Did you try creating a macro in ImageJ and do batch processing? Ref: http://imagej.net/How_to_apply_a_common_operation_to_a_complete_directory

Thanks for you answer! Yes, I did, and this reduces of course the time I need to sit besides the computer - still, it takes a lot of time. So I was wondering if there is another way of doing the cropping which is intrinsically faster.

Thanks for the idea - could you maybe share some details of the process? Thanks!

Thanks a lot, that is really helpful! I have written the code below, but I think it is not optimal. Do you mind to have a look at it?

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

Dear Antonios, thanks a lot for your help, I really appreciate it!

There is a bunch of free image-manipulation tools that come with EQUINOX-3D (equinox3d.com). These should do what you need, insanely fast, compared to any other options recommended here! (I just did a test with 720 files like you need. It took less than a second - see screenshot).

"icr" is image crop, "is" is image scale, etc.

Most of these tools are multi-threaded (including "icr"), and they scale automatically to the number of physical cores / threads you have.

For example, this command will crop all TIFFs in the current folder to the size you specified in your post, and put the resulting files in the folder, called "cropped", keeping the same file names.

icr -T  -c -159 -217 -279 -123 *.tif cropped/.tif

This will crop and convert to PNG, in one shot:

icr -T  -c -159 -217 -279 -123 *.tif cropped/.png

The -T option preserves the original time stamps of the images, which can be handy (just type "icr" with no options, for help).

As these are command-line tools, you can easily script and automate them. I actually use these tools in my Makefile, as part of the build process for EQUINOX-3D...

Just an idea..for those facing same problem but dont want/dont know how to code...

Maybe use Fiji (imageJ) to load partial stack (eg from 0-1000 1000-2000 2000-3000 etc or even every 500 pics) then aply the rectangular by its xy coordinates, then crop the partial-stacks and SaveAsImageSequence in separate folder with correct numbering/labeling.

When all images are processed and are saved in the same folder with correct sequence number ...Just Import as ImageSequence..

wouldnt this fit your purpose?