2.3 Cell Segmentation
Algorithm will find possible centers of individual cells inside the mask
- Adjust Segments Parameters
- Click Compute Features
- Click Next
- Min Distance: minimum distance between 2 centers (increase when you have more than one center per cell, decrease when there are none)
- Min Height: minimum euclidean distance to background (decrease when there are missing centers)
- Min Margin: minimum distance to image border
- Max peaks: maximum number of possible centers (chosen based on distance to background)
Watershed algorithm will define each individual cell
Cell computation
- Adjust Cell Computation Parameters
- Click Compute Cells
- Click Next
- Axial step: degrees between each rotation to find cell orientation (should not be changed)
- Force merge if area below (pxs): cells with an area below defined value will automatically be merged
-
Merged Dividing Cells: tries to find cells that are a single dividing cell (use with caution)
- Length tolerance merge: maximum accepted length increase
- Min Interface for merge: minimum number of “touching” pixels between 2 cells
- Merge/Split Cells: click on button and then right-click on cells. (only manually merged cells can be splitted)
- Define as noise: same procedure; removes from the analysis noise that was misidentified as possible cell