Aivia Software
Calcium Oscillation
The Calcium Oscillation recipe in Aivia detects regions that experience sharp intensity changes from baseline levels and tracks the intensities in those regions over time.
The detected regions are fixed in size and position throughout the analysis, allowing direct comparison of regional intensities across different time points.
This recipe is useful for characterizing calcium flux activity in cells.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Calcium Oscillation and their descriptions are summarized in the table below.
Preset Group | Parameter Name | Min Value | Max Value | Description |
|---|---|---|---|---|
Detection | Contrast Threshold | 0 | 255 | Adjusts the detection sensitivity on the segmentation image;
A lower value will detect bigger and more objects |
Background Removal Factor (Remove Background only) | 0 | 100 | Adjusts the sensitivity of the background removal operation on the temporal projection image; a lower value will preserve larger objects and more background variations | |
Bright Spot Size (Remove Background only) | 0 | 50 | Adjusts the sensitivity of the bright peak enhancement operation; a lower value will enhance smaller, individual peaks | |
Tracking | Object Size | 0 | 1,000,000 (px2 or µm2) | Specifies the range of objects to be included in the analysis results based on the area of the detected objects |
Separation Factor | 0 | 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 Tracking; each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are given in the following subsections.
Detection
Parameter Name | Low | Medium | High |
|---|---|---|---|
Contrast Threshold | 20 | 10 | 7 |
Background Removal Factor | 35 | 65 | 85 |
Bright Spot Size | 2 | 15 | 25 |
Tracking
Parameter Name | Low | Medium | High |
|---|---|---|---|
Object Size | 2 - 50 (px2 or µm2) | 50 - 2,000 (px2 or µm2) | 300 - 5,000 (px2 or µm2) |
Separation Factor | 80 | 80 | 80 |
Tutorial
Before beginning the tutorial, please download the Calcium Oscillation 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.
Load the demo image, “CaOscDemo.tif,” into Aivia.
Click Apply or Cancel on the Calibration Properties dialog to proceed with loading the image.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Calcium Oscillation recipe.
Select the Low presets for the Detection and Tracking groups.
Click the Start button or press the
F4key on your keyboard to begin applying the recipe to the image.
Results
Measurements
The Calcium Oscillation recipe generates intensity and position measurements. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia and find measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are in the table below.
Intensity | Position | Advanced |
|---|---|---|
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