I have a question about the definition of „percent touching“.
Here our project:
We want to determine the cells at the border of a cell colony. To do so, we only want to count cells that have less than 70 percent touching.
What I have done:
I created a pipeline to identify primary objects by using a smoothed Dapi image. Than this image was used to determine secondary objects in an actin image.
If I now use MeasureObjectNeighbors I have the problem to specify: what is a neighbor?
Using Adjacent or expand until adjacent resulted in values from 0 to 7 (see attached pdf file). Sometimes the results from adjacent and expand until adjacent are the same and sometimes not.
If I want to determine neighbors within a specific distance (5, 10, 20 or 50 pixel) I got values from 4 to 100 percent touching, which makes more sense to me. If an cell is in the middle of an colony I would expect that the boundary of this cell has nearly 100 percent touching to other cells.
I read the definitions in cell profiler manual, but so far I can´t really understand the results I got.
Here my questions:
What is percent touching really telling me?
What is the meaning if an object has 1 or 7 percent touching after using adjacent or expand until adjacent?
I know that there are a lot of more things in the pipeline, these are only for later quantifications.
Thanks a lot for your help. Fell free to contact me if it doesn´t come clear what I want to say.
neighbors_percent touching.pdf (137 KB)
pipeline measure everything_cell neighbors adj_expand until adj_specific distances.cp (14.7 KB)