Neurite Outgrowth

The Neurite Outgrowth recipe in Aivia detects neurons and their neuronal processes (e.g. axons, dendrites) in 2D fluorescence microscopy images. The recipe measures the morphology and intensity of the detected neurons as well as the length of the processes.

Parameters and Presets


Recipe parameters for Neurite Outgrowth and their descriptions are summarized in the table below.

Preset GroupParameter NameMin ValueMax ValueDescription

Background Removal Factor


Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations

Contrast Threshold


255 (8-bit)

65,535 (16-bit)

Adjusts the detection sensitivity on the background removed image; a lower value will detect bigger and more cell bodies
Fill Holes Size05,000Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
Smoothing Factor0100Adjusts the amount of smoothing applied to the outline of the detected objects; a lower value will preserve more of the object's morphological features
Subset Filtering

Object Size01,000,000Specifies the range of objects to be included in the analysis results based on the area of the detected objects
Separation Factor (Cell Partition only)0100Adjusts the sensitivity of the object separation operation; a lower value will preserve larger objects with multiple intensity peaks
Neurite DetectionBranch Sensitivity1100Adjusts the sensitivity of the neurite tracing operation; a lower value will result in detection of fewer short branches
Mean Neurite Width0.1100Specifies the typical width of neurites on the image; a lower value will result in higher sensitivity for detection of thinner neurites
Min Neurite Length01,000Specifies the minimum length of neurite branches to be included in the analysis result


There are three preset groups in the recipe: Detection, Subset Filtering and Neurite Detection; each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are as follows:


Parameter NameLowMediumHigh
Background Removal Factor255575

Contrast Threshold

Intensity Threshold

23 (8-bit)8 (8-bit)1 (8-bit)
5,898 (16-bit)1,966 (16-bit)262 (16-bit)
Fill Holes Size102550
Smoothing Factor444

Subset Filtering

Parameter NameSmallMediumLarge
Object Size1 - 25050 - 1,000150 - 6,000
Separation Factor507085

Neurite Detection

Parameter NameLowMediumHigh
Branch Sensitivity313846
Mean Neurite Width2715
Min Neurite Length1050


The Neurite Outgrowth recipe generates morphological and intensity measurements for each detected neuron as well as a count of the total number of neurites per cell. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia. The measurements generated by the recipe are as follows:

Measurement TypeMeasurement NameSomaNeurite
MorphologyLine Lengthxx

End Point Countxx

Branch Point Countxx



Component Countxx
Standard Deviationx


Before beginning the tutorial, please download the Neurite Outgrowth 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, NeuriteOutgrowthDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the Neurite Outgrowth recipe
  3. Expand the Input and Output section in the recipe and make sure the input image is set to the green channel
  4. Select the High preset for the Detection group and the Medium preset for the Subset Filtering and Neurite Detection groups
  5. Click on the Show Advanced Interface icon  to expand the Recipe Console and show parameter options for the recipe
  6. Modify the parameter values in the recipe as follows while leaving the other values intact:
    • Contrast Threshold: 100
    • Separation Factor: 6
    • Branch Sensitivity: 54
    • Mean Neurite Width: 2.6
    • Min Neurite Length: 5
  7. Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image

The detected objects outlines will be overlaid on the image.


Neurite Outgrowth results

Image credits

Ginger Withers, Whitman College, Cell Image Library (CIL:12566),