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.
On this page:
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 |
|---|---|---|---|---|
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 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:
|
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
| ||
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 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 | 255 (8-bit, Remove Background) 65,535 (16-bit, Remove Background) 255 (Enhance Bright Spots) | Specifies the lower intensity threshold for vesicle detection on the enhanced image, which has the background removed or bright spots enhanced | |
Intensity Threshold (Skip Remove Background only) | 0 | 255 (8-bit) 65,535 (16-bit) | Specifies the lower intensity threshold for vesicle detection on the smoothed (if smoothing is opted for) Vesicles [#] Input | |
Fill Holes Size (Remove Background and Skip Remove Background only) | 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 | |
Smoothing Factor (Remove Background and Skip Remove Background only) | 0 | 100 | Specifies the amount of smoothing applied to the detected vesicle boundaries; a higher value leads to more smoothing | |
Vesicles Diameter | 0 | 10,000 px or µm | Specifies the range of detected vesicles to keep based on their diameters | |
Min Edge-to-Center Distance (Apply Vesicles Partition only) | 0 | 10,000 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 | |
Presets
There are three preset groups in the recipe: Whole Cells Detection, Nuclei Detection, and Vesicles Detection. Each group has three pre-configured parameter groupings to help you get started on the analysis. The default preset values are given in the sections to follow.
In the Input and Output section, you may opt to not detect nuclei and/or to not detect vesicles (see right), in which case that/those parameter group(s) will not appear. Additionally, 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.
Whole Cells Detection
Parameter Name | Low | Medium | High |
|---|---|---|---|
Image Smoothing Filter Size | 3 | 9 | 13 |
Typical Cell Diameter | 5 px or µm | 20 px or µm | 50 px or µm |
Contrast Threshold | 23 (8-bit) | 8 (8-bit) | 1 (8-bit) |
5898 (16-bit) | 1966 (16-bit) | 262 (16-bit) | |
Intensity Threshold | 23 (8-bit) | 8 (8-bit) | 1 (8-bit) |
5898 (16-bit) | 1966 (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 |
Cells 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 |
Nuclei Detection
Parameter Name | Low | Medium | High |
|---|---|---|---|
Image Smoothing Filter Size | 1 | 3 | 5 |
Typical Nucleus Diameter | 3 px or µm | 8 px or µm | 15 px or µm |
Contrast Threshold | 23 (8-bit) | 8 (8-bit) | 1 (8-bit) |
5898 (16-bit) | 1966 (16-bit) | 262 (16-bit) | |
Intensity Threshold | 23 (8-bit) | 8 (8-bit) | 1 (8-bit) |
5898 (16-bit) | 1966 (16-bit) | 262 (16-bit) | |
Fill Holes Size | 0 px2 or µm2 (Remove Background) | 0 px2 or µm2 (Remove Background) | 0 px2 or µm2 (Remove Background) |
50 px2 or µm2 (Skip Remove Background) | 50 px2 or µm2 (Skip Remove Background) | 50 px2 or µm2 (Skip Remove Background) | |
Smoothing Factor | 2 (Remove Background) | 2 (Remove Background) | 2 (Remove Background) |
4 (Skip Remove Background) | 4 (Skip Remove Background) | 4 (Skip Remove Background) | |
Nuclei Diameter | 1 - 10 px or µm | 2 - 20 px or µm | 5 - 50 px or µm |
Min Edge-to-Center Distance | 3 | 6 | 10 |
Nuclei Correction | No Nuclei Correction | ||
Vesicles Detection
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 |
Contrast Threshold | 23 (8-bit, Remove Background) | 8 (8-bit, Remove Background) | 1 (8-bit, Remove Background) |
5898 (16-bit, Remove Background) | 1966 (16-bit, Remove Background) | 262 (16-bit, Remove Background) | |
125 (Enhance Bright Spots) | 65 (Enhance Bright Spots) | 15 (Enhance Bright Spots) | |
Intensity Threshold | 23 (8-bit) | 8 (8-bit) | 1 (8-bit) |
5898 (16-bit) | 1966 (16-bit) | 262 (16-bit) | |
Fill Holes Size | 0 px2 or µm2 | 0 px2 or µm2 | 0 px2 or µm2 |
Smoothing Factor | 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 |
Measurements
Cell Analysis generates morphological, intensity, position, and count measurements. You can add additional measurements to the analysis results by using the Measurement Tool in Aivia and view measurement definitions on the Measurement Definitions page. The measurements generated by the recipe are in the table below.
Object Set | Morphological | Intensity | Position | Count |
|---|---|---|---|---|
Cell Membranes |
|
|
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Nuclear Membranes |
|
|
|
|
Cells |
| None |
|
|
Cytoplasm |
| None |
|
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Nucleus |
| None |
|
|
Vesicles |
| None |
| None |