Analysis

Purpose

Analysis calculates and displays quantitative information about the brain regions identified in your images.

Procedure

1. Click Analysis to open the Analysis Viewer window.

2. Choose Brain Region Summary under Anatomic Region on the left hand side of the Analysis Viewer window.

3. Review parameters and adjust as needed:

   • Planes: Click All to include all registered experimental image-planes or type in the range of image planes to include in the analysis.

   • Show results for: Select one of the following:

     • All brain regions: All brain regions contained in the atlas will be included in the analysis.

     • Selected brain regions: Only brain regions that have been selected in the Atlas Ontology list will be included in the analysis.

     • Brain regions in group: If you set up groups of brain regions using the Atlas Ontology tools, they are listed in the drop-down menu. Click to select a group for analysis.

4. Click Run Analysis and results will be displayed in the right hand pane of the Analysis Viewer window.

   You can customize options for measurement units and numerical precision in the Numerical formatting preferences panel.

5. Export to Excel: Click to export the currently displayed data to Microsoft Excel. NeuroInfo software will open an Excel spreadsheet with the results chart from the Analysis Viewer window. Analysis results are not saved within the data file.

   Make sure to Export to Excel to save your data. Analysis results are note saved when you close the software.

Brain region summary

The Brain Region Summary provides the volume, number of markers (if applicable), and average pixel intensity for all brain regions, or for specific brain regions selected by the user. Data is collected across all sections that have been registered to an atlas and are contained within the user-defined range of image planes.

• Region: The full name of the brain region as defined by the atlas.
• Acronym: Acronym the atlas uses for the brain region.
• ID: The atlas ID assigned to the brain region.
• Hemisphere: Specifies which hemisphere the region is contained in.
• Volume (mm³): Volume of the brain region across the registered sections. Volume is calculated using the cumulative area of the brain region on each registered section and the distance between the image planes.
• Marker: The number of markers per region across the registered sections. Each marker type is tallied individually and is displayed in its own column.
• Channel Avg. Intensity: Average pixel intensity per region across the registered sections. Pixel intensity for each channel is calculated separately and is displayed in its own column.