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    3D Neuron Analysis - FL

    Owned by Hoyin Lai
    Last updated: Jan 13, 2023 by Aiden Maloney-Bertelli (Unlicensed)Version comment
    7 min read

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

    For tracing neurons in 3D electron microscopy images, use the 3D Neuron Analysis - EM recipe. 

    Automatic Parameter Selection

    Auto Icon

    3D Neuron Analysis - FL features Aivia That Learns: AI-powered automatic parameter selection.

    Click on the Auto icon (see right) 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.

    Auto icon for automatic parameter selection

     

    Active Tile

    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.

    Active Tiles

    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

    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 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 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

    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.

    Soma Detection

    Parameter Name

    Small

    Medium

    Large

    Parameter Name

    Small

    Medium

    Large

    Soma Diameter

    10 - 50 (px or µm)

    40 - 100 (px or µm)

    100 - 300 (px or µm)

    Min Intensity Threshold

    61 (8-bit)

    15,728 (16-bit)

    41 (8-bit)

    10,486 (16-bit)

    10 (8-bit)

    2,621 (16-bit)

     

    Dendrite Detection

    Parameter Name

    Small

    Medium

    Large

    Parameter Name

    Small

    Medium

    Large

    Dendrite Diameter

    2 (px or µm)

    5 (px or µm)

    15 (px or µm)

    Min Branch Length

    10 (px or µm)

    20 (px or µm)

    50 (px or µm)

    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

    10 (px or µm)

    25 (px or µm)

    50 (px or µm)

     

    Spine Detection

    Parameter Name

    Small

    Medium

    Large

    Parameter Name

    Small

    Medium

    Large

    Typical Spine Head Diameter

    1 (px or µm)

    2 (px or µm)

    5 (px or µm)

    Spine Head Diameter

    0.05 - 4 (px or µm)

    0.2 - 10 (px or µm)

    1 - 15 (px or µm)

    Max Spine Neck Length

    2 (px or µm)

    2 (px or µm)

    2 (px or µm)

    Spine Detection is disabled by default. Expand the preset group and select Enable Spine Detection or Enable Enhanced Spine Detection to enable the preset group and view the parameters. With Enable Enhanced Spine Detection, spines are detected with greater accuracy at the expense of processing time.

     

     

    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.

    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 - FL recipe.

    3. Click on the Show Advanced Interface icon to expand the Recipe Console and show the parameter options for 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 for the Spine Detection group 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 Start button or press the F4 key on your keyboard to begin applying the recipe to the image.

    The recipe generates three 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

     

     







    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

    Object Set

    Morphology

    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

    • Mean Intensity

    • Max Intensity

    • Min Intensity

    • Total Intensity

    • Std. Dev. Intensity

    None

    Spine Necks

    • Surface Area

    • Volume

    • Average Length

    • Top 5 Percent Length

    • CV Lengths

    • Average Angle

    • Mean Intensity

    • Max Intensity

    • Min Intensity

    • Total Intensity

    • Std. Dev. Intensity

    None

     

    Image Credits

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


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