Parameters and presets
Parameters
Recipe parameters for 3D Neuron Analysis - FL and their descriptions are summarized in the table below.
Preset Group
Parameter Name
Min Value
Max Value
Description
Soma Detection
Soma Diameter
0
1,000 (px or µm)
Specifies the average diameter of somas (neuron cell bodies); a lower value leads to detection of smaller objects on the image
Min Intensity Threshold
(Enable Soma Partition only)
0
255 (8-bit)
65,535 (16-bit)
Specifies the minimum intensity of somas on the image for partitioning touching somas; this parameter is only enabled when the Enable Soma Partition option is selected; a lower value reduces the number of partitions and preserves larger soma
Dendrite Diameter
0
50 (px or µm)
Specifies the diameter of a typical dendrite on the image; a lower value increases detection sensitivity for thin dendrites and decreases detection sensitivity for thicker dendrites (such as axons)
Min Branch Length
0
Automatic Parameter Selection
Parameters and Presets
Parameters
Recipe parameters for 3D Neuron Analysis - FL and their descriptions are summarized in the table below.
Preset Group | Parameter Name | Min Value | Max Value | Description |
---|---|---|---|---|
Soma Detection | Soma Diameter | 0 | 1,000 (px or µm) | Specifies the |
average diameter of somas (neuron cell bodies); a lower value leads to detection of smaller objects on the image | ||
Min Intensity Threshold (Enable Soma Partition only) | 0 | 255 (8-bit) 65,535 (16-bit) |
Specifies the intensity range for dendrite tracing using the voxel scooping algorithm; the lower threshold specifies the minimum intensity that is not considered background; the upper threshold specifies the minimum intensity above which the voxels are always considered as part of a dendrite
Mean Intensity Offset
0
255 (8-bit)
65,535 (16-bit)
Adjusts the detection sensitivity of the dendrite tracing algorithm; a higher value reduces the number of dendrites detected that are at or near the minimum intensity threshold specified above
Max Connection Distance
(Skip Soma Detection only)
Specifies the minimum intensity of somas on the image for partitioning touching somas; this parameter is only enabled when the Enable Soma Partition option is selected; a lower value reduces the number of partitions and preserves larger soma | ||||
Dendrite Detection | Dendrite Diameter | 0 | 50 (px or µm) | Specifies the diameter of a typical dendrite on the image; a lower value increases detection sensitivity for thin dendrites and decreases detection sensitivity for thicker dendrites (such as axons) |
Min Branch Length | 0 | 1,000 (px or µm) | Specifies the |
Spine Detection
(Enable Spine Detection and Enable Enhanced Spine Detection only)
Typical Spine Head Diameter
0
100 (px or µm)
Specifies the approximate diameter of a typical dendritic spine head; this parameter is only enabled when the Enable Spine Detection option or Enable Enhanced Spine Detection option is selected
Spine Head Diameter
0
minimum length of a traced branch to be included in the analysis results | |||
Intensity Threshold | 0 | 255 (8-bit) 65,535 (16-bit) | Specifies the intensity range for dendrite tracing using the voxel scooping algorithm; the lower threshold specifies the minimum intensity that is not considered background; the upper threshold specifies the minimum intensity above which the voxels are always considered as part of a dendrite |
Mean Intensity Offset | 0 | 255 (8-bit) 65,535 (16-bit) | Adjusts the detection sensitivity of the dendrite tracing algorithm; a higher value reduces the number of dendrites detected that are at or near the minimum intensity threshold specified above |
Max Connection Distance (Skip Soma Detection only) | 0 | 1,000 (px or µm) | Specifies the |
maximum gap distance between dendritic traces to join together; this parameter is only enabled when the Skip Soma Detection option is selected; a lower value increases the number of disconnected dendritic branches |
Spine Detection (Enable Spine Detection |
and Enable Enhanced Spine Detection |
only) | Typical Spine Head Diameter | 0 | 100 (px or µm) | Specifies the |
approximate diameter of a typical dendritic spine head; this parameter is only enabled when the Enable Spine Detection option or Enable Enhanced Spine Detection option is selected |
Presets
There are three (3) preset groups in the recipe: Soma Detection, Dendrite Detection, and Spine Detection; each group has three (3) pre-configured parameter groupings to help you get started on the analysis. The default preset values are given in the sections to follow.
3D Neuron Analysis - FL features Aivia That Learns: AI-powered automatic parameter selection. Click on the Automatic Parameter Selection icon (see figure below) in the recipe header to initiate parameter prediction, which feeds features from the specified input image channel into a model trained by human experts and then populates the Recipe Console with predicted parameters.
Another way to initiate parameter estimation for 3D Neuron Analysis - FL is through the Neuron Analysis Active Tile, which is accessed from the search bar at the top of the Aivia window. The Neuron Analysis Active Tile also adjusts the Aivia layout to one that is recommended for a neuron analysis recipe workflow. If the Neuron Analysis Active Tile is not shown when you click in the search bar, try clicking on the Expand icon in the lower-left corner of the search dropdown.
Spine Head Diameter | 0 | 100 (px or µm) | Specifies the size range for a spine to be included in the analysis results based on the diameter of the spine head; this parameter is only enabled when the Enable Spine Detection option or Enable Enhanced Spine Detection option is selected |
Max Spine Neck Length | 0 | 100 (px or µm) | Specifies the maximum distance between spine heads and dendritic branches; this parameter is only enabled when the Enable Spine Detection option or Enable Enhanced Spine Detection option is selected; a lower value reduces the search range for spine heads |
Presets
There are three preset groups in the recipe: Soma Detection, Dendrite Detection, and Spine Detection; each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are given in the sections to follow.
Measurements
TheObject Set
Morphological
Intensity
Count
Soma Set
Surface Area
Volume
Mean Intensity
Max Intensity
Min Intensity
Total Intensity
Std. Dev. Intensity
None
Dendrite Trees
Mean Diameter
Total Path Length
Longest Path Length
Shortest Path Length
None
Branch Count
Spine Count
Branch Order
Dendrite Segments
Mean Diameter
Branch Angle
Total Path Length
Longest Path Length
Shortest Path Length
Surface Area
Volume
Average Length
Top 5 Percent Length
CV Lengths
Average Angle
Mean Intensity
Max Intensity
Min Intensity
Total Intensity
Std. Dev. Intensity
Branch Count
Spine Count
Branch Order
Spines
Total Spine Length
Head Neck Length Ratio
Total Spine Volume
Total Spine Surface Area
Head Neck Volume Ratio
Spine Head Diameter
Spine Diameter Ratio
Length to Head Diameter Ratio
Spine Surface Area Ratio
Spine Convex Hull Volume Ratio
Spine Tortuosity
Branch Angle
None
None
Spine Heads
Surface Area
Volume
Average Length
Top 5 Percent Length
CV Lengths
Average Angle
Measurements
The 3D Neuron Analysis - FL recipe generates morphological, intensity, and count measurements for the somas, dendrites, and spines of each detected neuron. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are summarized in the table below.
Object Set | Morphology | Intensity | Count | ||
---|---|---|---|---|---|
Soma Set |
|
| None | Spine Necks
| None |
Dendrite Trees |
| None |
| ||
Dendrite Segments |
|
| None |
Tutorial
Before beginning the tutorial, please download the Neuron Analysis Demo image. For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console.
Unzip the demo file and load the demo image, "NeuronAnalysisDemo.tif," into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the 3D Neuron Analysis - FL recipe.
Click on the Show Advanced Interface icon to expand the Recipe Console and show the parameter options for the recipe.
Modify the parameter values in the recipe as follows for the Soma Detection and Dendrite Detection groups:
Soma Diameter: 8 - 15
Dendrite Diameter: 1.5
Min Branch Length: 5
Intensity Threshold: 18 - 200
Mean Intensity Offset: 0
To enable spine detection, go to Step 6; otherwise, go to Step 8.
Click on the Switch Recipe Operations icon to show the list of available recipe operations; select the Enable Spine Detection option from the dropdown menu.
Select the Small preset for the Spine Detection group.
Click the Start button or press the
F4
key on your keyboard to begin applying the recipe to the image.
The recipe generates three (3) output object sets: Soma Set, Dendrite Set and Spine Set. You can toggle the display of individual object sets as well as change their display colors from the Object Set Settings panel.
Results
| |||
Spines |
| None | None |
Spine Heads |
|
| None |
Spine Necks |
|
| None |
Image Credits
Maryann Martone and Eric Bushong, Cell Image Library (CIL:48401), http://www.cellimagelibrary.org/images/48401
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