Parameters and Presets
Parameters
Recipe parameters for Cell Tracking and their descriptions are summarized in the table below.
Preset Group | Parameter Name | Min Value | Max Value | Description |
|---|---|---|---|---|
Detection | Background Removal Factor (Remove Background only) | 0 | 100 | Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations |
Contrast Threshold (Remove Background) Intensity Threshold (Skip Remove Background) | 0 | 255 (8-bit) 65,535 (16-bit) | Adjusts the detection sensitivity on the segmentation image; when Remove Background is selected, the threshold will be applied to the background removed image; whereas when Skip Remove Background is selected, the threshold will be applied to the input image; a lower value will detect bigger and more objects | |
Fill Holes Size | 0 | 5,000 | Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection | |
Smoothing Factor | 0 | 100 | Adjusts the amount of smoothing applied to the outline of the detected objects; a lower value will preserve more of the object's morphological features | |
Tracking | Object Size | 0 | 50,000 | Specifies the range of objects to be included in the analysis results based on the area of the detected objects |
Max Search Range | 0 | 5,000 | Specifies the maximum distance for track-point matchmaking between successive time frames; a higher value will expand the search distance for fast-moving cells | |
Min Track Length | 0 | 50,000 | Specifies the minimum number of time frames before a detected object is considered a valid track; a lower value will generate more, and often shorter, tracks | |
Separation Factor | 0 | 100 | Adjusts the sensitivity of the object separation operation, a lower value will preserve larger objects with multiple intensity peaks | |
Track Lineage Option | Not applicable | Specifies whether to track cell divisions for quantifying lineages | ||
Tutorial
Before beginning the tutorial, please download the Cell Tracking 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.
Unzip the demo file and load the demo image, CellTrackDemo.tif, into Aivia
In the Recipe Console, click on the Recipe selection dropdown menu and select the Cell Tracking recipe
Select the Medium presets for both the Detection and Tracking preset groups
Click on the Show Advanced Interface
to icon to expand the Recipe Console and show parameter options for the recipe
Modify the parameter values in the recipe as follows while leaving the other values intact:
Smoothing Factor: 1
Object Size: 50 - 2000
Separation Factor: 57
Click the Start button to begin applying the recipe to the image
The detected objects outline and tracks will be overlaid on the image.
Results
Image credits
Chantal Brueggemann and Noelle L'Etoile, University of California - San Francisco
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