reading stk file failed

[yongshuo-Z]

Hi,

I am reading a MetaMorph stk file that contains a series of cryo-EM images, which contain 50 images.

Here is the code;

import tifffile
stk = tifffile.imread('particles_export.stk')

it returns an error:

KeyError                                  Traceback (most recent call last)
/opt/anaconda3/envs/cryo/lib/python3.6/site-packages/tifffile/tifffile.py in __init__(self, arg, name, offset, size, _multifile, _useframes, _master, **kwargs)
   2754             try:
-> 2755                 byteorder = {b'II': '<', b'MM': '>', b'EP': '<'}[header[:2]]
   2756             except KeyError:

KeyError: b'\x00\x00'

During handling of the above exception, another exception occurred:

TiffFileError                             Traceback (most recent call last)
<ipython-input-25-d5856ab518a1> in <module>()
      4 
      5 
----> 6 stk = tifffile.imread(filename)
      7 #stk = imageio.mimread(filename, format = 'SPIDER' ,is_stk = True)

/opt/anaconda3/envs/cryo/lib/python3.6/site-packages/tifffile/tifffile.py in imread(files, aszarr, **kwargs)
    710 
    711         if isinstance(files, (str, os.PathLike)) or hasattr(files, 'seek'):
--> 712             with TiffFile(files, **kwargs_file) as tif:
    713                 if aszarr:
    714                     return tif.aszarr(**kwargs)

/opt/anaconda3/envs/cryo/lib/python3.6/site-packages/tifffile/tifffile.py in __init__(self, arg, name, offset, size, _multifile, _useframes, _master, **kwargs)
   2755                 byteorder = {b'II': '<', b'MM': '>', b'EP': '<'}[header[:2]]
   2756             except KeyError:
-> 2757                 raise TiffFileError('not a TIFF file')
   2758 
   2759             version = struct.unpack(byteorder + 'H', header[2:4])[0]

TiffFileError: not a TIFF file

I am wondering how can I read this file? I want to save the images as several single tiff files.

You may find this file here. I've checked the stk file with ImageJ. It works fine, so the file is not corrupted.

Thanks for any advice.

[cgohlke]

The file is not a MetaMorph STK or TIFF file. It's a SPIDER file, which can be read (for example) with Pillow.