Cropping a tif stack

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Hey everyone,

I need to crop a stack of single tif-files. For example, I have a stack of 5000 512x512 tif images where I only need the regions from x=159 to 295 and y=279 to 389. Is there a way to do this fast in MATLAB? I have written the code below, using parfor, but it still takes a long time, and I have the impression that it could be done better...

Thanks!

im=imread('filename.tif');  
filename='filename.tif';   
info=imfinfo(filename);     
num_images=numel(info);    
parfor k = 1:num_images
A=imread(filename,k,'Info',info);   
Acrop=imcrop(A,[5 10 50 75]);
imwrite(Acrop,'stack_crop.tif','writemode','append');
end

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Huan Zheng 2020-9-19

Hi, I met the same issue now, do you have any solution after 3 years?

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Answer 1

Walter Roberson 2017-1-23

1 个投票

You can do slightly better by using array indexing instead of imcrop, since you already know the section you want to extract.

However, your output is not well defined. parfor does not execute the loop in-order, so the order of images is going to be random in 'writemode' 'append'

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mtmtmt 2017-1-23

Thanks a lot for your answer!

It is interesting that the images seem to be in order in my case... Though it would not be a problem if they were random.

Apart from that - can I do more than just using array indexing?

Walter Roberson 2017-1-23

Possibly switching to using the Tiff class might help. No promises.

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Cropping a tif stack

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