How to use saveas for binary images?

Dear all,

I would like to saveas jpg my DICOM images, which I transform to binary images. So I would like to save these binary images. But I only did, that all of these images are in one .jpg picture, but I want to save them separately, for example: binaryImage1.jpg, binaryImage2.jpg,.....binaryImage37.jpg. This is my code:

Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
for i=0;
    i = i+1;
for p = 48:86
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  grayImage(:,:,1,p - 47)= dicomread(filename);
  grayImage_pater(:,:,1,p - 47)= dicomread(filename);
  [rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
[rows, columns, numberOfColorChannels] = size(grayImage_pater);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage_pater = grayImage_pater(:, :, 2); % zelený kanál    
end
eq_grayImage_pater = histeq(grayImage_pater);

thresholdValue = 900;
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
binaryImage_okoli = bwareaopen(binaryImage_okoli, 750);

%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
imshow(binaryImage_okoli, []);
%     X(:,:,1,p - 47) = imadjust(X(:,:,1,p - 47),[0 0.022],[]); % increase contrast
 saveas(gcf(i),'Binarizace_okoli.png')     
end
end

Can you advise me? Thank you for your answers.

[Guillaume]

A bit off topic, but saving a binary image as JPEG is not a good idea. Unless you use the rarely used non-lossy compression option, JPEG will result in colour gradients at the transitions between black and white.

Thankfully, in the answers that have been provided I see that the format has been changed to PNG which is a much better format for saving binary images.

[Veronika]

Yes, I save images in PNG format, but still, first two are saved right, but the other images are only black.

Do you know, where is a problem, please?

This is my recent code:

Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';

for p = 54:86
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  grayImage(:,:,1,p - 53)= dicomread(filename);
  %grayImage_pater(:,:,1,p - 53)= dicomread(filename);
  [rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
    

%Práh pro vytvoření binárního obrazu okolí
thresholdValue = 900
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
 binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
imshow(binaryImage_okoli, []);
output_name = sprintf('Binarizace_okoli_%3d_%3d.png', p)
imwrite(logical(binaryImage_okoli), output_name);

Answer 1

[Walter Roberson]

http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F

[Veronika]

I´m so sorry, but I am really confused. I downoloaded export_fig toolbox http://www.mathworks.com/matlabcentral/fileexchange/23629-export-fig. And I really don´t know, how this toolbox works, there are so many functions and this is too hard for me. Is there any other simpler way to solve my problem? I want to only save images as png without overwritting each other.

[Walter Roberson]

 output_name = sprintf('Binarizace_okoli_%3d_%3d.png', i, p)
 saveas(gcf(i), output_name)

[Veronika]

This shows error message:

 Error using gcf
Too many input arguments.

Error in mujTIFF (line 33)
saveas(gcf(i), output_name)

[Walter Roberson]

I do not know why you wrote gcf(i) in your original code. I would suggest

saveas(gca, output_name)

... Actually, I would not do the imshow() or saveas() like that. I would use

   output_name = sprintf('Binarizace_okoli_%3d_%3d.png', i, p)
   imwrite(output_name, logical(binaryImage_okoli));

[Veronika]

I tried your advice:

Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
for i=0;
    i = i+1;
for p = 48:86
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  grayImage(:,:,1,p - 47)= dicomread(filename);
  grayImage_pater(:,:,1,p - 47)= dicomread(filename);
  [rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
[rows, columns, numberOfColorChannels] = size(grayImage_pater);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage_pater = grayImage_pater(:, :, 2); % zelený kanál    
end
eq_grayImage_pater = histeq(grayImage_pater);
thresholdValue = 900;
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
binaryImage_okoli = bwareaopen(binaryImage_okoli, 750);
%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
% imshow(binaryImage_okoli, []);
output_name = sprintf('Binarizace_okoli_%3d_%3d.png', i, p)
imwrite(output_name, logical(binaryImage_okoli));

But this error appears:

Error using imwrite>parse_inputs (line 515)
The first argument should not be a string.

Error in imwrite (line 418)
[data, map, filename, format, paramPairs] = parse_inputs(varargin{:});

Error in mujTIFF (line 33)
imwrite(output_name, logical(binaryImage_okoli));

[Walter Roberson]

imwrite(logical(binaryImage_okoli), output_name);

[Veronika]

Now, I have this error:

Error using imwrite (line 426)
Unable to determine the file format from the file name.

Error in mujTIFF (line 29)
imwrite(logical(binaryImage_okoli), output_name);

This is my code:

Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';

for p = 54:86
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  grayImage(:,:,1,p - 53)= dicomread(filename);
  %grayImage_pater(:,:,1,p - 53)= dicomread(filename);
  [rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
    

%Práh pro vytvoření binárního obrazu okolí
thresholdValue = 900
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
 binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
imshow(binaryImage_okoli, []);
output_name = sprintf('Binarizace_okoli_%3d_%3d.png', p)
imwrite(logical(binaryImage_okoli), output_name);

end

Can you please help me again?

[Walter Roberson]

output_name = sprintf('Binarizace_okoli_%3d.png', p);

[Veronika]

Thank you, so much.

And don´t you know,why is saved first two images right and the other are only black?

[Image Analyst]

What are the first two and the "other"? I only see that you called imwrite() once. Where are the other two calls to imwrite()? But the array always comes first, and the file name string comes second in the input argument list to imwrite().

[Veronika]

I have 32 DICOM images and these images I transferred into binary images and then I would like to these binary images save into file. Problem is, that first two binary images are saving right, and the other (56-86) are saving like black image. I attach for example 12 DICOM images. And my code:

Folder = 'path,where is CTslices is';
  
filePattern = fullfile(Folder, '/*.dcm*');
  ImageFiles = dir(filePattern);
  
  % Filter the list to pick out only files of
  % file types that we want (image and video files).
  for Index = 1:length(ImageFiles)
    end
for p = numel(Index)
for k = 1:p figure(k); 
    for p = 54:66
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  grayImage(:,:,1,p - 53)= dicomread(filename);
  grayImage_pater(:,:,1,p - 53)= dicomread(filename);
  [rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
[rows, columns, numberOfColorChannels] = size(grayImage_pater);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage_pater = grayImage_pater(:, :, 2); % zelený kanál    
end
eq_grayImage_pater = histeq(grayImage_pater);

thresholdValue = 900;
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
binaryImage_okoli = bwareaopen(binaryImage_okoli, 750);

%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
    imshow(binaryImage_okoli); 
%     temp=['fig',num2str(k),'.png']; 
uint8Image = uint8(255 * binaryImage_okoli);
     temp=['fig',uint8Image,'.png']; 
    saveas(gca,temp); 
    end
end
end

So, PLEASE, try this and answer, if you have the same (wrong) result as me. Or there is something wrong. Thank you for your time and answer.

[Image Analyst]

The poorly-named "temp" is, or should be a filename. However you're sticking an actual binary image into it for some reason. Why are you doing that? You should not.

Use sprintf() to make up a valid filename. Check what it is before you just blindly use it.

Also, why do you have this:

for p = numel(Index)
  for k = 1:p figure(k); 
    for p = 54:66

You have a loop over p inside an outer loop over p. What is your thought process there????

[Veronika]

So I must rename temp to binaryImage_okoli?

for p = numel(Index)

this I have for counting the number of images in file

for k = 1:p figure(k);

this is for create figure (1-33)

and this

   for p = 54:66

for better name of file.

Please, if you can, transform my code for better function.

Answer 2

[Image Analyst]

Try this:

uint8Image = uint8(255 * binaryImage_okoli);
imwrite(uint8Image, 'Binarizace_okoli.png') ;

[Akash Tomer]

Well is there anyone who can find out PSF of a blurred image and then deblur it. The problem is we don't have the Unblurred image so the input is the Blurred image which we need to deblur by using Wiener Filter.I have tried many techniques but nothing is working please help.

[Image Analyst]

What does this have to do with Veronika's question or my answer?

[Veronika]

I tried this, but my output is only one black figure.

Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
for i=0;
    i = i+1;
for p = 48:86
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  grayImage(:,:,1,p - 47)= dicomread(filename);
  grayImage_pater(:,:,1,p - 47)= dicomread(filename);
  [rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
[rows, columns, numberOfColorChannels] = size(grayImage_pater);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage_pater = grayImage_pater(:, :, 2); % zelený kanál    
end
eq_grayImage_pater = histeq(grayImage_pater);
thresholdValue = 900;
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
binaryImage_okoli = bwareaopen(binaryImage_okoli, 750);
%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
imshow(binaryImage_okoli, []);

uint8Image = uint8(255 * binaryImage_okoli);
imwrite(uint8Image, 'Binarizace_okoli.png') ;    
end
end

So I don´t know, if I did something wrong.

[Image Analyst]

Try

uint8Image = uint8(255 * mat2gray(binaryImage_okoli));

This should not be all black unless binaryImage_okoli is all false (=0 = black).

[Veronika]

I still don´t know what's wrong. Please check this code:

[fn pn] = uigetfile('*.dcm','select dcm file');
complete = strcat(pn,fn);
I = dicomread(complete);
fontSize = 15;

% Načtení obrazu.
grayImage = dicomread(complete);
grayImage_pater = dicomread(complete);

% Dimenze obrazu. 
% ***
[rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
end
eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
[rows, columns, numberOfColorChannels] = size(grayImage_pater);
if numberOfColorChannels > 1
  % Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
  grayImage_pater = grayImage_pater(:, :, 2); % zelený kanál
     %grayImage_pater(425:end, :) = 0;
end
eq_grayImage_pater = histeq(grayImage_pater);%ekvalizace pomocí histogramu obrazu

% Zobrazení obrazu.
figure(19)
imshow(grayImage, []);
axis on;
caption = sprintf('Originální černobílý obraz, %s');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo();

% Nastavení obrazu.
% Zvětšení obrazu na celou obrazovku.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Odstranění panelu nástrojů a rozbalovacího menu.
set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Přidání titulku okna.
set(gcf, 'Name', 'Segmentace', 'NumberTitle', 'Off') 

figure(20)
imhist(grayImage,500);
grid on;
caption = sprintf('Histogram originálního obrazu, %s');
title(caption, 'FontSize',fontSize, 'Interpreter', 'None');
ylabel('Četnost');
% Nastavení obrazu.
% Zvětšení obrazu na celou obrazovku.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Odstranění panelu nástrojů a rozbalovacího menu.
set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Přidání titulku okna.
set(gcf, 'Name', 'Histogram pro snadnější práhování', 'NumberTitle', 'Off')

thresholdValue = 180;
binaryImage = grayImage < thresholdValue;
% Odstranění okolí.
binaryImage = imclearborder(binaryImage);
% Vyplnění otvorů.
binaryImage = imfill(binaryImage, 'holes');
labeledImage = bwlabel(binaryImage);
binaryImage = bwareaopen(binaryImage, 750);

%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
labeledImage= imdilate(labeledImage,se);

%Práh pro vytvoření binárního obrazu páteře
% Práh pro vytvoření binárního obrazu páteře
thresholdValue = 1500;
binaryImage_pater =  grayImage_pater > thresholdValue;
% Odstranění okolí.
binaryImage_pater = imclearborder(binaryImage_pater);
% Vyplnění otvorů
binaryImage_pater = imfill(binaryImage_pater, 'holes');
labeledImage_pater = bwlabel(binaryImage_pater);
binaryImage_pater = bwareaopen(binaryImage_pater, 10);
% binaryImage_pater = binaryImage_pater-ismember(labeledImage_pater, 12);

se = strel('line',5,100);
binaryImage_pater= imdilate(binaryImage_pater,se);

% Práh pro vytvoření binárního obrazu okolí
thresholdValue = 900
binaryImage_okoli = grayImage > thresholdValue;
% Odstranění okolí.
binaryImage_okoli = imclearborder(binaryImage_okoli);
% Vyplnění otvorů.
binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
% Vymazání menších otvorů.
 binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);

%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);

figure(21)
subplot (2, 3, 1)
imshow(binaryImage_okoli, []);
axis on;
caption = sprintf('Binární obraz okolí');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
save binaryImage_okoli binaryImage_okoli
subplot (2, 3, 2)
imshow(binaryImage_pater, []);
axis on;
caption = sprintf('Binární obraz páteře');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
subplot (2, 3, 3)
imshow(binaryImage, []);
axis on;
caption = sprintf('Binární obraz plic');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
labeledImage = bwlabel(binaryImage);

% Nastavení obrazu.
% Zvětšení obrazu na celou obrazovku.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Odstranění panelu nástrojů a rozbalovacího menu.
set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Přidání titulku okna.
set(gcf, 'Name', 'Segmentace', 'NumberTitle', 'Off') ¨

I attach three of my DICOM images. This code binarized image in order. So I don´t understand, why in this code does not save the image correctly.

   Folder = 'Your path of CT slices/';
   for p = 54:86
     filename = fullfile(Folder, sprintf('%06d.dcm', p));
     grayImage(:,:,1,p - 53)= dicomread(filename);
  %   %grayImage_pater(:,:,1,p - 53)= dicomread(filename);
     [rows, columns, numberOfColorChannels] = size(grayImage);
  if numberOfColorChannels > 1
  %   % Máme barevný obraz, musíme ho převést na černobílý = vybereme %zelený kanál
  grayImage = grayImage(:, :, 2); % zelený kanál
  end
  eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
  %     
  % %Práh pro vytvoření binárního obrazu okolí
  thresholdValue = 900
  binaryImage_okoli = grayImage > thresholdValue;
  % % Odstranění okolí.
  binaryImage_okoli = imclearborder(binaryImage_okoli);
  % % Vyplnění otvorů.
  binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
 % % Vymazání menších otvorů.
  binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
  %Roztažení binárního obrazu pro přesnější segmentaci
  se = strel('line',5,100);
  binaryImage_okoli= imdilate(binaryImage_okoli,se);
  imshow(binaryImage_okoli, []);
  output_name = sprintf('Binarizace_okoli_%3d.png', p);
  imwrite(logical(binaryImage_okoli), output_name);
  end

Please, advice me where is the mistake?

[Walter Roberson]

What is your current directory at the time you try to do the imwrite() ? You cannot write under the directory where MATLAB is installed.

By the way, I recommend you change

    output_name = sprintf('Binarizace_okoli_%3d.png', p);

to

    output_name = sprintf('Binarizace_okoli_%03d.png', p);

[Veronika]

My current directory is

C:/Users/ced0005/DP/DP_framework/TIFF
and directory, where MATLAB is installed is: 

C:/ProgramFiles/MATLAB/R2016a.

Is it problem?

I changed the raw, which you mentioned, but still it doesn´t work.

[Image Analyst]

This works perfectly fine as far as I can tell.

% Initialization steps.
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;

% Specify the folder where the files live.
folder = 'C:\Users\Mark\Documents\MATLAB\work\Tests\Scans';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(folder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', folder);
  uiwait(warndlg(errorMessage));
  return;
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(folder, '*.dcm'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(folder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
  % Now do whatever you want with this file name,
  % such as reading it in as an image array with imread()
  grayImage= dicomread(fullFileName);
  subplot(1, 2, 1);
  imshow(grayImage, []);  % Display image.
  axis on;
  title(baseFileName, 'FontSize', fontSize);
  drawnow; % Force display to update immediately.
  
  % Convert to gra scale if necessary.
  [rows, columns, numberOfColorChannels] = size(grayImage);
  if numberOfColorChannels > 1
    %   % Máme barevný obraz, musíme ho převést na černobílý = vybereme %zelený kanál
    grayImage = grayImage(:, :, 2); % zelený kanál
  end
  
  % Do totally unnecessary histogram equalization.
  eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
  
  % Do morphological processing
  % Práh pro vytvoření binárního obrazu okolí
  thresholdValue = 900;
  binaryImage_okoli = grayImage > thresholdValue;
  % Odstranění okolí.
  binaryImage_okoli = imclearborder(binaryImage_okoli);
  % Vyplnění otvorů.
  binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
  % Vymazání menších otvorů.
  binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
  % Roztažení binárního obrazu pro přesnější segmentaci
  se = strel('line',5,100);
  binaryImage_okoli= imdilate(binaryImage_okoli,se);
  
  % Display the image.
  subplot(1, 2, 2);
  imshow(binaryImage_okoli, []);
  title('Binarized', 'FontSize', fontSize);
  % Enlarge figure to full screen.
  set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
  drawnow;
  
  % Save output image.
  baseOutputFileName = sprintf('Binarizace_okoli_%3d.png', k);
  fullOutputFileName = fullfile(folder, baseOutputFileName);
  imwrite(logical(binaryImage_okoli), fullOutputFileName);
  fprintf('Saved %s.\n', fullOutputFileName);
  
  promptMessage = sprintf('Do you want to Continue processing,\nor Quit processing?');
  titleBarCaption = 'Continue?';
  buttonText = questdlg(promptMessage, titleBarCaption, 'Continue', 'Quit', 'Continue');
  if strcmpi(buttonText, 'Quit')
    break;
  end
end
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Get rid of tool bar and pulldown menus that are along top of figure.
set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst for Veronika', 'NumberTitle', 'Off')

msgbox('Done with Program');

[Veronika]

Thank you, sooo much. You are amazing!

Answer 3

[Payam Khoshkenar]

I have a microscope image with three channels (RED, GREEN and BLUE), each channel is unit 16 intensity image. I want to show each channel in a subplot (1,3), but in their color form (RGB). I figured it out that with the following command, I can all channels into one RGB image, but I want to show each channel in one subplot.

overlay=cat(3,imadjust(mat2gray(RED)),imadjust(mat2gray(GREEN)),imadjust(mat2gray(BLUE)));

Is there anyway to show/convert my intensity grayscale images into RGB format? I also found in one of your replies that following line can show each channel in RGB format but the output image is not adjusted and also I cannot adjust the output of following code by imadjust because it's not grayscale anymore:

red_IM = cast(cat(3, RED, zeros(size(RED)), zeros(size(RED))), class(RED));

I would appreciate if you could help me.

Thanks

[Walter Roberson]

red_IM = cast(cat(3, imadjust(mat2gray(RED)), zeros(size(RED)), zeros(size(RED))), class(RED));