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 |
---|---|---|---|---|
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:
|
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
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:
|
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
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
| ||
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:
|
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
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 |