Critical_reorganization_of_adolescent_prefrontal_circuitry/code/morphology/CalcInt.m

function [results,Int]=CalcInt(MGstack,MGvolume,res,PunctaWanted,Pvolume_total,spMarker)


MGPuncta=  MGstack + PunctaWanted;                        
MGPuncta(MGPuncta == 1) = 0;                                      
MGPuncta(MGPuncta == 2) = 1;     

PunctaWanted_labeled  =  bwlabeln(PunctaWanted,8);  
MGPuncta =  MGPuncta .* PunctaWanted_labeled; 
[MGPuncta_size, ~]  = histcounts(MGPuncta,1 : max(MGPuncta(:)));
MGPuncta_size(MGPuncta_size<=1)=0;

[PunctaWanted_size, ~]  = histcounts(PunctaWanted_labeled ,1 : max(PunctaWanted_labeled(:)));
PunctaWanted_size(PunctaWanted_size<=1)=0;



%if parts extending Microglias

if spMarker<1
    MGPuncta_size(MGPuncta_size<=res.pixel_width_um/10)=0;
    PunctaWanted_size(PunctaWanted_size<=res.pixel_width_um/10)=0;
    
    [Psize, ~]  =  histcounts(PunctaWanted_labeled, 1 : max(PunctaWanted_labeled(:)));
    MGPuncta_size(end : length(Psize)) = 0;
    size_ratio = MGPuncta_size ./ Psize;
    MGPuncta_size = find(size_ratio == 1);
    MGPuncta = ismember(MGPuncta,MGPuncta_size);
end

%% count number of inclusions and number of pixels in the intersection in the desired microglia

results.number_inclusions  = nnz(MGPuncta_size);        
results.number_inclusions_per_um = results.number_inclusions / MGvolume;
results.volume_inclusions_um = sum(sum(sum(MGPuncta)))* (res.pixel_width_um*res.pixel_height_um*res.pixel_depth_um);
results.volume_inclusions_per_um = results.volume_inclusions_um / MGvolume;
results.microglia_volume=MGvolume;
results.number_inclusions_total=nnz(PunctaWanted_size); 
results.volume_inclusions_total=Pvolume_total;

Int=MGPuncta;