Neurite Outgrowth

The Neurite Outgrowth recipe in Aivia detects neurons and their neuronal processes (e.g., axons and dendrites) in 2D fluorescence microscopy images.

This recipe also measures the morphology, intensity, and count of the detected neurons.

On this page:

1 Parameters and Presets
- 1.1 Parameters
- 1.2 Presets
2 Tutorial
3 Measurements
4 Image Credits
5 Related Articles

Parameters and Presets

Parameters

Recipe parameters for Neurite Outgrowth 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
Detection	Background Removal Factor	0	100	Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations
	Contrast Threshold	0	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 Size	0	5,000 px² or µm²	Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
	Smoothing Factor	0	100	Adjusts the amount of smoothing applied to the outlines of the detected objects; a lower value will preserve more of the objects' morphological features
Subset Filtering	Object Size	0	1,000,000 px² or µm²	Specifies the range of objects to be included in the analysis results based on the areas of the detected objects
Subset Filtering	Separation Factor (Cell Partition only)	0	100	Adjusts the sensitivity of the object separation operation; a lower value will preserve larger objects with multiple intensity peaks
Neurite Detection	Branch Sensitivity	1	100	Adjusts the sensitivity of the neurite tracing operation; a lower value will result in detection of fewer short branches
	Mean Neurite Width	0.1 px or µm	100 px or µm	Specifies the typical width of neurites on the image; a lower value will result in higher sensitivity for detection of thinner neurites
	Min Neurite Length	0	1,000 px or µm	Specifies the minimum length of neurite branches to be included in the analysis result

Presets

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:

Detection

Parameter Name	Low	Medium	High
Background Removal Factor	25	55	75
Contrast Threshold	23 (8-bit)	8 (8-bit)	1 (8-bit)
Contrast Threshold	5,898 (16-bit)	1,966 (16-bit)	262 (16-bit)
Fill Holes Size	10 px² or µm²	25 px² or µm²	50 px² or µm²
Smoothing Factor	4	4	4

Subset Filtering

Parameter Name	Small	Medium	Large
Object Size	1 - 250 px² or µm²	50 - 1,000 px² or µm²	150 - 6,000 px² or µm²
Separation Factor	50	70	85

Neurite Detection

Parameter Name	Low	Medium	High
Branch Sensitivity	31	38	46
Mean Neurite Width	2 px or µm	7 px or µm	15 px or µm
Min Neurite Length	0 px or µm	10 px or µm	50 px or µm

Tutorial

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.

Unzip the demo file and load the demo image, “NeuriteOutgrowthDemo.tif,” into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Neurite Outgrowth recipe.
Expand the Input and Output section in the recipe and make sure the input image is set to the green channel.
Select the High preset for the Detection group and the Medium preset for the Subset Filtering group.
Click on the Show Advanced Interface icon to expand the Recipe Console and show parameter options for the recipe.
Modify the parameter values in the recipe as follows while leaving the other values intact:
- Contrast Threshold: 100
- Branch Sensitivity: 54
- Mean Neurite Width: 2.6
- Min Neurite Length: 5
Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image.

The detected object outlines will be overlaid on the image.

Show Advanced Interface icon

Results

Neurite Outgrowth tutorial results

Measurements

The Neurite Outgrowth recipe generates morphological, intensity, and count measurements for each detected neuron, including the total number of neurites per cell. You can add additional measurements to the analysis results with the Measurement Tool in Aivia and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are given in the table below.

Object Set	Morphology	Intensity	Count	Advanced

Object Set	Morphology	Intensity	Count	Advanced
Soma	Area Circularity	Pixel-based Mean Intensity Pixel-based Standard Deviation Intensity Pixel-based Total Intensity	Component Count	Neurite Count Cell Count
Neurite	None	None	Component Count	None

Image Credits

Ginger Withers, Whitman College, Cell Image Library (CIL:12566), http://www.cellimagelibrary.org/images/12566