Producing and exporting analysis results

Purpose 

There are two methods for producing and exporting analysis results. The first is by running a single type of analysis at a time which will open results window(s) directly in Neurolucida Explorer. This method enables you to visualize the results: select a structure to see the corresponding data in the results table, or click in the results table to highlight the corresponding structure. Some results will also show a graphic of the analysis, such as the Sholl or Convex Hull analyses. The results can then be exported to Excel by using the Current windows tool.

The second way to produce results is by using the Batch analysis tool which can export one or more analyses in one or more data files directly into Excel. Note that Batch analysis will not open results windows in Neurolucida Explorer.

You can find all analyses in the Neuron Data, Region Data and Vessel Data sections of the Analyze ribbon.

The analyses available will depend on what objects are present in the data file.

You can find the Current Windows and Batch Analysis tools in the Export section of the Analyze ribbon.

Procedure

Batch analysis

If you want to analyze all the data in your file(s) (rather than selecting specific structures for analysis) and don’t need to visualize the data, the Batch analysis function is ideal.

  1. Click Batch analysis on the Analyze ribbon.

  2. A dialog box will open that asks if you want to include other files in the batch analysis:

    • Click no to include only the file currently open in Neurolucida Explorer and skip to step 4.
    • Click yes to include files that are not currently open in Neurolucida Explorer.

  3. In the Add Files window that opens, select your data files. Note that if a file is open in Neurolucida Explorer, it will already be listed.

  4. In the Run in Batch window that opens next, select the analyses you want to run.

    In the Run in Batch window, if you hover the mouse over an analysis in the list on the left hand side, a description of each analysis will be displayed on the right hand side. If applicable, settings for certain analyses will also be displayed and can be adjusted as desired. For example, the Starting radius and Radius increment in Sholl analysis.

  5. Select Save Options and the Save to: location for your output.

    • Check Separate by Set to provide separate analyses for groups of objects saved as sets in a single file. For example, the soma, dendrites and axon that make up a neuron are a group of objects.

      To use Separate by Set, sets of modeled structures must have been created in Neurolucida, Neurolucida 360, or Vesselucida 360.

    • Select one of the following:

      • One Excel file for each data file: An Excel file will be exported for each data file individually with each analysis type as a different sheet within the Excel file.

      • One Excel file for each analysis: Each analysis type will be exported to its own Excel file and contain the results of that one analysis for all the data files.

      • One Excel file: A single Excel file with be exported containing all data files and all analyses. Each sheet will be a separate analysis and all data for that analysis across all data files will be listed in that sheet.

    • Check Open Excel spreadsheet on completion to view the results immediately. You need to save the data file to a local drive to use this option.

  6. Click Run. The results are saved in Excel files.

Current windows

Current windows is used to export data from results windows that are visible on the screen after running one or more analyses on a data file that is currently open in Neurolucida Explorer.

  1. Open your data file: Go to File>Open data file and select your file, or drag and drop your file into Neurolucida Explorer.

  2. Select the structures you want to analyze by clicking or dragging with your mouse in the viewing window, using selection tools, or by clicking on structures or their names in the Traced Structures panel.

  3. In the Neuron Data, Region Data or Vessel Data sections of the Analyze ribbon, click on a desired analysis.

  4. Check the boxes corresponding to the metrics you’re interested in, adjust settings if needed, then click OK. Results are displayed in tables.

  5. To export the results to Excel, click Current windows on the Analyze ribbon, select a destination folder, change the file name if desired, then click save.

If you don’t need data from a specific analysis, close the corresponding data table in the program before exporting.

Visualizing results

If you are running analyses on a data file that is open in Neurolucida Explorer, the program has the ability to show you the exact structure that a result belongs to.

To visualize a result, you can do one of the following:

  • Click on a cell in a results table to highlight the corresponding structure in the viewing window.

  • Select a structure in the viewing window and the results for that structure will be highlighted in the results table.

Some analyses have graphics, such as the spheres in Sholl analysis, that will also be displayed in the viewing window when analysis results are generated.

To remove the graphics, click Remove analysis graphics on the Analyze or View ribbon.