Identity of Neighbours

cellprofiler

#1

Hello,

We are using cell profiler to identify objects and the number of neighbours of every object. Our problem is that we would like to get the identity of these neighbours for posterior analysis. We think that the program have this information but we are not able to extract it. Can we get any help please?

Thank you very much in advance.

Luisma Escudero


Cell neighbours identification for cell intercalation measurements
#2

Hi Luisma,

Indeed we do record this information, but since this is an unusual measurement (i.e. a variable number of measurements per object), we can’t run this information through our ExportTo* modules. You need to use Matlab to access this data and it is within handles.Measurements.Neighbors.IdentityOfNeighbors. Take a look at the MeasureObjectNeighbors.m code, which I quote from:

"
% This field is different from the usual measurements. To avoid problems with export modules etc we don’t
% add a IdentityOfNeighborsFeatures field. It will then be “invisible” to
% export modules, which look for fields with ‘Features’ in the name.
handles.Measurements.Neighbors.IdentityOfNeighbors(handles.Current.SetBeingAnalyzed) = {IdentityOfNeighbors};

%%% Example: To extract the number of neighbor for objects called Cells, use code like this:
%%% handles.Measurements.Neighbors.IdentityOfNeighborsCells{1}{3}
%%% where 1 is the image number and 3 is the object number. This
%%% yields a list of the objects who are neighbors with Cell object 3.
"

Hope this helps,
Dave