Recipe Description


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.

Parameters and Presets


Parameters

Parameters 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 objects 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 (found typically 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
Partition
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
Partition
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 objects partition more aggressively resulting in smaller, more uniform objects
Tracking
Min 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
Tracking
Max Search Range
0
1,000
Specifies the maximum distance for track point match-making between successive time frames; a higher value will expand the search distance for fast-moving cells
Tracking
Motion vs Intensity
0
10
Adjusts the relative weighting between motion and object intensity for track point match-making between successive frames; a value of 5 will apply equal weights to motion and intensity for match-making
Tracking
Track Lineages \
Skip Lineage
Toggles tracking of object division and lineages

Presets

There are two preset groups in the recipe: Detection and Partition; each group has three pre-configured parameter grouping 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)
2621 (16-bit)
5 (8-bit)
1311 (16-bit)
3 (8-bit)
655 (16-bit)

Partition

Parameter Name
Small
Medium
Large
Object Radius
2 - 5
20 - 50
100 - 300
Smoothing Factor
1
2
5
Min Edge-to-Center Distance
2
20
100

Tracking

Parameter Name
Motion
Mixted
Intensity
Min Track Length
2 - 5
20 - 50
100 - 300
Smoothing Factor
1
2
5
Min Edge-to-Center Distance
2
20
100

Measurements


The 3D Object Tracking recipe generates morphological, intensity and motility measurements for each detected 3D object 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
    • Surface Area
    • Volume
    • Convex Hull Volume
    • Volume Ratio
  • Intensity (measured on the input channel)
    • Average
    • Maximum
    • Minimum
    • Total
  • Track
    • Total Time
    • First Frame
    • Last Frame
    • X
    • Y
    • Z
    • Velocity Magnitude (Instantaneous)

Tutorial


Before beginning the tutorial, please download the 3D Object Tracking Demo image (3DObjTrackDemo.zip). For information on how to select presets or modify parameter values, please refer to the tutorial on how to use the Recipe Console. You can download the image directly here.

  1. Unzip the demo file and load the demo image, 3DObjTrackDemo.aivia.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the 3D Object Tracking recipe
  3. Select Small for the Partition preset and Intensity for the Tracking preset
  4. Click on the Show Advanced Interface icon showAdvOptions.PNG to expand the Recipe Console
  5. Click on the Switch Recipe Operations icon SwapIcon.png to show the list of available recipe operations; select the Remove Background option from the dropdown menu
  6. Select the following settings on the recipe, leaving the others in tact:
    • Average Object Radius: 4
    • Min Edge Intensity: 3
    • Min Edge-to-Center Distance: 4
  7. Click the From beginning 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

3D Object Tracking results

Image Credits


Stegmaier J, Mikut R. Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines. PLoS One. 2017 Nov 2; 12(11):e0187535. https://doi.org/10.1371/journal.pone.0187535