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The Cell Proliferation recipe in Aivia detects cell regions and measures the change in confluency over time. The recipe applies a machine learning-based algorithm for cell segmentation and works for both phase contrast and fluorescence microscopy images.

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Table of Contents

maxLevel	3
exclude	[4]

Parameters and Presets

Parameters

Recipe parameters for Cell Proliferation and their descriptions are summarized in the table below.

Preset Group	Parameter Name	Max Value	Description
Detection	Background Flattening Factor (Enhance Image only)	100	Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations
Detection	Contrast Threshold (Enhance Image) Intensity Threshold (Skip Enhance Image)	255 (8-bit) 65,535 (16-bit)	Adjusts the detection sensitivity on the segmentation image; When Enhance Image is selected, the threshold will be applied to the enhanced image with the maximum value set to 255 regardless of image bit-depth When Skip Enhance Image is selected, the threshold will be applied to the input image A lower value will detect bigger and more objects
Subset Filtering	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
	Min Object Size	1,000,000	Specifies the minimum size of objects to be included in the analysis results based on the area of detected regions

Presets

There are two preset groups in the recipe: Detection and Subset Filtering; 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 Flattening Factor

50

60

63

Contrast Threshold

(Enhance Image only)

20

Intensity Threshold

(Skip Enhance Image only)

51 (8-bit)

13,107 (16-bit)

20 (8-bit)

5,243 (16-bit)

5 (8-bit)

1,311 (16-bit)

Measurements

The Cell Proliferation recipe generates morphological measurements for the confluency of the detected regions. 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	Summary
Area Percent Total Image	Cell region area over time Percent area of cells over time

Tutorial

Before beginning the tutorial, please download the Cell Proliferation 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, CellProDemo.tif, into Aivia
In the Recipe Console, click on the Recipe selection dropdown menu and select the Cell Proliferation recipe
Select the High preset for the Detection group and the Medium preset for the Subset Filtering group
Click on the caret Image Modified to the left of the Subset Filtering preset group to show the preset parameters
Change the Subset Filtering preset parameter below as follows, leaving the others intact:
- Fill Holes Size: 500
Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image

The detected cell region outline will be overlaid on the image.

Results

Multimedia

name	CellProDemo_output.mp4
autostart	true

Cell Proliferation results

Versions Compared

Old Version 13

New Version 14

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