Table 2.
Setup to recognize nuclei in CellPathfinder
| Parameter | Note | |||
|---|---|---|---|---|
| ImageFIlter | [1] Gaussian | IN Previous Output | Mask Size (μm) | Set to 1.0 μm for HeLa cells. |
| Binarization | [2] DynamicThreshold | IN Previous Output | Mask Size (μm) | – |
| Detect Factor | – | |||
| Min. Gray Offset [gray level] | – | |||
| BinarizeTransform | [3] ClosingCircle | IN Previous Output | Diameter (μm) | Adjust the value depending on the staining intensity. |
| [4] OpeningCircle | IN Previous Output | Diameter (μm) | – | |
| [5] Find MaximumDistance | IN Previous Output | Minimum Point Distance (μm) | – | |
| Remove Size (μm) | – | |||
| [6] DilationCircle | IN Previous Output | Diameter (μm) | Set to 5.0. | |
| Labeling | [7] Labeling | IN Previous Output | – | – |
| [8] Labeling | IN Nucleus [4] OpeningCircle | – | – | |
| LabelTransform | [9] ExpandRegion3D | IN Nucleus [7] Labeling, Nucleus [8] Labeling | – | – |
| [10] CompactnessFilter(2D) | IN Previous Output | Range | Recognize the nuclei with abnormal shapes. | |
| [11] SizeFilter | IN Previous Output | Range | Adjust the value depending on the cell type or the treatment. | |
| [12] Subregion | IN Nucleus [9] ExpandRegion-3D, Nucleus [10] Compactness-Filter(2D) | – | Exclude the nuclei with abnormal shapes. | |
| [13] ErodeRegion | IN Previous Output | Length (μm) | Recognize the dots at the interface between the nucleus and the cytoplasm. |
This table shows how to set algorithm for the recognition of nuclei. See step 8e i.