Cell count
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% Octave script for cell count in .jpg images.
%%%%%%%%%%%%%%%%%%%%%%%%%%
files = dir('file.jpg'); % Read all images in current folder.
fileID = fopen('CellCount.txt','w');
pas=pwd;
for i=1:length(files)
[pathname,filename,extension] = fileparts(files(i).name);
I = imread(files(i).name);
%I_cropped = I(400:900, 465:965); % Crop image.
imshow(I)
%Adjust color intensity (0=max intensity; 1=less intensity).
RED=1;
GREEN=1;
BLUE=0.1;
I = imadjust(I,[0 0 0; RED GREEN BLUE],[]);
imshow(I)
I = rgb2gray(I); % Convert to grayscale.
imshow(I)
I = imcomplement(I); % Invert image colors (optional) Useful for very bright images.
% Equalize
I_eq=imadjust(I);
imshow(I_eq)
% Convert to black and white.
bw = im2bw(I_eq, graythresh(I_eq));
imshow(bw)
bw2 = imfill(bw,'holes');
imshow(bw2)
bw3 = imopen(bw2, ones(5,5));
imshow(bw3)
bw4 = bwareaopen(bw3, 20000);
imshow(bw4)
bw4_perim = bwperim(bw4);
imshow(bw4_perim)
% Cell count.
[L, num] = bwlabel(bw4); num
fprintf(fileID, ' %s %s %s\t %s\t %6.0f\n', pas, '/', filename,'CellCount= ', num);
end
fclose(fileID);