Table 3.
Setup to recognize cytoplasm in CellPathfinder
| Parameter | Note | |||
|---|---|---|---|---|
| ImageFilter | [1] Gaussian | IN Previous Output | Mask Size (μm) | Set to 1.0 μm for HeLa cells. |
| Binarization | [2] Threshold | IN Previous Output | Threshold [gray level] | Adjust the value depending on the luminance of the background and the cytoplasm. |
| BinarizationTransform | [3] ClosingCircle | IN Previous Output | Diameter (μm) | – |
| [4] OpeningCircle | IN Previous Output | Diameter (μm) | – | |
| Labeling | [5] Labeling | IN Previous Output | – | – |
| LabelTransform | [6] ExpandRegion3D | IN Nucleus [9] ExpandRegion3D, cytoplasm [5] Labeling | – | – |
| [7] ExcludeEdge | IN Previous Output | Range | Exclude the cells on the edge of the image. | |
| [8] ErodeRegion | IN Previous Output | Range | Shrink the recognized area to separate the individual cells, which are closely attached. | |
| [9] ExpandRegion3D | IN Nucleus [9] ExpandRegion-3D, Nucleus [10] Compactness-Filter(2D) | – | – | |
| [10] SubRegion | IN Cytoplasm [8] ErodeRegion, Cytoplasm [9] ExpandRegion3D | – | – | |
| [11] SubRegion | IN Previous Output, Nucleus Result | – | Exclude the nucleus region from the entire cell body. | |
| [12] SizeFilter | IN Previous Output | Range | – |
This table shows how to set algorithm for the recognition of cytoplasm. See step 8e ii.