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 px2 or µm2 | 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 |
objects' |
morphological features | ||
Tracking | Object Size | 0 |
100,000 px2 or µm2 | Specifies the range of objects to be included in the analysis results based on the |
areas of the detected objects | |||
Max Search Range | 0 | 5,000 px or µm | 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 |
Results
Measurements
Image creditsThe Cell Tracking recipe generates morphological, intensity, and position measurements for each detected cell. You can add additional measurements to the analysis results with the Measurement Tool in Aivia and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are in the table below.
Image Credits
Chantal Brueggemann and Noelle L'Etoile, University of California - San Francisco
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