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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 GroupParameter NameMin ValueMax ValueDescription
Detection

Contrast Threshold

0255

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)

0100Adjusts 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)

050Adjusts the sensitivity of the bright peak enhancement operation; a lower value will enhance smaller, individual peaks
Tracking


Object Size01,000,000Specifies the range of objects to be included in the analysis results based on the area of the detected objects
Separation Factor0100Adjusts 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 to help you get started on the analysis. The default preset values are as follows:

Detection

Parameter NameLowMediumHigh

Contrast Threshold

20107
Background Removal Factor356585
Bright Spot Size21525

Partition

Parameter NameSmallMediumLarge
Object Size2 - 5050 - 2,000300 - 5,000
Separation Factor808080


Measurements

The Cell Tracking 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.


MorphologicalIntensity
  • 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 From beginning button or the F4 key on your keyboard to begin applying the recipe to the image.

Results

Calcium Oscillation result







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