findClosestGM.asv

function closeGM = findClosestGM(sertoli, connectedGerm, ND)
sertoliLbl = bwlabel(sertoli,4);
germBoundary = imdilate(connectedGerm,strel('disk',1)) - connectedGerm;
germBoundaryLbl = bwlabel(germBoundary,8);
stats = regionprops(sertoliLbl, 'Centroid');
num = numel(stats);
% cell of 2D that the first column store a list of direct germ mass
% neighbors and their distance. The second column store the list of germ
% Mass that connected to the current sertoli cell via another sertoli
% cells. So, it includes germ mass label, distance and connecting sertoli.
closeGM = cell(num,2);

GMandSertoli = sertoliLbl - germBoundaryLbl;
[row, col] = size(GMandSertoli);
centers = round(cat(1,stats.Centroid));
for i = 1 : num
    cntr = centers(i,:);
    NS = neighboringSertoli(i, cntr, row,col,GMandSertoli,ND);
    if numel(NS) > 0
        directNS = directNeighbor(i, centers(i,:), NS, centers, lbl, row, col);
        %  if you want to have pair of connected region uncomment following line
        %         for j= 1 : numel(directNS)
        %             NRG{directNS(j)} = [NRG{directNS(j)}, i];
        %         end
        NRG{i} = [NRG{i}, directNS];
    end
end
end

function NS = neighboringSertoli(currentR, centroid, row,col,lbl,ND)
currentBox = lbl(max(1,centroid(2)-ND): min(centroid(2)+ND, row), ...
    max(1,centroid(1)-ND): min(centroid(1)+ND, col));
[~, ~, v] = find(currentBox);
NS = {[], [], []};
v = sort(v);
for j = 1 : numel(v)-1
    if (v(j) ~= currentR && v(j) ~= v(j+1))
        if v(j) > 0
            NS{1} = [NS{1}, v(j)];
        else
            NS{2} = [NS{2}, v(j)];
        end
    end
end

if (numel(v) > 0 && v(end) ~= currentR )
    if v(end) > 0
        NS{1} = [NS{1}, v(end)];
    else
        NS{2} = [NS{2}, v(end)];
    end
end
numGM = numel(NS{2});
if numGM > 0
    tmpNS = zeros(numGM,4);
    cntrInROI = min(centroid, [80 80]);
    bridgeRegion = cell(numGM,1);
    for l = 1 : numGM
        [r,c] = find(currentBox == NS{2}(l));
        D = sqrt((r-cntrInROI(2)).^2 + (c-cntrInROI(1)).^2);
        [val, ind] =min(D);
        tmpNS(l,1) = - NS{2}(l); % germ mass label
        tmpNS(l,2) = val; % ditance of centriod and nerest pixel in boundary
        % first coordinate of nearest pixel or row
        tmpNS(l,3) = r(ind)+ max(1,centroid(2)-ND)- 1;
        % second coordinate of nearest pixel or column
        tmpNS(l,4) = c(ind)+max(1,centroid(1)-ND) - 1;
        BR = checkBridgeRegion()
    end
    NS{2} = tmpNS;
end
end

function directNS = directNeighbor(currentR, centroid, NS, centers, lbl, row, col)
%neighborhood distance of centroid that is applied to check direct conection
n= 5;

directNS = [];
for i = 1 : numel(NS)
    % collecting some pixels in between regions
    connectingPixels = [];
    NCentroid = centers(NS(i), :);
    [x, y, cp] = improfile(lbl, ...
        [centroid(1), NCentroid(1)], [centroid(2), NCentroid(2)]);
    connectingPixels = [connectingPixels; cp];
    cp = improfile(lbl, ...
        max([centroid(1)-n, NCentroid(1)-n],1), [centroid(2), NCentroid(2)]);
    connectingPixels = [connectingPixels; cp];
    cp = improfile(lbl, ...
        min([centroid(1)+n, NCentroid(1)+n], col), [centroid(2), NCentroid(2)]);
    connectingPixels = [connectingPixels; cp];
    cp = improfile(lbl, ...
        [centroid(1), NCentroid(1)], max([centroid(2)-n, NCentroid(2)-n], 1));
    connectingPixels = [connectingPixels; cp];
    cp = improfile(lbl, ...
        [centroid(1), NCentroid(1)], min([centroid(2)+n, NCentroid(2)+n], row));
    connectingPixels = [connectingPixels; cp];
    
    for j = 1 : numel(connectingPixels)
        if (connectingPixels(j) ~= 0 && connectingPixels(j) ~= currentR ...
                && connectingPixels(j) ~= NS(i))
            break;
        end
    end
    if j == numel(connectingPixels)
        directNS = [directNS, NS(i)];
    end
end
end