LymphNodeReconstruction/vasC.m at main · Gleghorn-Lab/LymphNodeReconstruction · GitHub

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%function [cc, BW] = vasFunc(p,r, I)
%
%mike = imbinarize(imread("VasculatureGT section30.tif"));
p = imread('Purple_30.tif');
%I0 = rgb2gray(p);
maskp = hysteresis3d(p,0.45,0.4,8);
se =  strel('sphere',8);% se =offsetstrel('ball',12,12);
maskp1 = imdilate(maskp,se);
maskp2 = imerode(maskp1,se);
maskp2 = rgb2gray(maskp2);
imshow(maskp2)
%
%load('masks.mat');
I = im2double(imread('merged_30.tif'));
%I = im2double(imread('30.tif'));

%I = imread('mask2.PNG');
r= im2double(imread('Red_30.tif'));
% g1 = g1+maskedRGBImage;x
% p = imread('purple.tif');
% g0 = imread('green.tif');
%r = im2double(imread('redtwo.tif'));
main =I-maskp2;
gr = (rgb2gray(main));
%gr = (rgb2gray(I));

I2 = ordfilt2(gr,22,true(5));
% I2 = medfilt2(gr>10,[3 3]);
% imshow(I2)
%load('masks.mat');
%I = im2double(imread('S4_LYVE1_Align_06_07_21_1_2.tif'));
%I = imread('mask2.PNG');
% g1= imread('S4_LYVE1_Align_06_07_21_1.tif');
% g1 = g1+maskedRGBImage;x
% p = imread('purple.tif');
% g0 = imread('green.tif');
%g=rgb2gray(maskedRGBImage-r);

%g = imgaussfilt(g,1);
%g=rgb2gray(I);
%
% se = offsetstrel('ball',2,2);
% g = imdilate(g,se);
% g = imerode(g,se);
% % %imshow(g)
%I2 = medfilt2(medfilt2(medfilt2(medfilt2(gr>89,[2 2]))));

% imshow(I2);

%BW1 = edge(g,'canny',0.9);
%figure
%imshow(g)
img= hysteresis3d(gr,0.44,0.4,8);
figure
imshow(img)

% se1 =  strel('sphere',4);% se =offsetstrel('ball',12,12);
% se2 =  strel('sphere',1);% se =offsetstrel('ball',12,12);
%
% img1 = imdilate(img,se1);
% img2 = imerode(img1,se1);
%
%
% imshow(img2)
%img = imbinarize(imfill(img,'holes'));
%img1 = 1- img;

cc = bwconncomp(img);
%img =imgaussfilt(img,1);
% figure
BW = bwareafilt(imbinarize(img),[5 2550]);
%BW = bwareafilt(BW,[10 1000]);

% se1 =  strel('sphere',8);% se =offsetstrel('ball',12,12);
% maskp3 = imdilate(BW,se1);
% maskp4 = imerode(maskp3,se1);
% %maskp4 = rgb2gray(maskp4);
% imshow(maskp4)
% BW = bwareaopen(img, 10);
 imshow(BW)
% labeledImage = bwlabel(img);
% labeledImage(labeledImage == 8) = 3;  % Blob #8 is now merged with 3

se1 =  strel('sphere',4);% se =offsetstrel('ball',12,12);
se2 =  strel('sphere',3);% se =offsetstrel('ball',12,12);

BW1 = imdilate(BW,se1);
BW2 = imerode(BW1,se2);

BW3 = bwareafilt(BW2,[15 1550]);

%BW = bwareafilt(imbinarize(img), 16);
imshow(BW3)

%img1 = bwconvhull(img,'objects');
    [B,L,N] = bwboundaries(BW);
       figure;
       imshow(I);
       hold on;
       for k = 1:length(B)
           boundary = B{k};
%            if(k > N)
                plot(boundary(:,2), boundary(:,1), 'y', 'LineWidth', 1.5);
%             else
%                 plot(boundary(:,2), boundary(:,1), 'r', 'LineWidth', 2);
%            end
       end