Difference between revisions of "SNT: Analysis"

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=Measurements=
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[[Image:Snt-Measurements-List.png|right|thumb|200px|''Measure...'' dialog]]
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SNT provides several ways to measure reconstructions. A comprehensive selection of measurements can be found by going to {{bc|Analysis|Measure...}}. in the main SNT dialog. To quickly measure tracings with a common set of statistics, choose {{bc|Analysis|Quick Measurements}}. In both cases the results of the measurements are displayed in a table. To get measurements only on a select group of Paths, first select the Paths you want to measure in the Path Manager and choose either option from the  {{bc|Analyze}} menu in the Path Manager. Batch measurements of reconstructions can be accomplished via scripting. See ''Measure_Multiple_Files.py'' in the SNT [[https://imagej.net/SNT:_Scripting#Script_Templates Script Templates]] for a basic example.
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[[Image:Snt-Measure-Results-Table.png|thumb|200px|''Measure...''
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=Custom Analyses=
 
=Custom Analyses=

Revision as of 19:09, 11 January 2020

Home Manual Walk-throughs Screencasts Shortcuts Analysis Rec. Viewer SciView Cx3D Scripting FAQ


Sholl Analysis

There are two Sholl Analysis commands available in SNT's Analysis menu. The Analysis › Shuoll Analysis... option provides a set of pre-defined focal points the user can choose from. Note for the morphology-based focal points (e.g., Soma, Root node(s): Primary apical dendrite(s)) , the relevant morphology tag(s) must be assigned to the set of paths considered by the analysis. To select a focal point manually, see the following section.

Sholl Analysis (by Focal Point)

Initiating Sholl Analysis: coarse method

It is also possible to initiate Sholl Analysis on a tracing in the canvas by manually selecting a focal point. You can do it coarsely by right-clicking near a node and choosing Sholl Analysis at Nearest Node from the contextual menu (Shortcut: Alt + Shift + A.

Alternatively, for precise positioning of the center of analysis:

  1. Mouse over the path of interest. Press G to activate it.
  2. Press Alt+ Shift to select a node along the path.
  3. Press Alt+ Shift+A to start analysis.
  • 1) Select path
  • 2) Snap cursor to node
  • 3) Sholl dialog


The Sholl dialog created by this approach differs slightly from the dialog created by running the Analyze › Sholl › Sholl Analysis (From Tracings)... plugin in the main Fiji menu. First, the center of analysis is automatically taken from the nearest (or exact) node where the user clicks. In addition to morphology and custom tag filters, the Path filtering drop-down menu provides an additional option to restrict the analysis to the subset of paths selected in the Path Manager. Another advantage is that the display canvas allows the radius step size to be previewed visually. To do this, toggle on the Preview checkbox under the Sampling section and experiment with different step sizes.

  • Step Size = 0
  • Step Size = 5

In addition to the Sholl Profile plot and table, the output of the analysis can be visualized as a color mapping of the reconstruction and as a Sholl Image. To color code the tracing, choose Color coded paths from the Annotations drop-down menu and select a Lut from the Annotations Lut drop-down menu before pressing Run Analysis. To output the Sholl Image, choose 3D viewer labels image from the Annotations drop-down menu and select the desired Lut before running the analysis.

  • Sholl Profile Plot
  • Sholl Profile Table
  • Color Coded Tracing - Ice Lut
  • Sholl Image - Ice Lut

Strahler Analysis

To conduct Strahler Analysis on the current contents of the Path Manager, choose the Utilities › Strahler Analysis command in the main SNT dialog. This command will output the results of the analysis as a table and plot. These figures contains statistics on the group of paths associated with each Horton-Strahler Number. Note that this feature analyzes traced reconstructions. To run Strahler analysis on images, use the Analyze › Skeleton › Strahler Analysis... plugin in the main Fiji dialog.

  • Strahler Analysis table
  • Strahler Analysis plot

Path Order Analysis

Found at Analysis › Path Order Analysis in the main SNT dialog, this option analyzes the Paths in the Path Manager based on Branch Order. Produces a table of results and a plot similar to the Strahler Analysis option.

  • Path Order Analysis table
  • Path Order Analysis plot


Measurements

Measure... dialog

SNT provides several ways to measure reconstructions. A comprehensive selection of measurements can be found by going to Analysis › Measure.... in the main SNT dialog. To quickly measure tracings with a common set of statistics, choose Analysis › Quick Measurements. In both cases the results of the measurements are displayed in a table. To get measurements only on a select group of Paths, first select the Paths you want to measure in the Path Manager and choose either option from the Analyze menu in the Path Manager. Batch measurements of reconstructions can be accomplished via scripting. See Measure_Multiple_Files.py in the SNT [Script Templates] for a basic example.

Measure... results


Custom Analyses

It is possible to script your own analysis routines. See SNT:_Scripting for the link to SNT's API as well as script templates demonstrating a range of analysis possibilities.

Home Manual Walk-throughs Screencasts Shortcuts Analysis Rec. Viewer SciView Cx3D Scripting FAQ