MATLAB Answers

bwconncomp doesn't count correctly

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Eilaf Badr
Eilaf Badr on 13 Dec 2018
Answered: Rahul punk on 15 Feb 2019
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
90 c.jpg

  2 Comments

KSSV
KSSV on 13 Dec 2018
Attach your original image..so that people here can give you better solution.
Image Analyst
Image Analyst on 13 Dec 2018
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.

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Answers (1)

Rahul punk
Rahul punk on 15 Feb 2019
use this
https://www.mathworks.com/matlabcentral/fileexchange/70220-rahulpunk?s_tid=prof_contriblnk

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