How to choose a ROI of an image and make rest transparent, then save it?

I have two images of the same object: 1) bright-field, 2) a luminescence intensity. To create an overlay, I would like to define a ROI of the image 2), and then overlay this to the image 1). The area outside of ROI in image 2) should be transparent.

I got the ROI working and it also displays as the region outside of the ROI is transparent, but then exporting/saving fails

I=imread('cameraman.tif');
I=double(I); %convert to my typical form of input
% Define the Region of Interest
c = [100 200 200 100];
r = [100 100 200 200];
% Creates a Mask
BW = roipoly(I,c,r);
BW = double(BW);
BW(BW==0) = NaN;    %set elements outside to NaN
filter_1 = I.*BW;   % multipliy to get old intensity

image(filter_1);
transparent=image(I, 'AlphaData', filter_1); 
imwrite(I, 'test.png', 'Alpha', filter_1) %doesn't work

Answer 1

[Thiago Henrique Gomes Lobato]

To write the image I has to be either a double normalized to 1 or a uint8 with values from 0 to 255, in your case you had double values from 0 to 255. Alpha also has to be between 0 and 1. Changing just the last line of your code produces the results that you want

imwrite(uint8(I), 'test.png', 'Alpha', filter_1/max(filter_1(:)))

Answer 2

[Pascal Gschwend]

Thank you Thiago, that works. I could even shorten the code a bit. But this brings me to my next problem: I would like to save the image with a colormap, but this always give me the following error message:

Error using writepng (line 35)
Cannot specify alpha channel with an indexed image.

Here's my updated code

I=imread('cameraman.tif');
I=double(I); %convert to my typical form of input
% Define the Region of Interest
c = [100 200 200 100];
r = [100 100 200 200];
% Creates a Mask
BW = roipoly(I,c,r);
BW2=double(BW); 

I_norm=I/255; %normalize to values between 0 and 1
imwrite(I_norm, 'test.png', 'Alpha', BW2)

imwrite(I_norm, jet,'test.png', 'Alpha', BW2) % does not work

[Thiago Henrique Gomes Lobato]

You have to first convert your image to the desired colormap as a rgb image and then save

rgbImage = ind2rgb( uint8(255*I_norm), jet);
imwrite(rgbImage,'test.png', 'Alpha', BW2)

[Image Analyst]

You can convert your indexed image to an RGB image before saving, but you don't have to. You can save indexed images along with their colormaps. See the code below:

grayImage = imread('moon.tif');
cmap = hsv(256);
imshow(grayImage, 'Colormap', cmap);
colorbar
% Save indexed image along with it's color map to disk.
imwrite(grayImage, cmap, 'deleteme.tif');
% Read it back in and apply the colormap and observe it looks the same.
figure
[grayImage2, cmap2] = imread('deleteme.tif');
imshow(grayImage2, 'Colormap', cmap2);  % Looks exactly the same

[Pascal Gschwend]

@Thiago: Thank you, that fixed the problem.

@Image Analyst: Thanks for your comment. Are you sure though that this also works using the transparency (alpha)?