MATLAB: Count and measure yeast cells from an image

Question

Hello. I am trying to detect, count and measure yeast cells from various images like in this example,

First I made the background uniform using a morphological opening, followed by an increase of the contrast using "imadjust". Then, I found the edges of the image using the 'canny' function to create a mask that overlays on the adjusted image to remove all the background and some of the cells glow. Next, I turned the pixels below 50 into black and converted the image into a binary one. Finally, I cleaned the image and used the “watershed” transformation to separate the connected cells.

Here’s my code:

        clear all
        close all
        se1=strel('disk',2);
        X=imread('t132-1.png');
        I=X(:,:,2);
        figure
        imshow(I)
        title('original')
        drawnow
        %%background removal
        background = imopen(I,strel('disk',15));
        I2=I-background;
        I3 = imadjust(I2);
        % figure




        % imshow(I3);
        % title('Adjusted image')
        % drawnow





        %%edge detection
        Iedge=edge(I3,'canny',0.3);
        Iedge=bwmorph(Iedge,'dilate');
        Iedge=bwmorph(Iedge,'bridge');
        Iedge=imfill(Iedge,'holes');
        % figure 
        % imshow(Iedge)
        % title('edge')
        % drawnow
        Iclean=bwmorph(Iedge,'erode',2);
        Iclean=bwareaopen(Iclean,500);
        % figure
        % imshow(Iclean);
        % drawnow
        %%Image masking
        Icut=255-I3;
        Icut(Iclean==0)=0;
        figure;
        imshow(Icut);
        title('cut')
        drawnow
        Iadjust=Icut;
        Iadjust(Iadjust<50)=0;
        % figure
        % imshow(Iadjust);
        % title('black pixels below 50');
        % drawnow
        Ibw=im2bw(Iadjust,0.1);
        % figure
        % imshow(Ibw);
        % title('BW');
        % drawnow
        Ibw=imerode(Ibw,se1);
        Ibw=imdilate(Ibw,se1);
        Iclean2=bwareaopen(Ibw,150);
        % figure
        % imshow(Iclean2);
        % title('clean')
        % drawnow
        %%watershed function
        D=-bwdist(~Iclean2);
        mask=imextendedmin(D,7);
        D2=imimposemin(D,mask);
        Ld2=watershed(D2);
        bw3=Iclean2;
        bw3(Ld2==0)=0;
        figure
        imshow(bw3)
        title('Final')
        drawnow

I plan to make the measurements using the “regionprops” command. My problem is that the resulting image (shown below) lost many of the cells forms and have outter holes that difficult the measuring process. I’m wondering if you have any suggestion for a better general detection process that I could apply on all my 36 images, thanks in advance!

Answer 1

Maybe try either imfill() or bwconvhull().