Aivia Software
Filament Tracking
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
- Casey McBride
The Filament Tracking recipe in Aivia detects the leading edges (or "heads") of thin filaments and tracks their motility over time in fluorescence time-lapse microscopy images.
This recipe is well-suited for the detection and analysis of thin filaments in gliding assays.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Filament Tracking and their descriptions are summarized in the table below.
Preset Group | Parameter Name | Min Value | Max Value | Description |
|---|---|---|---|---|
Detection | Background Removal Factor | 1 | 100 | Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations |
Contrast Threshold | 0 | 255 | Adjusts the detection sensitivity on the background-removed image; a lower value will detect more objects | |
Frame Offset | 1 | 1,000 | Specifies the time offset (in frames) the detection will look at to determine whether a filament endpoint represents the leading edge ("head") or the trailing edge ("tail") by the change in intensity; a higher value will improve the detection of slow-moving filaments | |
Min Head Separation Distance | 1 | 100 | Specifies the minimum distance between two filament heads | |
Tracking | Max Search Range | 0 | 1,000 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 objects |
Min Track Length | 0 | 10 | 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 | |
Gap Length | 0 | 10 | Specifies the maximum number of time frames for linking tracks that are spatially colocated; a higher value will preserve particle tracks for longer |
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 in the sections to follow.
Detection
Parameter Name | Low | Medium | High |
|---|---|---|---|
Background Removal Factor | 25 | 55 | 75 |
Contrast Threshold | 24 | 16 | 13 |
Frame Offset | 100 | 20 | 1 |
Min Head Separation Distance | 15 | 5 | 1 |
Tracking
Parameter Name | Low | Medium | High |
|---|---|---|---|
Max Search Range | 10 px or µm | 15 px or µm | 30 px or µm |
Min Track Length | 5 | 5 | 5 |
Gap Length | 5 | 5 | 5 |
Tutorial
Before beginning the tutorial, please download the Filament 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, “FilamentTrackDemo.tif,” into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Filament Tracking recipe.
Select the Medium preset for the Detection group and the Tracking group.
Click on the caret to the left of the Detection preset group to show the preset parameters.
Modify the parameter value as follows, leaving the other parameters intact:
Contrast Threshold: 50
Click the Start button or press the
F4key on your keyboard to begin applying the recipe to the image.
The detected filament head tracks will be overlaid on the image.
Results
Measurements
The Filament Tracking recipe generates morphology and position measurements for each detected object. 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 given in the table below.
Morphology | Position | Advanced |
|---|---|---|
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