sphere or hemisphere was used.

  • Radius (µm): Radius of the spaceball.

  • Surface Area of Probe (µm²): Surface area of the spaceball.

  • Sampling Grid (X) (µm): Distance between sampling sites along the X-axis.

  • Sampling Grid (Y) (µm): Distance between sampling sites along the Y-axis.

  • Sampling Grid Area (XY) (µm²): Area of each grid step (Sampling Grid Width x Sampling Grid Height).

  • Virtual Section Thickness: Value used for section thickness across all sections that were sampled.

  • Volume Associate with Sphere (µm³): Volume of the spaceball.

  • Section Evaluation Interval: The interval of the tissue sections used for counting. Since Image Volume Spaceballs uses virtual sections that are stacked directly on top of each other (rather than physically cut sections which can be separated out into interval sets), the section evaluation interval always equals 1. See Image Volume Spaceballs equation.

Print Displayed Results Prints the currently displayed results category for all selected probe runs.

Print All Results Prints results of all selected probe runs.

Copy Displayed Results to Clipboard Copies the currently displayed results category for all selected probe runs to the Windows Clipboard.

Copy All Results to Clipboard Copies results of all selected probe runs to the Windows Clipboard.

Equations Displays the equations used for the probe runs.

Export to Excel Exports results of all selected probe runs directly to Excel (2003 or later).

Close Closes the Sampling Results window

About export to Excel

Click Export to Excel in the Sampling Results window. Results of all selected probe runs are exported directly to Excel (2003 or later). Each category in left hand panel of the Sampling results window is exported to a separate worksheet within a single Excel file.

  • Summary: Length estimates and Coefficients of Error (CE) for each individual marker.

  • Parameters: File information and parameters associated with the selected probe runs. This information should be added to the Methods section of a publication to enable other researchers to test the reproducibility of the results.

  • Counts by Site: Lists the number of markers at each site. This information can be used to calculate your own CE, or to compare number of intercepts within a section or between sections.

  • Coefficient of Error: Lists all Coefficients of Error. Note: CEs will only be calculated if a minimum of three sections have been analyzed.

  • CE Variance Details: Raw variance data used in the Gundersen CE calculation. See Coefficients of Error.

  • Section Details: Lists marker counts by section.

  • All Markers Z Histogram and Individual Markers Z Histogram: Distribution of marked intercepts within the tissue.

  • Z Depth: Lists how many markers are contained in Z-depth bins of 1 micron each. These values are used to generate the Z depth histograms.

  • Z Depth Details: Lists the Z values for each marker. These values are used to sort markers into Z-depth bins.

  • Smoothness : Distribution of markers within your region of interest.

  • Planimetry : Area of each section and volume calculated from this area.

    Note that planimetry is biased; for an unbiased estimate of area/volume, use the Cavalieri Estimator.

  • Z Order : Z value of the sections and the actual Z at which the contours were drawn in each section.

  • Raw Report : Number of markers and tissue thickness per site.