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TheNeurite 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.

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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
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	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 outline of the detected objects; a lower value will preserve more of the object's morphological features
Subset Filtering	Object Size	0	1,000,000	Specifies the range of objects to be included in the analysis results based on the area 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	100	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	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 Intensity Threshold	23 (8-bit)	8 (8-bit)	1 (8-bit)
Contrast Threshold Intensity Threshold	5,898 (16-bit)	1,966 (16-bit)	262 (16-bit)
Fill Holes Size	10	25	50
Smoothing Factor	4	4	4

Measurements

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 Type	Measurement Name	Soma	Neurite
Morphology	Line Length	x	x
	End Point Count	x	x
	Branch Point Count	x	x
	Area	x
	Circularity	x
	Component Count	x	x
Intensity	Mean	x
	Standard Deviation	x
	Total	x

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 and Neurite Detection groups
Click on the Show Advanced Interface

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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 objects outlines will be overlaid on the image.

Results

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Neurite Outgrowth results

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Image credits

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

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

Versions Compared

Old Version 10

New Version 11

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