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Analysis

Although NeuronStudio's primary purpose is for constructing a model and spines from image stacks, a sholl analysis feature is available in the current version to allow analysis of spine distributions.

Sholl Analysis

Sholl analysis creates a series of concentric circles (spheres in 3D) around the soma of the neuron. Within each sphere various metrics can be obtained such as the number of spines that intersect it, or the total length of intersecting neurites. This feature can be run be selecting the main menu item Run >> Sholl Analysis.

IMPORTANT: There must be only one origin (soma) in the model for Sholl Analysis to be run.

The images below show a Sholl Analysis being run on a model and spines. The leftmost image shows a model of a cell before the analysis has been run. The center image shows the resulting spheres drawn around the model in the 2D display after the analysis has been run. Note that the menu item View >> Sholl Spheres (2D Only) must be checked in order to see the rendering of the sholl spheres. The rightmost image shows a closeup view of a simple model with a few spines. For each concentric sphere, a number of metrics are obtained.

Sholl Analysis Image 1 Sholl Analysis Image 2 Sholl Analysis Image 3

You can control the size of the sholl spheres by opening up the .ns file in any text editing program. Look for the following section in the file:

[sholl]
min_radius=0.000000
max_radius=500000.000000
radius_delta=1.000000

The min_radius is the offset from the soma where the first concentric sphere will start. By default it is set to zero. The max_radius sets how far from the soma the last concentric sphere will end. Note that if this setting is larger than the radial extent of the model and spines, NeuronStudio will automatically clip this value. However, you may set it to a value less than the radial extent of the model and spines if desired. The radius_delta is the increment in radius between each concentric circle. Since NeuronStudio automatically clips the max_radius parameter, the increment of the last concenctric circle is not guaranteed to be equal to the radius_delta. In the center image above, you can see how this has occurred for the last concentric circle.

After setting these parameters to the desired values, simply save the .ns file and run the sholl analysis.

After the Sholl Analysis has completed, a dialog box will appear prompting you to choose the location of a text file that will be created containing the various metrics that were obtained during the analysis. This text file is a simple column format that can be opened with text editors and spreadsheet programs. See below for an example of the text file generated by NeuronStudio. Note that each row in the file, except for the first one containing column names, defines the metrics obtained for a single concentric circle.

    START-RADIUS      END-RADIUS     DEND-LENGTH     DEND-VOLUME         DEND-SA   BRANCH-POINTS     SPINE-COUNT    STUBBY-COUNT      THIN-COUNT  MUSHROOM-COUNT     OTHER-COUNT
          0.0000          5.0000         44.3836        114.5242        220.6643               6               0               0               0               0               0
          5.0000         10.0000        111.8297         17.0385        139.6092               9               0               0               0               0               0
         10.0000         15.0000        132.7414         14.3937        149.2009              10               0               0               0               0               0
         15.0000         20.0000        134.6922         12.4768        140.9804               3               0               0               0               0               0
         20.0000         25.0000        133.7809         11.4747        133.6965               5               0               0               0               0               0
         25.0000         30.0000         90.0517          7.1328         87.4335               2               0               0               0               0               0
         30.0000         35.0000         61.3024          4.9704         60.3928               0               0               0               0               0               0
         35.0000         40.0000         18.2389          1.5659         18.6814               0               0               0               0               0               0
         40.0000         45.0000          5.1803          0.5488          5.9952               0               0               0               0               0               0
         45.0000         46.7921          1.6961          0.2062          2.1021               0               0               0               0               0               0

Column Details

START-RADIUS: The starting radius of the concentric circle.

END-RADIUS: The ending radius of the concentric circle.

DEND-LENGTH: The total dendritic length between the starting and ending radius.

DEND-VOLUME: The total dendritic volume between the starting and ending radius.

DEND-SA: The total dendritic surface area between the starting and ending radius.

BRANCH-POINTS: The toal number of dendritic branch points between the starting and ending radius. A branch point is any vertex with a parent edge (the one leading back to the soma) and two or more children edges.

SPINE-COUNT: The total number of spines between the starting and ending radius.

STUBBY-COUNT: The total number of stubby spines between the starting and ending radius.

THIN-COUNT: The total number of thin spines between the starting and ending radius.

MUSHROOM-COUNT: The total number of mushroom spines between the starting and ending radius.

OTHER-COUNT: The total number of "other" spines between the starting and ending radius.

IMPORTANT: If you are using a trainable spine classifier the STUBBY-COUNT, THIN-COUNT, MUSHROOM-COUNT, and OTHER-COUNT columns will be replaced by columns matching the classes defined in the classifier.

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Send questions or comments to: alfredo.rodriguez@mssm.edu