Aivia Software
Nuclei Count
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
- Casey McBride
The Nuclei Count recipe in Aivia detects nuclei in 2D fluorescence microscopy images and measures the morphology, intensity, and count of the detected nuclei.
This recipe can be used for detection of any compact, bright foreground objects against a dark background.
On this page:
Parameters and Presets
Parameters
Recipe parameters for Nuclei Count 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 | |
Nuclei Partition | 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 (Nuclei Partition only) | 0 | 100 | Adjusts 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 Nuclei Partition. 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 | 25 | 55 | 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 |
Nuclei Partition
Parameter Name | Low | Medium | High |
|---|---|---|---|
Object Size | 10 - 500 px2 or µm2 | 50 - 3,000 px2 or µm2 | 100 - 5,000 px2 or µm2 |
Separation Factor | 50 | 70 | 85 |
Tutorial
Before beginning the tutorial, please download the Nuclei Count 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, “NucleiCountDemo_01.tif,” into Aivia.
In the Recipe Console, click on the Recipe selection dropdown menu and select the Nuclei Count recipe.
Select the Low preset for both the Detection group and the Nuclei Partition group.
Click on the caret to the left of the Detection preset group to show the preset parameters.
Change the Detection preset parameter below as follows:
Contrast Threshold: 120
Click the Start button or press the
F4key on your keyboard to begin applying the recipe to the image.
The detected object outlines will be overlaid on the image.
Results
Measurements
The Nuclei Count recipe generates morphological and intensity measurements for each detected nucleus as well as a count of the total number of nuclei on the image. 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 | Count | Advanced |
|---|---|---|---|
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