Recipe Description


The Cell Count recipe in Aivia detects cells in fluorescence microscopy images. The recipe measures the morphology and intensity of the detected cells. This recipe can be used for detection of any bright foreground objects against a dark background.

Parameters and Presets


Parameters

Parameters and their descriptions are summarized in the table below.

Preset Group
Parameter Name
Min Value
Max Value
Description
Detection
Background Removal Factor
0
100
Adjusts the sensitivity of the background removal operation; a lower value will preserve larger objects and more background variations
Detection
Contrast Threshold
0
255 (8-bit)
65,535 (16-bit)
Adjusts the detection sensitivity on the background removed image; a lower value will detect bigger and more objects
Detection
Fill Holes Size
0
5,000
Adjusts the maximum size threshold for filling in gaps inside a detected object; a lower value will preserve more holes in the detection
Detection
Smoothing Factor
0
100
Adjusts the amount of smoothing applied to the outline of the detected objects; a lower value will preserve more of the object's morphological features
Subset Filtering
Object Size
0
50,000
Specifies the range of objects to be included in the analysis results based on the area of the detected objects
Subset Filtering
Separation Factor
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 Subset Filtering; 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
Background Removal Factor
25
55
75
Contrast Threshold
23 (8-bit)
5,898 (16-bit)
8 (8-bit)
1,966 (16-bit)
1 (8-bit)
262 (16-bit)
Fill Holes Size
10
25
50
Smoothing Factor
4
4
4

Subset Filtering

Parameter Name
Low
Medium
High
Object Size
1 - 250
50 - 1,000
150 - 6,000
Separation Factor
50
70
85

Measurements


The Cell Count recipe generates morphological and intensity measurements for each detected cell as well as a count of the total number of cells 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
    • Area
    • Circularity
    • Component Count
  • Intensity (measured on the input channel)
    • Mean
    • Standard
    • Total
  • Summary
    • Total Component Count
    • Average Mean Intensity

Tutorial


Before beginning the tutorial, please download the Cell Count Demo Image (CellCountDemo.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, CellCountDemo.tif, into Aivia
  2. In the Recipe Console, click on the Recipe selection dropdown menu and select the Cell Count recipe
  3. Select the High preset for the Detection group and the Small preset for the Subset Filtering group
  4. Click on the Show Advanced Interface icon showAdvOptions.PNG to expand the Recipe Console and show parameter options on the recipe
  5. Modify the parameter values in the recipe as follows while leaving the other values intact
    • Contrast Threshold: 90
    • Separation Factor: 81
  6. Click the From beginning button or press the F4 key on your keyboard to begin applying the recipe to the image

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

Results

CellCountDemo_output.png
Cell Count results