3D Cell Analysis - Meshes/Spots

The 3D Cell Analysis - Meshes and 3D Cell Analysis - Spots recipes in Aivia can detect cells, nuclei, and vesicles.

The 3D Cell Analysis - Meshes recipe creates surface reconstructions of all detected cellular components, while the 3D Cell Analysis - Spots recipe creates surface reconstructions of cells and nuclei and spot representations of vesicles. Spots are spherical objects with fixed size that lower the rendering cost for visualizing vesicle counts and positions.

Both recipes establish relationships between 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 calculated.

On this page:

1 Automatic Parameter Selection
2 Parameters and Presets
- 2.1 Parameters
- 2.2 Presets
3 Measurements
4 Related Articles

Automatic Parameter Selection

3D Cell Analysis - Meshes/Spots features automatic parameter selection for Min Cells Intensity, Min Nuclei Intensity, and Min Vesicles Intensity. Click on Auto (see figure below) in the recipe header to initiate parameter estimation, which uses the image data in the processing region as well as the smoothing and background removal options that you have selected (see “Parameters” section) to approximate reasonable minimum intensity values.

Auto button for automatic parameter selection

Parameters and Presets

Parameters

Recipe parameters for 3D Cell Analysis - Meshes and 3D Cell Analysis - Spots 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 applies a morphological filter consisted of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size. Average Filter Smoothing applies an average filter that outputs the average intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size. Gaussian Filter Smoothing applies a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size. Median Filter Smoothing applies a median filter that outputs the median intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size.
	Typical Cells Diameter (Remove Background only)	0	65,535 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
	Min Cells Intensity	0	255 (8-bit) 65,535 (16-bit)	Specifies the lower intensity threshold for cell detection When Skip Remove Background is selected, the threshold is applied to the smoothed (if smoothing is opted for) Cells Input When Remove Background is selected, the threshold is applied to the enhanced image, which has the background removed A lower value leads to the detection of bigger and more cells
	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
	Cell Diameter	0	100,000 px or µm	Specifies the range of detected cells to keep based on their diameters
	Min Edge to Center Distance (Apply Partition only)	0	100,000 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
	Mesh Smoothing Factor	0	100	Specifies the amount of smoothing applied to the surface reconstructions of the detected cells; a lower value leads to the creation of surfaces with greater similarity to the input image
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 applies a morphological filter consisted of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size. Average Filter Smoothing applies an average filter that outputs the average intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size. Gaussian Filter Smoothing applies a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size. Median Filter Smoothing applies a median filter that outputs the median intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size.
	Typical Nuclei Diameter (Remove Background only)	0	100,000 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
	Min Nuclei Intensity	0	255 (8-bit) 65,535 (16-bit)	Specifies the lower intensity threshold for nuclei detection When Skip Remove Background is selected, the threshold is applied to the smoothed (if smoothing is opted for) Nuclei Input When Remove Background is selected, the threshold is applied to the enhanced image, which has the background removed A lower value leads to the detection of bigger and more nuclei
	Fill Holes Size	0	1,000,000 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
	Nuclei Diameter	0	100,000 px or µm	Specifies the range of detected nuclei to keep based on their diameters
	Min Edge to Center Distance (Apply Partition only)	0	100,000 px or µm	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
	Mesh Smoothing Factor	0	100	Specifies the amount of smoothing applied to the surface reconstructions of the detected nuclei; a lower value leads to the creation of surfaces with greater similarity to the input image
	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 applies a morphological filter consisted of an average filter and morphological opening/closing operations based on the value of the Image Smoothing Filter Size. Average Filter Smoothing applies an average filter that outputs the average intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size. Gaussian Filter Smoothing applies a Gaussian filter with a filter width specified by the value of the Image Smoothing Filter Size. Median Filter Smoothing applies a median filter that outputs the median intensity value for each voxel across a circular region, with diameter specified by the value of the Image Smoothing Filter Size.
	Typical Vesicles Diameter (Remove Background only)	0	100,000 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 preserving smaller objects
	Min Vesicles Intensity	0	255 (8-bit) 65,535 (16-bit)	Specifies the lower intensity threshold for vesicle detection When Skip Remove Background is selected, the threshold is applied to the smoothed (if smoothing is opted for) Vesicles [#] Input When Remove Background is selected, the threshold is applied to the enhanced image, which has the background removed A lower value leads to the detection of bigger and more vesicles
	Fill Holes Size	0	1,000,000 px² or µm²	Specifies the maximum size of gaps in detected vesicles that are filled; a lower value leads to the preservation of more holes in the detected vesicles
	Vesicles Diameter	0	100,000 px or µm	Specifies the range of detected vesicles to keep based on their diameters
	Min Edge to Center Distance (Apply Partition only)	0	100,000 px or µm	Specifies the minimum distance from the center of a vesicle to the edge that is touching its closest neighboring vesicle; a lower value leads to more aggressive partitioning, which results in smaller, more uniform vesicle objects
	Mesh Smoothing Factor (3D Cell Analysis - Meshes only)	0	100	Specifies the amount of smoothing applied to the surface reconstructions of the detected vesicles; a lower value leads to the creation of surfaces with greater similarity to the input image

Presets

There are three preset groups in the recipes: Whole Cells Detection, Nuclei Detection, and Vesicles Detection. Each group has three pre-configured parameter groupings to help you get started on the analysis.

In the Input and Output section, you may choose whether to detect nuclei and specify how many vesicle sets to detect (see right), which dictates what parameter groups are shown. You may choose to detect up to five vesicle sets at once. Each vesicle set has its own Vesicles Detection section, and all Vesicles Detection sections have the same default preset values. The default preset values are given in the sections to follow.

Whole Cells Detection

Parameter Name	Low	Medium	High

Parameter Name	Low	Medium	High
Image Smoothing Filter Size	3	9	13
Typical Cells Diameter	5 px or µm	20 px or µm	50 px or µm
Min Cells Intensity	102 (8-bit)	51 (8-bit)	13 (8-bit)
Min Cells Intensity	26,214 (16-bit)	13,107 (16-bit)	3,277 (16-bit)
Fill Holes Size	0	0	0
Cell Diameter	1 - 30 px or µm	2 - 100 px or µm	20 - 200 px or µm
Min Edge to Center Distance	4 px or µm	8 px or µm	25 px or µm
Mesh Smoothing Factor	0	0	0

Output Options menu where you can add and remove nucleus and vesicle output sets

Nuclei Detection

Parameter Name	Low	Medium	High

Parameter Name	Low	Medium	High
Image Smoothing Filter Size	1	3	5
Typical Nuclei Diameter	3 px or µm	8 px or µm	15 px or µm
Min Nuclei Intensity	102 (8-bit)	51 (8-bit)	13 (8-bit)
Min Nuclei Intensity	26,214 (16-bit)	13,107 (16-bit)	3,277 (16-bit)
Fill Holes Size	0	0	0
Nuclei Diameter	1 - 10 px or µm	2 - 20 px or µm	5 - 50 px or µm
Min Edge to Center Distance	3 px or µm	6 px or µm	10 px or µm
Mesh Smoothing Factor	0	0	0

Vesicles Detection

Parameter Name	Low	Medium	High

Parameter Name	Low	Medium	High
Image Smoothing Filter Size	1	1	1
Typical Vesicles Diameter	0.2 px or µm	0.5 px or µm	1 px or µm
Min Vesicles Intensity	102 (8-bit)	51 (8-bit)	13 (8-bit)
Min Vesicles Intensity	26,214 (16-bit)	13,107 (16-bit)	3,277 (16-bit)
Fill Holes Size	0	0	0
Vesicles Diameter	0.1 - 5 px or µm	0.2 - 10 px or µm	0.5 - 20 px or µm
Min Edge to Center Distance	0.2 px or µm	0.6 px or µm	2 px or µm
Mesh Smoothing Factor	0	0	0

Measurements

The 3D Cell Analysis - Meshes and 3D Cell Analysis - Spots recipes generate a few morphological, intensity, position, and count measurements. 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.

Object Set	Morphology	Intensity	Position	Count

Object Set	Morphology	Intensity	Position	Count
Cell Membranes	Sphericity Surface Area Surface Area to Volume Ratio Volume	Mean Intensity - [Cells Input]	Centroid X Centroid Y Centroid Z	Contained Vesicle Count
Nuclear Membranes	Sphericity Surface Area Surface Area to Volume Ratio Volume	Mean Intensity - [Nuclei Input]	Centroid X Centroid Y Centroid Z	Contained Vesicle Count
Cells	Cell/Nucleus Volume Ratio Cell/Cytoplasm Volume Ratio	None	Center to Nucleus Center Distance Cytoplasm to Nucleus Vesicle Ratio (3D Cell Analysis - Meshes only) Min Edge to Nucleus Edge Distance Centroid X Centroid Y Centroid Z	Contained Vesicle Count
Cytoplasm	Volume (3D Cell Analysis - Meshes only) Volume to Contained Vesicle Volume Ratio (3D Cell Analysis - Meshes only)	None	Centroid X Centroid Y Centroid Z	Contained Vesicle Count
Nucleus	Mean Contained Vesicle Volume (3D Cell Analysis - Meshes only)	None	Min Center of Mass to Cell Edge Distance Centroid X Centroid Y Centroid Z	Contained Vesicle Count
Vesicles	Sphericity (3D Cell Analysis - Meshes only) Volume (3D Cell Analysis - Meshes only)	None	Distance to Center of Cell Distance to Center of Nucleus Distance to Nearest Edge of Cell Distance to Nearest Edge of Nucleus Centroid X Centroid Y Centroid Z	None

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