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Cell Analysis

Aivia Software

Cell Analysis

The Cell Analysis recipe detects cells, nuclei, and vesicles in 2D fluorescence microscopy images.

The recipe establishes relationships between detected objects so that nucleus and vesicle measurements can easily be done on a per-cell basis and so that measurements between cellular components can be made.

Parameters and Presets

Parameters

Recipe parameters for Cell Analysis 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

Whole Cells Detection

Image Smoothing Filter Size

(without Skip Smooth Image only)

1

100

Specifies the diameter of the filter that is used to smooth the Cells Input before further processing

The available smoothing types are the following:

  • Morphological Smoothing uses a morphological filter consisting of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size.

  • Average Filter Smoothing uses an average filter that outputs the average intensity value for each pixel across a circular region with a diameter specified by the value of the Image Smoothing Filter Size.

  • Gaussian Filter Smoothing uses a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size.

  • Binomial Filter Smoothing uses a binomial filter with a filter width specified by the value of the Image Smoothing Filter Size.

Typical Cell Diameter

(Remove Background only)

0

10,000 px or µm

Specifies the diameter of a typical cell in the image; the diameter is used for object enhancement and background removal, with a lower value preserving smaller objects

Contrast Threshold

(Remove Background only)

0

255 (8-bit)

65,535 (16-bit)

Specifies the lower intensity threshold for cell detection on the enhanced image, which has the background removed; a lower value leads to the detection of more and bigger cells

Intensity Threshold

(Skip Remove Background only)

0

255 (8-bit)

65,535 (16-bit)

Specifies the lower intensity threshold for cell detection on the smoothed (if smoothing is opted for) Cells Input

Fill Holes Size

0

1,000,000 px2 or µm2

Specifies the maximum size of gaps in detected cells that are filled; a lower value leads to the preservation of more holes in the detected cells

Smoothing Factor

0

100

Specifies the amount of smoothing applied to the detected cell boundaries; a higher value leads to more smoothing

Cells Diameter

0

10,000 px or µm

Specifies the range of detected cells to keep based on their diameters

Min Edge-to-Center Distance

(Apply Cells Partition only)

0

10,000 px or µm

Specifies the minimum distance from the center of a cell to the edge that is touching its closest neighboring cell; a lower value leads to more aggressive partitioning, which results in smaller, more uniform cell objects

Nuclei Detection

(optional)

Image Smoothing Filter Size

(without Skip Smooth Image only)

1

100

Specifies the diameter of the filter that is used to smooth the Nuclei Input before further processing

The available smoothing types are the following:

  • Morphological Smoothing uses a morphological filter consisting of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size.

  • Average Filter Smoothing uses an average filter that outputs the average intensity value for each pixel across a circular region with a diameter specified by the value of the Image Smoothing Filter Size.

  • Gaussian Filter Smoothing uses a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size.

  • Binomial Filter Smoothing uses a binomial filter with a filter width specified by the value of the Image Smoothing Filter Size.

Typical Nucleus Diameter

(Remove Background only)

0

10,000 px or µm

Specifies the diameter of a typical nucleus in the image; the diameter is used for object enhancement and background removal, with a lower value preserving smaller objects

Contrast Threshold

(Remove Background only)

0

255 (8-bit)

65,535 (16-bit)

Specifies the lower intensity threshold for nucleus detection on the enhanced image, which has the background removed; a lower value leads to the detection of more and bigger nuclei

Intensity Threshold

(Skip Remove Background only)

0

255 (8-bit)

65,535 (16-bit)

Specifies the lower intensity threshold for nucleus detection on the smoothed (if smoothing is opted for) Nuclei Input

Fill Holes Size

0

50,000 px2 or µm2

Specifies the maximum size of gaps in detected nuclei that are filled; a lower value leads to the preservation of more holes in the detected nuclei

Smoothing Factor

0

100

Specifies the amount of smoothing applied to the detected nucleus boundaries; a higher value leads to more smoothing

Nuclei Diameter

0

10,000 px or µm

Specifies the range of detected nuclei to keep based on their diameters

Min Edge-to-Center Distance

(Apply Nuclei Partition only)

0

10,000

Specifies the minimum distance from the center of a nucleus to the edge that is touching its closest neighboring nucleus; a lower value leads to more aggressive partitioning, which results in smaller, more uniform nucleus objects

Nuclei Correction

Not applicable

Specifies how to deal with detected nuclei that lie partially outside of detected cells

  • When No Nuclei Correction is selected, no post-processing is done to detected nuclei and cells, even when nuclei are partially outside of cells

  • When Extend Cell To Nucleus is selected, the detected cells are expanded so that they fully encapsulate their detected nuclei

  • When Crop Nucleus To Cell is selected, detected nuclei are cut off at the edges of their detected cells so that all cells fully encapsulate their nuclei

Vesicles [#] Detection

Up to five (5) vesicle sets can be detected.

(optional)

Image Smoothing Filter Size

(without Skip Smooth Image only)

1

100

Specifies the diameter of the filter that is used to smooth the Vesicles [#] Input before further processing

The available smoothing types are the following:

  • Morphological Smoothing uses a morphological filter consisting of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size.

  • Average Filter Smoothing uses an average filter that outputs the average intensity value for each pixel across a circular region with a diameter specified by the value of the Image Smoothing Filter Size.

  • Gaussian Filter Smoothing uses a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size.

  • Binomial Filter Smoothing uses a binomial filter with a filter width specified by the value of the Image Smoothing Filter Size.

Typical Vesicles Diameter

(Remove Background and Enhance Bright Spots only)

0

10,000 px or µm

Specifies the diameter of a typical vesicle in the image; the diameter is used for object enhancement and background removal, with a lower value enhancing/preserving smaller objects

Contrast Threshold

(Remove Background and Enhance Bright Spots only)

0