• Ready for review
  • Aivia Software

    Cell Count

    The Cell Count recipe in Aivia detects cells in fluorescence microscopy images. This recipe is designed for 2D data.

    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

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

    Preset Group

    Parameter Name

    Min Value

    Max Value

    Description

    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; when Remove Background is selected, the threshold will be applied to the background-removed image; whereas when Skip Remove Background is selected, the threshold will be applied to the input image; a lower value will detect bigger and more objects

    Fill Holes Size

    0

    1,000,000 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 outline of the detected objects; a lower value will preserve more of the object's morphological features

    Subset Filtering

    Object Size

    0

    1,000,000,000 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 (Cell 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 Subset Filtering. Each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are in the sections to follow.

     

    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

    10 px2 or µm2

    25 px2 or µm2

    50 px2 or µm2

    Smoothing Factor

    4

    4

    4



     

    Subset Filtering

    Parameter Name

    Small

    Medium

    Large

    Object Size

    1 - 250 px2 or µm2

    50 - 1,000 px2 or µm2

    150 - 6,000 px2 or µm2

    Separation Factor

    50

    70

    85

     

     

    Tutorial (written steps)

    Before beginning the tutorial, please download the Cell 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.

    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 to expand the Recipe Console and show parameter options for 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 Start button or press the F4 key on your keyboard to begin applying the recipe to the image.

    The detected object outlines will be overlaid on the image.

     

    Cell Count tutorial results

     

    Tutorial (videos)

     

    Video: Cell Count Tutorial Worked Example (59s)

     

     

    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 and explore measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are in the table below.

    Morphological

    Intensity

    Summary

    Morphological

    Intensity

    Summary

    • Area

    • Circularity

    • Component Count

    • Pixel-based Mean Intensity

    • Pixel-based Total Intensity

    • Pixel-based Standard Deviation Intensity

    • Total Component Count

    • Average Mean Intensity

     

    Related Articles