indv_cell_coloc.m

function [C2_intMean, C0_cell_size, objBoundVol]=indv_cell_coloc(segCell, C2_indiv)
%% Adam Tyson | 2018-03-27 | adam.tyson@icr.ac.uk
% function to take segmented images of cells, mask a second channel, and
% return mean fluroescence.
% also returns mean cell size

%% TO DO
% remove loops
% check picking cells individually

for obj=1:length(segCell)

    objSeg=segCell{obj};
    
    % vol of object (using convex bounding box)
    for z=1:size(objSeg,3)
        boundBox(:,:,z) = bwconvhull(objSeg(:,:,z));
    end
    objBoundVol(obj) = sum(boundBox(:));
    
    % secondary marker expression & cell vol
    C2im=C2_indiv{obj};
    for cell=1:max(objSeg(:))
        % orig note-  "first "cell" is oversegmented noise"
        % not sure what this referred to
        
        tmpIm=objSeg;
        tmpIm(tmpIm~=cell)=0; % not sure why have to use -ve
        tmpIm(tmpIm>0)=1;
        
        C0_cell_size{obj, cell}=nnz(tmpIm>0); % num non-zero elements
        
        mask=zeros(size(tmpIm));
        for z=1:size(tmpIm,3)
            mask(:,:,z) = bwconvhull(tmpIm(:,:,z));
        end
        
        maskedC2=mask.*double(C2im);
        C2_intMean{obj, cell}=mean(nonzeros(maskedC2(:))); % non-zero mean
    end
    
    clear objSeg
    clear boundBox
end

end