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The Filament Tracking recipe in Aivia detects the leading edge (or "head") of thin filaments and tracks their motility over time in fluorescence time-lapse microscopy images. The recipe is well-suited for the detection and analysis of thin filaments in gliding assays.

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Table of Contents

maxLevel	3
exclude	[4]

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 end point represents the leading edge ("head") or the trailing edge ("tail") by the change in intensity; a higher value will improve the detection of slower-moving filaments
	Min Head Separation Distance	1	100	Specifies the minimum distance between two filament heads
Tracking	Max Search Range	0	1,000	Specifies the maximum distance for track-point match-making 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 grouping groupings to help you get started on the analysis. The default preset values are as follows:

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

Measurements

The Filament Tracking recipe generates track measurements for each detected object. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia. The measurements generated by the recipe are as follows.

Tracking
Total Time
First Frame
Last Frame
Path Length (Total)
X
Y
Velocity Magnitude (instantaneous)
Mean Square Displacement
Average Velocity Magnitude (moving window of 6 frames)

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 following preset for each preset group:
- Detection: Medium
- Tracking: Medium
Click on the caret Image Modified 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 From beginningStart button or press the F4 key on your keyboard to begin applying the recipe to the image

The detected filament head tracks will be overlaid on the image.

Results

Multimedia

name	FilamentTrackDemo_output.mp4
autostart	true

Filament Tracking results

Versions Compared

Old Version 6

New Version 7

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