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

maxLevel	3
exclude	[4]

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	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 grouping groupings to help you get started on the analysis. The default preset values are as follows:

Detection

Parameter Name	Low	Medium	High
Contrast Threshold	20	10	7
Background Removal Factor	35	65	85
Bright Spot Size	2	15	25

Partition

Parameter Name	Small	Medium	Large
Object Size	2 - 50	50 - 2,000	300 - 5,000
Separation Factor	80	80	80

Measurements

The Cell Tracking 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.tiff, into Aivia
Click Apply or Cancel on the Calibration Properties dialog to proceed with the loading
In the Recipe Console, click on the Recipe selection dropdown menu and select the Calcium Oscillation recipe
Select the following settings on the recipe:
- Detection Preset: Low
- Tracking Preset: Low
Click the From beginningStart button or the F4 key on your keyboard to begin applying the recipe to the image.

Results

Multimedia

name	CaOscDemo_output.mp4
autostart	true

Calcium Oscillation result

Versions Compared

Old Version 6

New Version 7

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