Measure intensities corresponding to segments
Parameters:
| Name |
# |
Type |
Description |
| Channel Number for Cell or Nucleus Stain |
1 |
integer |
Channel number associated with the image. Use Edit/Rename to view or change channel number. |
| Channel Number to be measured |
2 |
integer |
Channel number associated with the image. Use Edit/Rename to view or change channel number. |
| Background Level (Percentile) |
3 |
real |
Background is calculated as frame-by-frame mean of those pixels that are the darker than this percentile of image histogram for the duration of the entire recording. |
| Approximate nucleus diameter |
4 |
integer |
Diameter of the nucleus in pixels |
| Debris cutoff (percentile) |
5 |
real |
Brighter details of the image than this will be ignored |
| Minimum cell fluorescence (%) |
6 |
real |
Cells dimmer than this will be rejected. Increase this value if debris dimmer than the cells is detected. |
Description:
Segments an image of cytosolic or nuclear stain into single cells or nuclei, and then measures intensities in an other channel, after performing background subtraction.
The output is a row of intensities, one mean intensity value for each detected object.
To adjust segmentation:
*If single nuclei are detected as multiple segments, increase the approximate cell diameter. In addition, you may turn segment welding on.
*If multiple nuclei are detected as single segments, decrease the approximate cell diameter. In addition, you may turn segment welding off.
*If debris is detected a nuclei, increase minimum cell fluorescence.
*If dimmer cells are missed, decrease minimum cell fluorescence.
*If bright debris outshines cells, decrease debris cutoff percentile.
Pipelines Glossary
