Here is a bit of code to get you going. It creates a dialog title to allow the user to select the folder containing tiff files (you can change to other extensions if you want) to crop, then store the images in a cell array and use a loop to actually crop the images using imcrop. For the example I'm assuming a grayscale image, but it can easily be modified.
clear all
clc
dialog_title = 'Select the directory containing the images to be processed';
folder_name = uigetdir('',dialog_title);
addpath(folder_name);
% select current folder
cd(folder_name);
ImagesToRead = dir('*.tif');
ImageCell = cell(1,length(ImagesToRead));
CroppedImageCell = cell(1,length(ImagesToRead));
for k = 1:length(ImagesToRead)
ImageCell{k} = imread(ImagesToRead(i).name); % Read image and store in cell array.
CroppedImageCell{k} = imcrop(ImageCell{k},CropRectangle); % See comments below
end
% Save to resulting images in a sequence or a stack:
% 1) Sequence:
SequenceName = 'DummyName' ; name of the sequence...change as you wish.
for k = 1:length(ImagesToRead)
ExportedName = sprintf('%s%d.tif',SequenceName,k); % Add the frame # after the name
imwrite(CroppedImageCell{k},ExportedName,'tif','WriteMode','overwrite','Compression','none');
end
% 2) Stack
SequenceName = 'DummyName' ; name of the sequence...change as you wish.
for k = 1:length(ImagesToRead)
imwrite(CroppedImageCell{k},SequenceName,'tif','WriteMode','append','Compression','none'); % Note the "append" writing mode.
end
In the above code, you will want to change "CropRectangle" to a rectangle with the size/position that best fits your need. Consult the link I provided above to know how to do so.
If it's not clear please ask for more details :)
