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The Nuclei Count recipe in Aivia detects nuclei in fluorescence microscopy images. The recipe measures the morphology and intensity of the detected nuclei. This recipe can be used for detection of any compact, bright foreground objects against a dark background.

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Table of Contents

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Parameters and Presets

Parameters

Recipe parameters for Nuclei Count and their descriptions are summarized in the table below.

Preset Group	Parameter Name	Max Value	Description
Detection	Background Removal Factor (Remove Background only)	100	Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations
	Contrast Threshold (Remove Background) Intensity Threshold (Skip Remove Background)	255 (8-bit) 65,535 (16-bit)	Adjusts the detection sensitivity on the segmentation image When Remove Background is selected, the threshold will be applied to the background removed image When Skip Remove Background is selected, the threshold will be applied to the input image A lower value will detect bigger and more objects
	Fill Holes Size	1,000,000	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	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
Nuclei Partition	Object Size	1,000,000,000	Specifies the range of objects to be included in the analysis results based on the area of the detected objects
Nuclei Partition	Separation Factor (Cell Partition only)	100	Adjusts the sensitivity of the object separation operation, a lower value will preserve larger objects with multiple intensity peaks

Presets

There are two preset groups in the recipe: Detection and Nuclei Partition; 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 Nuclei Count recipe generates morphological and intensity measurements for each detected cell as well as a count of the total number of cells on the image. 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.

Morphological

Morphology	Intensity	Summary
Area Circularity Component Count	Mean Total Standard Deviation	Total Component Count Average Mean Intensity

Tutorial

Before beginning the tutorial, please download the Nuclei Count 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, NucleiCountDemo_01.tif, into Aivia
In the Recipe Console, click on the Recipe selection dropdown menu and select the Nuclei Count recipe
Select the Low preset for both the Detection group and the Nuclei Partition group
Click on the caret

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to the left of the Detection preset group to show the preset parameters
Change the Detection preset parameter below as follows:
- Contrast Threshold: 120
Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image

The detected objects outline and tracks will be overlaid on the image.

Results

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Nuclei Count results

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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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