Aivia Software
Nuclei Tracking
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
- Casey McBride
The Nuclei Tracking recipe in Aivia detects nuclei and tracks their motility over time in fluorescence time-lapse microscopy images.
This recipe measures morphological, intensity, and motion attributes of the detected nuclei for comprehensive characterization of nuclei migrations. In addition, the recipe tracks nuclei divisions and generates lineages for all detected nuclei.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Nuclei Tracking and their descriptions are summarized in the table below.
Preset Group | Parameter Name | Min Value | Max Value | Description |
|---|---|---|---|---|
Detection | Background Removal Factor (Remove Background only) | 0 | 100 | Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations |
Contrast Threshold (Remove Background) Intensity Threshold (Skip Remove Background) | 0 | 255 (8-bit) 65,535 (16-bit) | Adjusts the detection sensitivity on the segmentation image:
A lower value will detect bigger and more objects | |
Fill Holes Size | 0 | 50,000 px2 or µm2 | Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection | |
Smoothing Factor | 0 | 100 | Adjusts the amount of smoothing applied to the outlines of the detected objects; a lower value will preserve more of the objects' morphological features | |
Tracking | Object Size | 0 | 50,000 px2 or µm2 | Specifies the range of objects to be included in the analysis results based on the areas of the detected objects |
Separation Factor | 0 | 100 | Adjusts the sensitivity of the object separation operation; a lower value will preserve larger objects with multiple intensity peaks | |
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 | |
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 | |
Matchmaking Option | Not applicable | Toggles the tracking algorithm used for track-point matchmaking between time points; the available options are the Greedy Algorithm and the Hungarian Algorithm | ||
Track Lineage Option | Not applicable | Specifies whether to track divisions for quantifying lineages | ||
Presets
There are two preset groups in the recipe: Detection 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 |
|---|---|---|---|
Background Removal Factor | 75 | 75 | 75 |
Contrast Threshold Intensity Threshold | 23 (8-bit) | 8 (8-bit) | 1 (8-bit) |
5,898 (16-bit) | 1,966 (16-bit) | 262 (16-bit) | |
Fill Holes Size | 50 px2 or µm2 | 50 px2 or µm2 | 50 px2 or µm2 |
Smoothing Factor | 4 | 4 | 4 |
Tracking
Parameter Name | Low | Medium | High |
|---|---|---|---|
Object Size | 10 - 500 px2 or µm2 | 50 - 3,000 px2 or µm2 | 100 - 6,000 px2 or µm2 |
Separation Factor | 75 | 75 | 75 |
Max Search Range | 20 px or µm | 20 px or µm | 20 px or µm |
Min Track Length | 4 | 4 | 4 |
Tutorial
Before beginning the tutorial, please download the Nuclei 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, “NucleiTrackDemo.tif,” into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Nuclei Tracking recipe.
Select the Low presets for both the Detection and Tracking preset groups.
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:
Separation Factor: 92
Click the Start button or press the
F4key on your keyboard to begin applying the recipe to the image.
The detected object outlines and tracks will be overlaid on the image.
Results
Measurements
The Nuclei Tracking recipe generates morphological, intensity, position, and count measurements for each detected cell. You can add additional measurements to the analysis results with the Measurement Tool in Aivia and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are given in the table below.
Morphology | Intensity | Position | Count |
|---|---|---|---|
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Image Credits
Harvard Stem Cell Institute, Harvard University, Boston MA