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The Calcium Oscillation recipe in Aivia detects regions that experiences experience sharp intensity changes from baseline level 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.

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Table of Contents

minLevel	1
maxLevel	53

Parameters and Presets

Parameters

Recipe parameters for Calcium Oscillation and their descriptions are summarized in the table below.

Preset Group	Parameter Name	Max Value	Description
Detection	Contrast Threshold	255	Adjusts the detection sensitivity on the segmentation image; When Remove Background is selected, the threshold will be applied to the temporal projection image with image background removed; When Skip Remove Background is selected, the threshold will be applied to the temporal projection image A lower value will detect bigger and more objects
	Background Removal Factor (Remove Background only)	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)	50	Adjusts the sensitivity of the bright peak enhancement operation; a lower value will enhance smaller, individual peaks
Tracking	Object Size	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
Tracking	Separation Factor	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 as follows:given in the following subsections.

Partition

SmallLarge

Measurements

The Calcium Oscillation recipe generates morphological and intensity measurements for each detected cell as well as a count of the total number of cells on the image. 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	Intensity
Centroid in X Centroid in Y	Mean Total Standard Deviation DeltaF/F

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

“CaOscDemo.

tiff

tif,” into Aivia.
Click Apply or Cancel on the Calibration Properties dialog to proceed with loading the

loading

Detection Preset: Low

Tracking Preset: Low

image.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Calcium Oscillation recipe.
Select the

following settings on the recipe:

Low presets for the Detection and Tracking groups.
Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image.

Results

CaOscDemo_output.mp4

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.

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

Versions Compared

Old Version 10

New Version Current

Key

Parameters and Presets

Parameters

Presets

Detection

Tracking

Tutorial

Results

Measurements

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