How to remove the grey margin from the imshow image

I'm analysing the MRI data with the imshow function. But every time the image pop out in a small window with a large grey (or white if I save it) margin around it. I have to zoom in the image in order to select the ROI.

Is there a code that can remove or reduce the margin as well as show the image in a larger window so that I don't have to double click it to full screen every single time?

Please see my code below. Thank you very much!

%% Draw kidney left t1 ROIs
slice =4 ; 
figure; imshow(Maps.kidney.t1(:,:,slice),[0 1500]); colormap('jet');
r = drawrectangle('Position',[32 84 3 3]), wait(r);

Answer 1

[Image Analyst]

You're probably saving it with exportgraphics or saveas instead of imwrite. Use imwrite instead when you save your image.

[Shuyang Zhang]

Thanks for your reply. I use the save icon, so probably saveas.

I tried to use umwrite but error ocurred. please see my completed code below

slice = 6; %choose the slice number

figure; imshow(Maps.kidney.t2(:,:,slice),[0 150]); colormap('jet'); % show the image

r = drawrectangle('Position',[64 64 3 3]), wait(r); %draw the ROI and wait for next command

mask = createMask(r);

kidney_left_mask(:,:,slice) = mask;

map = Maps.kidney.t2(:,:,slice);

val_mean = mean(map(mask==1)) %record the mean

kidney_left_t2_Mean_ROI1(slice) = val_mean

%try to use the imwrite here but failed

r2 = imwrite(figure,'kidney.jpg')

[DGM]

What exactly are you trying to save?

• The entire slice of the image
• The portion of the slice selected by the ROI
• The entire figure with the blue ROI rectangle

[Shuyang Zhang]

The entire image with ROIs, no white margin. Please see the example below.

[Image Analyst]

You can't have figure (a built-in function) be the first argument to imwrite. The first argument is the image array variable name, for example:

imwrite(Maps.kidney.t2(:,:,slice),'kidney.jpg');

and you don't need to accept anything from imwrite. No return value needs to be accepted from it.

[Shuyang Zhang]

Thank you for the explanation. using the following code does save the image.

imwrite(Maps.kidney.t2(:,:,slice),'kidney.jpg');

However, I got a black and white image, instead of color image with ROIs.

Do you know the reason?

Thank you!

[DGM]

If your goal is to save the image and the overlaid ROI objects, then you're stuck trying to capture the figure/axes. If you want to retain the image geometry, that might be a minor challenge.

% an image
inpict = imread('cameraman.tif'); % 256x256

% display the image and create an ROI object
imshow(inpict,'colormap',hot);
ROI = drawrectangle(gca,'position',[75 75 100 100]);

% try to force the saved image to have the same geometry as the original
% this won't work if the figure is docked
truesize(gcf,size(inpict))

% take a screenshot of the axes and save it
screenshot = frame2im(getframe(gca)); % should also be 256x256
imwrite(screenshot,'myscreenshot.png') % save nothing as JPG

[Shuyang Zhang]

I'm sorry, I couldn't follow what you say here "stuck trying to capture the figure/axes" and "retain the image geometry"

I can easily save the image with ROIs by clicking the "save" icon. The only problem is that the saved image has a large margin.

I'm looking for a possible solution to save the image and ROIs without a large margin.

Thank you.

[DGM]

That's my point. If you need to include objects other than the image itself, you can't trivially use imwrite() to do it. You need to somehow capture the figure or axes.

If you rely on print(), saveas() or the "save" buttons in the figure or axes toolbars, you'll lose control over the image scaling. You'll just get something that's dependent on the figure geometry.

If you use getframe(), you have a bit more control, but only if the image is scaled correctly.

% an image
inpict = imread('cameraman.tif'); % 256x256

% display the image and create an ROI object
% by default, imshow() uses loose borders, which does nothing but waste space
% i have my preferences set to use tight borders, so i'm explicitly using defaults here.
% set this to 'tight' in preferences if you never want to deal with that again
imshow(inpict,'colormap',hot,'border','loose','initialmagnification','fit'); % DEFAULT BEHAVIOR
ROI = drawrectangle(gca,'position',[75 75 100 100]);

% try to force the saved image to have the same geometry as the original
% this won't work if the figure is docked
truesize(gcf,size(inpict))

% take a screenshot of the axes and save it
screenshot = frame2im(getframe(gca)); % should also be 256x256
imwrite(screenshot,'myscreenshot.png') % save nothing as JPG

That has no white borders. The image size has not changed, so it's not been damaged by interpolation.

% do the same thing using saveas()/print
saveas(gcf,'screenshotfig.png')
saveas(gca,'screenshotax.png')
print(gcf,'printoutfig.png','-dpng')

All of those include white padding. All of those are rescaled to some uncontrolled geometry.

Use truesize()

Don't move the view (or just restore it after you do)

Use getframe() instead of saveas().

Since it looks like you have a tiny image, you may not be able to save the image at the original size and still have the resolution to render the ROI objects. If that's the case, you can scale the output size in the call to truesize()

truesize(gcf,size(inpict)*2) % scale by some integer

Can exportgraphics() help? Maybe. I don't have it, so I can't test that.

Of course, if you're manually panning and zooming the image all over the place before saving it, all bets are off. Even with getframe(), you'll have to deal with rescaling and (sometimes) a few pixels of white padding if things get moved.

[Shuyang Zhang]

The image with a small white padding is good enough for me. Thank you very much for your help!