Aivia Software
Wound Healing
The Wound Healing recipe in Aivia detects wound regions and measures the rate of wound closure over time in scratch assay images.
This recipe applies machine-learning-based technology for cell segmentation and works for both phase contrast and fluorescence microscopy images.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Wound Healing 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 | Adjusts the detection sensitivity on the machine-learning-enhanced image; a lower value will detect bigger and more objects | |
Fill Holes Size | 0 | 100,000 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 outlines of the detected objects; a lower value will preserve more of the objects' morphological features | |
Subset Filtering | 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 areas of the 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 Removal Factor | 60 | 60 | 60 |
Contrast Threshold | 85 | 65 | 50 |
Fill Holes Size | 10,000 px2 or µm2 | 10,000 px2 or µm2 | 10,000 px2 or µm2 |
Smoothing Factor | 10 | 4 | 1 |
Subset Filtering
Parameter Name | Small | Medium | Large |
|---|---|---|---|
Min Object Size | 1,000 px2 or µm2 | 10,000 px2 or µm2 | 50,000 px2 or µm2 |
Tutorial
Before beginning the tutorial, please download the Wound Healing 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, “WoundHealDemo.tif,” into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Wound Healing recipe.
Select the Low preset for the Detection group and the Small 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 wound region outline will be overlaid on the image.
Results
Measurements
The Wound Healing recipe generates morphological measurements for the the detected regions. You can add additional measurements to the analysis results with the Measurement Tool in Aivia and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are given in the table below.
Morphology | Advanced |
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