crop a region of interest on images and create new files only with this region

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Dear all,
I am writing to you because I am new to Matlab and I would be very grateful if you could help me. I have images from 20 sections from t=0 to t=70 (which would make for 1420 images, beginning with z0000_t0000, z0001_t0000... leading up to z00019_t0069, size of the field 200x200, pixels 521x512), that I normally put into Z-stack and analyse over time with ImageJ. However, I would like to have a Matlab program that would extract only one region of the image (that I would choose, either draw manually or by establishing coordinates, but I have no idea how establish the coordinates?) and create 1420 images (either new 1420 images, or transform the original image into images with the ROI) only with that region. Is it possible, and could you please help me do it? Thank you very much.

Accepted Answer

MHN on 9 Mar 2016
Edited: MHN on 9 Mar 2016
Im = imread('ngc6543a.jpg'); %load your image
x_start = 50; % start x
x_end = 500; % end x
y_start = 50; % start y
y_end = 500; % end x
Im1 = Im([x_start:x_end],[y_start:y_end],:);
imwrite(Im1,'newimage.jpg') % save the croped image
To find your coordinates, you can see the original picture (Im), use the "data cursor" and you can find your min\max x and min\max y.

More Answers (2)

Anastasia on 9 Mar 2016
Thank you very much for your response! Is it possible to create a program (or something like that), so that I could put all the pictures from one folder (from z0000_t0000 to z0019_t0069, and not one by one? Thank you again!!
MHN on 12 Mar 2016
If I want to integrate the answers (Just save the following code in the same path as your image's files):
for i = 0 : 19;
for j = 0 : 69;
filename = ['z00' sprintf('%02d',i) '_t00' sprintf('%02d',j) '.jpg'];
Im = imread(filename);
x_start = 50; % start x
x_end = 500; % end x
y_start = 50; % start y
y_end = 500; % end x
Im_new = Im([x_start:x_end],[y_start:y_end],:);
imwrite(Im_new, filename) % replace the croped image

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Anastasia on 3 Apr 2016
Thank you so much, it works perfectly!!! Thank you!
  1 Comment
Image Analyst
Image Analyst on 3 Apr 2016
Be very careful when using MHN's code because he made the common mistake of swapping x and y.
Images are arrays, and are indexed like arrays as (row, column), NOT (x,y) as he had. You will need to swap all of his x,y with y,x to get his code to work properly.

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