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The 3D Object Tracking recipe in Aivia detects objects (such as cells and nuclei), generates surface reconstructions, and tracks their movement in 3D+time volumetric images. The recipe provides a count of the number of detected objects as well as morphological, intensity and motility measurements of the detected objects.

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Table of Contents

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Parameters and Presets

Parameters

Recipe parameters for 3D Object Tracking and their descriptions are summarized in the table below.

Preset Group	Parameter Name	Min Value	Max Value	Description
Detection	Average Object Radius (Remove Background only)	0	1,000	Specifies the radius of a typical object in the image for object enhancement and background removal; a lower value will preserve smaller objects
Detection	Min Edge Intensity	0	255 (8-bit) 65,535 (16-bit)	Specifies the minimum object intensity that is typically found at the edge of the object for detection; when Remove Background is enabled, this parameter value is used to specify the minimum object intensity on the enhanced image; a lower value will detect bigger and more objects
Partition	Object Radius	0	1,000	Specifies the range of objects to be included in the analysis results based on the radius of the detected objects
	Smoothing Factor	0	10	Adjusts the amount of smoothing applied to the surface reconstructions of the detected objects; a lower value will generate surfaces with greater similarity to the input image
	Min Edge-to-Center Distance (Apply Partition only)	0	1,000	Specifies the minimum distance from the center of an object to the edge that is touching its closest neighboring object; this parameter is enabled only when Apply Partition is enabled; a lower value will apply object partitioning more aggressively, resulting in smaller, more uniform objects
Tracking	Minimum Track Length	1	100	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
	Maximum Search Range	0	1,000	Specifies the maximum distance for track-point matchmaking between successive time frames; a higher value will expand the search distance for fast-moving cells
	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
	Track Lineage Option	Not applicable		Toggles tracking of object division and lineages
	Matchmaking Option	Not applicable		Toggles the tracking algorithm used for track-point matchmaking between time points; the available options are Greedy Matching and Hungarian Matching

Presets

There are three preset groups in the recipe: Detection, Partition and Tracking; each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are as follows:

Detection

Parameter Name	Low	Medium	High
Average Object Radius	5	20	100
Min Edge Intensity	10 (8-bit)	5 (8-bit)	3 (8-bit)
Min Edge Intensity	2,621 (16-bit)	1,311 (16-bit)	655 (16-bit)

Measurements

The 3D Object Tracking recipe generates morphological, intensity and motility measurements for each detected 3D object as well as a count of the total number of 3D objects on the image. 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.

Morphological	Intensity	Track
Surface Area Volume	Average Maximum Minimum Total	Total Time First Frame Last Frame X Y Z Acceleration Magnitude (instantaneous) Velocity Magnitude (instantaneous)

Tutorial

Before beginning the tutorial, please download the 3D Object 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, 3DObjTrackDemo.aivia.tif, into Aivia
In the Recipe Console, click on the Recipe selection dropdown menu and select the 3D Object Tracking recipe
Click on the Small button for the Partition preset and the Intensity button for the Tracking preset, leave the Detection preset as is for now
Click on the Show Advanced Interface icon Image Modified to expand the Recipe Console
Under the Detection preset, click on the Switch Recipe Operations icon Image Modified next to the Min Edge Intensity parameter to show the list of available recipe operations; select the Remove Background option from the dropdown menu
Change the parameters listed below to the specified values, leaving the others intact:
- Detection
  - Average Object Radius: 4
  - Min Edge Intensity: 3
- Partition
  - Min Edge-to-Center Distance: 4
Click the Start button or press the F4 key on your keyboard to begin applying the recipe to the image

The surface reconstructions can be viewed in 3D View, while all tracks can be viewed in both 2D and 3D Views. Please note that in 2D View, tracks that are out of the current plane are also overlaid on the image.

Results

Multimedianame

3D Tracking results.mp4

autostarttrue3D Object Tracking results

Image credits

Stegmaier J, Mikut R. (2017) Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines. PLoS One. 12(11):e0187535. doi:10.1371/journal.pone.0187535

Versions Compared

Old Version 15

New Version 16

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