Recipe Description


The 3D Neuron Analysis recipe in Aivia detects and automatically traces dendrites in fluorescent 3D volumetric images. The recipe has options for tracing dendrites with or without soma, as well as options for automatic detection of dendritic spines. After applying the recipe, you can extend the analysis by applying the pre-trained neuron classifier to classify the detected neurons.

Parameters and Presets


Parameters

Parameters and their description are summarized in the table below.

Preset Group
Parameter Name
Min Value
Max Value
Description
Soma Detection
Soma Diameter
0
1,000
Specifies the average diameter of the soma (neuron cell body); a lower value will detect smaller sized objects on the image
Soma Detection
Min Intensity Threshold
(Enable Soma Partition only)
0
255 (8-bit)
65,535 (16-bit)
Specifies the minimum intensity of the soma on the image for partitioning touching somas; this parameter is only enabled when Enable Soma Partition option is selected; a lower value will reduce the number of partitions and preserve larger soma
Dendrite Detection
Dendrite Diameter
0
50
Specifies the diameter of a typical dendrite on the image; a lower value will increase detection sensitivity for thin dendrites while decreasing detection sensitivity for thicker dendrites (such as axons)
Dendrite Detection
Min Branch Length
0
1,000
Specifies the minimum length of a traced branch to be included in the analysis results
Dendrite Detection
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 above background; the upper threshold specifies the minimum intensity above which the voxels are always considered as part of a dendrite
Dendrite Detection
Mean Intensity Offset
0
255 (8-bit)
65,535 (16-bit)
Adjusts the detection sensitivity of the dendrite tracing algorithm; a higher value will reduce the number of dendrites detected that are at or near the minimum intensity threshold specified above
Dendrite Detection
Max Connection Distance
(Skip Soma Detection only)
0
1,000
Specifies the maximum gap distance between dendritic traces to join together; this parameter is only enabled when Skip Soma Detection option is selected; a lower value will increase the number of disconnected dendritic branches
Spine Detection
Typical Spine Head Diameter
0
100
Specifies the approximate diameter of a typical dendritic spine head; this parameter is only enabled when Enable Spine Detection option is selected
Spine Detection
Spine Head Diameter
0
100
Specifies the size range of spine to be included in the analysis results based on the diameter of the spine head; this parameter is only enabled when Enable Spine Detection option is selected
Spine Detection
Max Spine Neck Length
0
100
Specifies the maximum distance between spine heads and dendritic branches; this parameter is only enabled when Enable Spine Detection option is selected; a lower value will reduce 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 grouping to help you get started on the analysis. The default preset values are as follows:

Soma Detection

Parameter Name
Small
Medium
Large
Soma Diameter
10 - 50
40 - 100
100 - 300
Min Intensity Threshold
Disabled by default

Dendrite Detection

Parameter Name
Small
Medium
Large
Dendrite Diameter
2
5
15
Min Branch Length
10
20
50
Intensity Threshold
10 - 50 (8-bit)
2,621 - 12,845 (16-bit)
40 - 80 (8-bit)
10,289 - 20,578 (16-bit)
60 - 100 (8-bit)
15,401 - 25,690 (16-bit)
Mean Intensity Offset
0
0
0
Max Connection Distance
Disabled by default

Spine Detection

Parameter Name
Small
Medium
Large
Typical Spine Head Diameter
1
2
5
Spine Head Diameter
0.05 - 4
0.2 - 10
1 - 15
Max Spine Neck Length
2
2
2
Note: Spine Detection is disabled by default


Measurements


The 3D Neuron Analysis recipe generates morphological and intensity measurements for the soma, dendrites and spines of each detected neuron. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia. The measurements generated by the recipe are summarized in the table below.

Measurement
Soma
Dendrite
Dendrite Segments
Spines
Spine Heads
Spine Necks
Surface Area
x
x
x

x
x
Volume
x
x
x

x
x
Center Line Length

x
x

x
x
Average Length

x
x

x
x
Top 5% Length

x
x

x
x
CV of Lengths

x
x

x
x
Average Angle

x
x

x
x
Average Intensity
x
x
x

x
x
Maximum Intensity
x
x
x

x
x
Minimum Intensity
x
x
x

x
x
Total Intensity
x
x
x

x
x
Standard Deviation
x
x
x

x
x
Additional Measurements
  • Dendrite Count
  • Width
  • Height
  • Depth
  • Total Spine Length
  • Head Neck Length Ratio
  • Total Spine Volume
  • Total Spine Surface Area
  • Spine 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



Tutorial


Before beginning the tutorial, please download the Neuron Analysis Demo (NeuronAnalysisDemo.zip). For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console. You can download the image directly here.

  1. Unzip the demo file and load the demo image, NeuronAnalysisDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the 3D Neuron Analysis recipe
  3. Click on the Show Advanced Interface icon MultiViewIcon.png to expand the Recipe Console and show the parameter options on the recipe
  4. 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
  5. To enable spine detection, go to Step 6; otherwise, go to Step 8
  6. Click on the Switch Recipe Operations icon SwapIcon.png to show the list of available recipe operations; select the Enable Spine Detection option from the dropdown menu
  7. Select the Small preset for the Spine Detection group
  8. Click the From beginning button or press the F4 key on your keyboard to begin applying the recipe to the image

The recipe will generate three output object groups: Soma Set, Dendrite Set and Spine Set. You can toggle the display of individual object sets as well as change its display color using Display Settings.

Results
NeuronAnalysisDemo_z111_t000.png
Neuron Analysis results with different colors for soma, dendrites and spine object groups

Image Credits

Maryann Martone and Eric Bushong, Cell Image Library (CIL:48401), http://www.cellimagelibrary.org/images/48401