bwconncomp doesn't count correctly

I'm having troubles counting bacterial colonies using bwconncomp function ......as it counts adjecent colonies as one single spot and also count the outer boundaries of the plate holding the bacteria ..... , This is my first time to write full code and I have to handle this project soon so I'm in desperate need of help .

I=imread('2010-07-28-17.06.301.jpg');
imshow(I);
h = imfreehand; %draw something 
M = ~h.createMask();
I(M) = 0; % mask out the borders
imshow(I);
dim=size(I);
g=rgb2gray(I);
bw = im2bw(I,0.6);
se=strel('disk',4);
T=imopen(bw,se);
imshow(T);
T=imcomplement(T);
T=flipud(T);
BW_filled = imfill(T,'holes');
TT=imcrop(T); % remove borders
N=imcomplement(TT);
CC = bwconncomp(N,8);
imshow(T);
disp(CC);

original image

[KSSV]

Attach your original image..so that people here can give you better solution.

[Image Analyst]

If you're so desparate to get this done soon, then attach '2010-07-28-17.06.301.jpg'

In the meantime, try this link

Also, are you sure you need to count the number of colonies rather than just the area fraction? What happens if there was so many that about half the dish was covered? There would be no way to identify separate colonies in that case. So I'd just reconned computing the area fraction.

Answer 1

[Rahul punk]

use this

https://www.mathworks.com/matlabcentral/fileexchange/70220-rahulpunk?s_tid=prof_contriblnk