Aivia Software
Cell Proliferation
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.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Cell Proliferation and their descriptions are summarized in the table below.
Preset Group | Parameter Name | Min Value | Max Value | Description |
|---|---|---|---|---|
Detection
| Background Flattening Factor (Enhance Image only) | 0 | 100 | Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations |
Contrast Threshold (Enhance Image) Intensity Threshold (Skip Enhance Image) | 0 | 255 (8-bit) 65,535 (16-bit) | Adjusts the detection sensitivity on the segmentation image:
A lower value will detect bigger and more objects | |
Subset Filtering | Fill Holes Size | 0 | 1,000,000 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 outline of the detected objects; a lower value will preserve more of the object's morphological features | |
Min Object Size | 0 | 1,000,000 px2 or µm2 | 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 | 20 | 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) |
Subset Filtering
Parameter Name | Small | Medium | Large |
|---|---|---|---|
Fill Holes Size | 50 px2 or µm2 | 500 px2 or µm2 | 1,000 px2 or µm2 |
Smoothing Factor | 1 | 2 | 4 |
Object Size | 50 px2 or µm2 | 500 px2 or µm2 | 5,000 px2 or µm2 |
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 the Start button or press the
F4key on your keyboard to begin applying the recipe to the image.
The detected cell region outlines will be overlaid on the image.
Results
Measurements
The Cell Proliferation recipe generates 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:
Morphology | Advanced |
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