Difference between revisions of "SNT: Analysis"

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The Sholl dialog created by this approach differs slightly from the dialog created by running the {{bc|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.
 
The Sholl dialog created by this approach differs slightly from the dialog created by running the {{bc|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.
 
 
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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 [https://imagej.net/Simple_Neurite_Tracer:_Sholl_analysis#Sholl_Image 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.
 
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 [https://imagej.net/Simple_Neurite_Tracer:_Sholl_analysis#Sholl_Image 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.
 
 
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=Strahler Analysis=
 
=Strahler Analysis=
 
To conduct [https://imagej.net/Strahler_Analysis Strahler Analysis] on the current contents of the Path Manager, choose the {{bc|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 {{bc|Analyze|Skeleton|Strahler Analysis...}} plugin in the main Fiji dialog.
 
To conduct [https://imagej.net/Strahler_Analysis Strahler Analysis] on the current contents of the Path Manager, choose the {{bc|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 {{bc|Analyze|Skeleton|Strahler Analysis...}} plugin in the main Fiji dialog.
 
 
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=Path Order Analysis=
 
=Path Order Analysis=
 
Found at {{bc|Analysis|Path Order Analysis}} in the main SNT dialog, this option analyzes the Paths in the Path Manager based on [https://www.mbfbioscience.com/help/nx11/Content/Branch%20order/Branch_Order.htm Branch Order]. Produces a table of results and a plot similar to the ''Strahler Analysis'' option.  
 
Found at {{bc|Analysis|Path Order Analysis}} in the main SNT dialog, this option analyzes the Paths in the Path Manager based on [https://www.mbfbioscience.com/help/nx11/Content/Branch%20order/Branch_Order.htm Branch Order]. Produces a table of results and a plot similar to the ''Strahler Analysis'' option.  
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=Measurements=
 
=Measurements=
[[Image:Snt-Measurements-List.png|right|thumb|150px|''Measure...'' dialog]]
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[[Image:Snt-Measurements-List.png|right|thumb|120px|''Measure...'' dialog]]
 
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.  
 
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.  
 
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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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.
 
[[Image:Snt-Measure-Results-Table.png|none|thumb|1000px|''Measure...''  
 
[[Image:Snt-Measure-Results-Table.png|none|thumb|1000px|''Measure...''  
 
  results]]
 
  results]]
 
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=Create Dendrogram=
 
[[Image:Snt-Dendrogram-Shortcuts.png|right|thumb|300px|Dendrogram Viewer shortcuts]]
 
Found at {{bc|Utilities|Create Dendrogram}}, this option generates a [[https://en.wikipedia.org/wiki/Dendrogram Dendrogram]] based off the contents of the Path Manager, providing a high-level overview of neurite branching topology.
 
  
The viewer provides controls for orientation, zoom level, panning as well as options to display vertex labels and edge weights (which by default are the euclidean distances between adjacent vertices).  
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=Dendrogram Viewer=
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[[Image:Snt-Dendrogram-Shortcuts.png|right|thumb|140px|Dendrogram Viewer shortcuts]]
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Found at {{bc|Utilities|Create Dendrogram}}, this option generates a [https://en.wikipedia.org/wiki/Dendrogram Dendrogram] based off the contents of the Path Manager, providing a high-level overview of neurite branching topology.  
  
The plot may be exported in several file formats, including HTML, PNG and SVG. To see the available key shortcuts, right click on the viewer and choose ''Available Shortcuts...''.
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The viewer provides controls for orientation, zoom level, panning, vertex editing and traversal as well as options to display vertex labels and edge weights (which by default are the euclidean distances between adjacent vertices). To see the available key shortcuts, right click on the viewer and choose ''Available Shortcuts...''. The plot may be exported in several file formats, including HTML, PNG and SVG.
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Fine-grained programmatic control over SNT's Graph objects is achieved using the [https://jgrapht.org/javadoc/ JGraphT API] in a script.  Also relevant is the [http://fiji.github.io/SNT/sc/fiji/snt/analysis/graph/package-frame.html sc.fiji.snt.analysis.graph] package which provides high-level tools for Graph creation and conversion.
 
[[Image:Snt-Dendrogram-Viewer.png|none|thumb|300px|Dendrogram Viewer]]
 
[[Image:Snt-Dendrogram-Viewer.png|none|thumb|300px|Dendrogram Viewer]]
  
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=Comparing Reconstructions=
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The {{bc|Utilities|Compare Reconstructions...}} command will bring up a prompt which gives the user the option to compare two single reconstruction files or multiple groups of reconstruction files.
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[[Image:Snt-Compare-Reconstructions-Single-Or-Group-Choice.png|left|thumb|200px|]]
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If you select, ''Compare two files'' and press ''OK'', a file chooser dialog will appear allowing the user to select the two reconstruction files and their respective colors for display in Reconstruction Viewer.
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[[Image:Snt-Compare-Reconstructions-Single-File-Chooser.png|left|thumb|200px|]]
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[[Image:Snt-Compare-Reconstructions-Single-3DViewer-Result.png|right|thumb|200px|]]
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Use the ''Browse'' button to select the two files and press 'OK' to run the analysis. The results will include a table containing results of the ''Quick Measurements'' function for both reconstructions, as well as an instance of the 3D Reconstruction Viewer displaying both reconstructions.
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[[Image:Snt-Compare-Reconstructions-Single-Measurements-Table.png|left|thumb|900px|]]
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=Custom Analyses=
 
=Custom Analyses=
 
It is possible to script your own analysis routines. See [https://imagej.net/SNT:_Scripting SNT:_Scripting] for the link to SNT's API as well as script templates demonstrating a range of analysis possibilities.
 
It is possible to script your own analysis routines. See [https://imagej.net/SNT:_Scripting SNT:_Scripting] for the link to SNT's API as well as script templates demonstrating a range of analysis possibilities.
  
 
{{SNTNavBar}}
 
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Revision as of 16:55, 12 January 2020

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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


Dendrogram Viewer

Dendrogram Viewer shortcuts

Found at Utilities › Create Dendrogram, this option generates a Dendrogram based off the contents of the Path Manager, providing a high-level overview of neurite branching topology.

The viewer provides controls for orientation, zoom level, panning, vertex editing and traversal as well as options to display vertex labels and edge weights (which by default are the euclidean distances between adjacent vertices). To see the available key shortcuts, right click on the viewer and choose Available Shortcuts.... The plot may be exported in several file formats, including HTML, PNG and SVG.

Fine-grained programmatic control over SNT's Graph objects is achieved using the JGraphT API in a script. Also relevant is the sc.fiji.snt.analysis.graph package which provides high-level tools for Graph creation and conversion.

Dendrogram Viewer

Comparing Reconstructions

The Utilities › Compare Reconstructions... command will bring up a prompt which gives the user the option to compare two single reconstruction files or multiple groups of reconstruction files.

Snt-Compare-Reconstructions-Single-Or-Group-Choice.png

If you select, Compare two files and press OK, a file chooser dialog will appear allowing the user to select the two reconstruction files and their respective colors for display in Reconstruction Viewer.

Snt-Compare-Reconstructions-Single-File-Chooser.png
Snt-Compare-Reconstructions-Single-3DViewer-Result.png

Use the Browse button to select the two files and press 'OK' to run the analysis. The results will include a table containing results of the Quick Measurements function for both reconstructions, as well as an instance of the 3D Reconstruction Viewer displaying both reconstructions.

Snt-Compare-Reconstructions-Single-Measurements-Table.png


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