Array shape

[open-science-tools]

Array shape

[rbnvrw]

Thank you for your bug report.

Can you post the output of:

imReader.bundle_axes
imReader.iter_axes
imReader.metadata

Thank you!

[fjorka]

The output looks as follows (with edited list of frames):

imReader.bundle_axes
['y', 'x']
imReader.iter_axes
['t']
imReader.metadata
{'channels': ['DIC cam'],
 'date': datetime.datetime(2018, 5, 28, 22, 23, 1),
 'experiment': {'description': '',
  'loops': [{'duration': 345600000.0,
    'sampling_interval': 600000.0,
    'start': 0,
    'stimulation': False}]},
 'fields_of_view': [0],
 'frames': [0,
  1,
  2,
  3,
...
  440,
  441,
  442],
 'height': 973,
 'num_frames': 443,
 'pixel_microns': 0.647298582015452,
 'total_images_per_channel': 443,
 'width': 973,
 'z_levels': []}

[rbnvrw]

Thank you for the information. The output looks fine, so I'll need the nd2 file to really debug it.

Please send the ND2 file to the temporary mail address [email protected] (e.g. via WeTransfer) and I'll have a look!

[rbnvrw]

Comment: the stack was collected using Jobs module of Elements using both binning (4) and stitching (2x2). The file can be open both by Elements and ImageJ (BioFormats) and the shape is as specified in metadata.

[rbnvrw]

@hanasha I'm not sure what is causing the problem, but I've added a workaround that at least let's you open the file. Can you test with the latest development code from the master branch on GitHub if you can also open your file now?