Aivia Software

Calcium Oscillation

Owned by Hoyin Lai
Last updated: Jan 20, 2023 by Aiden Maloney-Bertelli (Unlicensed)Version comment
2 min read

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.

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

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 (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

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

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.

  1. Load the demo image, “CaOscDemo.tif,” into Aivia.

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

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

  4. Select the Low presets for the Detection and Tracking groups.

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

 

Results

 

Calcium Oscillation tutorial 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

Intensity

Position

Advanced

  • Pixel-based Mean Intensity

  • Pixel-based Standard Deviation Intensity

  • Pixel-based Total Intensity

  • Centroid X

  • Centroid Y

  • deltaF/F

 

 

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