@LMC by cropping, I meant, cutting a fragment of an image and saving as another file. So, for example

img[500:1500, 500:1500]

would give an image from 500th to 1500th pixel "vertically" and from 500th to 1500th pixel "horizontally".

@Konstantin Makarov there are two issues with your codes (both not working for me):

1. I want to save an image as .dcm file, not .png. The reason why I need a cropped dcm file is because I got many layers from the scanner, each in the different resolutions; and I need them in the same resolution in order to be able to read them in the segmentation program, as ITKSnap or 3DSlicer.
2. As far as I understand your codes, you assumed that I got one .dcm file with many layers - this is not true for me, I got separate files for the each layer. I mean, each layer is lets say in (x,y) coordinates, and the next layer is some distance (in z direction) from the previous one.
   Could you please edit the code, given the above clarification?

@etauger I got numpy. Your code doesnt work for me. It gives an error for the last line of code (saving file). The error is below:

"C:\Program Files\Python\Python313\python.exe" D:\praca\GUMED\serce\testy2.py 
Traceback (most recent call last):
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\tag.py", line 29, in tag_in_exception
    yield
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\filewriter.py", line 826, in write_dataset
    write_data_element(fp, get_item(tag), dataset_encoding)
    ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\filewriter.py", line 686, in write_data_element
    raise ValueError(
    ...<3 lines>...
    )
ValueError: The (7FE0,0010) 'Pixel Data' element value hasn't been encapsulated as required for a compressed transfer syntax - see pydicom.encaps.encapsulate() for more information

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "D:\praca\GUMED\serce\testy2.py", line 10, in <module>
    ds.save_as(r"D:\praca\GUMED\dicom\mrxs\1_AORTA\AO_1_014_Masson\3_0-test-cropping.dcm")
    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\dataset.py", line 2642, in save_as
    pydicom.dcmwrite(
    ~~~~~~~~~~~~~~~~^
        filename,
        ^^^^^^^^^
    ...<6 lines>...
        **kwargs,
        ^^^^^^^^^
    )
    ^
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\filewriter.py", line 1455, in dcmwrite
    write_dataset(fp, dataset)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\filewriter.py", line 825, in write_dataset
    with tag_in_exception(tag):
         ~~~~~~~~~~~~~~~~^^^^^
  File "C:\Program Files\Python\Python313\Lib\contextlib.py", line 162, in __exit__
    self.gen.throw(value)
    ~~~~~~~~~~~~~~^^^^^^^
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\tag.py", line 33, in tag_in_exception
    raise type(exc)(msg) from exc
ValueError: With tag (7FE0,0010) got exception: The (7FE0,0010) 'Pixel Data' element value hasn't been encapsulated as required for a compressed transfer syntax - see pydicom.encaps.encapsulate() for more information
Traceback (most recent call last):
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\tag.py", line 29, in tag_in_exception
    yield
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\filewriter.py", line 826, in write_dataset
    write_data_element(fp, get_item(tag), dataset_encoding)
    ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\marci\AppData\Roaming\Python\Python313\site-packages\pydicom\filewriter.py", line 686, in write_data_element
    raise ValueError(
    ...<3 lines>...
    )
ValueError: The (7FE0,0010) 'Pixel Data' element value hasn't been encapsulated as required for a compressed transfer syntax - see pydicom.encaps.encapsulate() for more information


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