Aivia Software
Particle Tracking
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
- Casey McBride
- Lindsey Marshall
The Particle Tracking recipe in Aivia detects subcellular particles and tracks their motility over time in fluorescence time-lapse microscopy images.
This recipe measures intensity and motion attributes of the detected objects for comprehensive characterization of intracellular dynamics.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Particle Tracking and their descriptions 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 |
Object Enhancement Factor | 0 | 50 | Adjusts the sensitivity of the bright peak enhancement operation; a lower value will enhance smaller, individual peaks | |
Contrast Threshold | 0 | 255 | Adjusts the detection sensitivity on the background-removed image; a lower value will detect more objects | |
Motion vs Intensity | Motion vs Intensity | 0 | 10 | Adjusts the relative weighting between motion and object intensity for track-point matchmaking between successive frames; a value of 5 will apply equal weights to motion and intensity for matchmaking |
Tracking | 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 |
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 | |
Max Search Range | 0 | 50,000 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 |
Presets
There are three preset groups in the recipe: Detection, Motion vs Intensity, 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 subsections to follow.
Detection
Parameter Name | Low | Medium | High |
|---|---|---|---|
Background Removal Factor | 75 | 75 | 75 |
Object Enhancement Factor | 2 | 2 | 2 |
Contrast Threshold | 125 | 65 | 15 |
Motion vs Intensity
Parameter Name | Motion | Mixed | Intensity |
|---|---|---|---|
Motion vs Intensity | 0 | 5 | 10 |
Tracking
Parameter Name | Low | Medium | High |
|---|---|---|---|
Gap Length | 5 | 5 | 5 |
Min Track Length | 3 | 3 | 3 |
Max Search Range | 5 px or µm | 5 px or µm | 65 px or µm |
Tutorial (written steps)
Before beginning the tutorial, please download the Particle 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, “ParticleTrackDemo.tif,” into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Particle Tracking recipe.
Select the following presets for each preset group:
Detection: Medium
Motion vs Intensity: Motion
Tracking: Low
Click on the caret to the left of the Tracking preset group to show the preset parameters.
Modify the parameter value as follows, leaving the other parameters intact:
Max Search Range: 0.7
Click the Start button or press the
F4key on your keyboard to begin applying the recipe to the image.
The detected particle tracks will be overlaid on the image.
Tutorial (video)
Measurements
The Particle Tracking recipe generates intensity and position measurements for each detected particle. You can add additional measurements to the analysis results with the Measurement Tool in Aivia and explore measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are in the table below.
Intensity | Position |
|---|---|
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Image Credits
Laura Anne Lowery, Boston College, Boston MA; David Van Vactor, Harvard Medical School, Boston MA