Recipe Description


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.

Parameters and Presets


Parameters

Parameters and their descriptions are summarized in the table below.

Preset Group
Parameter Name
Min Value
Max Value
Description
Detection
Background Flattening Factor
0
100
Adjusts the sensitivity of the background flattening operation; a lower value will preserve larger objects and more background variations
Detection
Contrast Threshold
0
255
Adjusts the detection sensitivity on the machine learning-enhanced image; a lower value will detect bigger and more objects
Detection
Fill Holes Size
0
50,000
Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
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
Min Object Size
0
50,000
Specifies the minimum size of objects to be included in the analysis results based on the area of the detected regions

Presets

There are two preset groups in the recipe: Detection and Subset Filtering; each group has three pre-configured parameter grouping 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
20
20
20
Fill Holes Size
50
500
1,000
Smoothing Factor
1
1
4

Subset Filtering

Parameter Name
Small
Medium
Large
Min Object Size
50
500
5,000

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
    • Area
    • Percent Total Image
  • Summary
    • Cell region area over time
    • Percent area of cells over time

Tutorial


Before beginning the tutorial, please download the Cell Proliferation Demo Image (CellProDemo.zip). For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console. You can download the image directly here.
  1. Unzip the demo file and load the demo image, CellProDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the Cell Proliferation recipe
  3. Select the High preset for the Detection group and the Medium preset for the Subset Filtering group
  4. Click on the caret (>) to the left of the Detection preset group to show the preset parameters
  5. Change the Detection preset parameter below as follows, leaving the others intact:
    • Fill Holes Size: 500
  6. Click the From beginning 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

Cell Proliferation results