Measure cells at the edge of clumps

Hi,

I’m trying to identify cells that are at edges of clusters. My idea was to identify the cells, then expand the identified objects until adjacent cells touch each other, then use the MeasureObjectNeighbor to suss out cells that are on the border of clusters. However, the results from MeasureObjectNeighbor (in “Adjacent” mode) aren’t really what I expected. I expected the measurement “PercentTouching” to range from 0-100% (or 0-1) so that I could use that to filter out cells which did not touch other cells 100% (i.e. border cells). Is this a bug, or have I misunderstood how the PercentTouching measurement works? I’ve attached a screendump to show what I mean.

Also, is there a way to filter out expanded objects that touch the edge of the image?

Edit: I’m using CellProfiler version 11248.

Thanks,
Karl


Hi Karl,

I believe this is a bug. We will repost here with a clarification or a bugfix; stay tuned.

The easiest way to do this is to use IdentifySecondaryObjects with Distance-N as the method to expand the objects rather than ExpandOrShrinkObjects. That way, you can make use of the “Discard secondary objects that touch the edge of the image” setting.

Regards,
-Mark

Alright, thanks Mark.

cheers,
Karl

Hi Karl,

The trunk build of CP which includes the fix for MeasureObjectNeighbors is here.
-Mark

Great, thank you!

cheers,
Karl