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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.

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;

  • 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)

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

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 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 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.

  1. Load the demo image, CaOscDemo.tiff, into Aivia

  2. Click Apply or Cancel on the Calibration Properties dialog to proceed with the loading

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

  4. Select the following settings on the recipe:

    • Detection Preset: Low

    • Tracking Preset: Low

  5. Click the Start button or the F4 key on your keyboard to begin applying the recipe to the image.

Results

CaOscDemo_output.mp4


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