Recipe Description



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.


Parameters and Presets


Parameters

Parameters and their description are summarized in the table below.

Preset Group
Parameter Name
Min Value
Max Value
Description
Detection
Background Removal Factor
0
100
Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations
Detection
Contrast Threshold
0
255
Adjusts the detection sensitivity on the background removed and temporally projected image; a lower value will detect bigger and more objects
Detection
Bright Spot Size
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 result based on the size of the detected objects
Tracking
Separation Factor
0
100
Adjusts the sensitivity of the object separation operation; a lower value will preserve larger objects with multiple local 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 Name
Low
Medium
High
Background Removal Factor
35
65
85
Contrast Threshold
20
10
7
Bright Spot Size
2
15
25

Tracking

Parameter Name
Low
Medium
High
Object Size
2 - 50
50 - 2000
300 - 5000
Separation Factor
80
80
80

Tutorial


Before beginning the tutorial, please download the Calcium Oscillation Demo image (CaOscDemo.zip). For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console. You can download the image directly here.

  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
CaOscDemo_output.png