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The Phase Cell Tracking recipe in Aivia detects cells and tracks their motility over time in time-lapse phase contrast microscopy images. The recipe applies a machine learning-based algorithm for cell segmentation. The recipe measures the motion attributes of the detected cells for comprehensive characterization of cell migrations.



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Parameters and Presets

Parameters

Recipe parameters for Phase Cell Tracking and their descriptions are summarized in the table below.

Preset GroupParameter NameMin ValueMax ValueDescription
Detection

Background Flattening Factor

0100

Adjusts the sensitivity of the background flattening operation; a lower value will preserve larger objects and more background variations

Contrast Threshold

0

255

Adjusts the detection sensitivity on the machine learning-enhanced image; a lower value will detect bigger and more objects
Fill Holes Size050,000Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
Smoothing Factor0100Adjusts the amount of smoothing applied to the outline of the detected objects; a lower value will preserve more of the object's morphological features
Tracking


Object Size01,000,000Specifies the range of objects to be included in the analysis results based on the area of the detected objects
Max Search Range01,000Specifies the maximum distance for track-point match-making matchmaking between successive time frames; a higher value will expand the search distance for fast-moving cells
Min Track Length01,000Specifies 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
Separation Factor1100Adjusts the sensitivity of the object separation operation, a lower value will preserve larger objects with multiple intensity peaks



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 NameLowMediumHigh
Background Flattening Factor506063

Contrast Threshold

18512070
Fill Holes Size505001,000
Smoothing Factor124




Partition

Parameter NameSmallMediumLarge
Object Size1 - 25050 - 1,000150 - 6,000
Max Search Range202020
Min Track Length888
Separation Factor507085




Measurements

The Phase Cell Tracking recipe generates track measurements for each detected cell. 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.


MorphologicalTrack
  • Area
  • Circularity
  • Total Time
  • First Frame
  • Last Frame
  • Straight Line Length (instantaneous)
  • Straight Line Velocity (instantaneous)
  • Acceleration Magnitude (instantaneous)
  • Velocity Magnitude (instantaneous)




Tutorial

Before beginning the tutorial, please download the Phase Cell 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.

  1. Unzip the demo file and load the demo image, PhCellTrackDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the Phase Cell Tracking recipe
  3. Select the Medium presets for both the Detection and Tracking preset groups
  4. Click the From beginningStart button or press the F4 key on your keyboard to begin applying the recipe to the image


The detected objects outline object outlines and tracks will be overlaid on the image.

Results

Multimedia
namePhCellTrackDemo_output.mp4
Phase Cell Tracking results




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