Datasets:

autoencodix
/

OrganMNIST3D-subsample

Error code:   FeaturesError
Exception:    UnicodeDecodeError
Message:      'utf-8' codec can't decode byte 0x80 in position 78: invalid start byte
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 244, in compute_first_rows_from_streaming_response
                  iterable_dataset = iterable_dataset._resolve_features()
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 4645, in _resolve_features
                  features = _infer_features_from_batch(self.with_format(None)._head())
                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2866, in _head
                  return next(iter(self.iter(batch_size=n)))
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 3073, in iter
                  for key, pa_table in ex_iterable.iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2581, in _iter_arrow
                  yield from self.ex_iterable._iter_arrow()
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 558, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 440, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/csv/csv.py", line 196, in _generate_tables
                  csv_file_reader = pd.read_csv(file, iterator=True, dtype=dtype, **self.config.pd_read_csv_kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/streaming.py", line 73, in wrapper
                  return function(*args, download_config=download_config, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1275, in xpandas_read_csv
                  out = pd.read_csv(f, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
                  return _read(filepath_or_buffer, kwds)
                File "/usr/local/lib/python3.14/site-packages/pandas/io/parsers/readers.py", line 620, in _read
                  parser = TextFileReader(filepath_or_buffer, **kwds)
                File "/usr/local/lib/python3.14/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
                  self._engine = self._make_engine(f, self.engine)
                                 ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
                  return mapping[engine](f, **self.options)
                         ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
                  self._reader = parsers.TextReader(src, **kwds)
                                 ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "pandas/_libs/parsers.pyx", line 574, in pandas._libs.parsers.TextReader.__cinit__
                File "pandas/_libs/parsers.pyx", line 663, in pandas._libs.parsers.TextReader._get_header
                File "pandas/_libs/parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
                File "pandas/_libs/parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
                File "pandas/_libs/parsers.pyx", line 2053, in pandas._libs.parsers.raise_parser_error
                File "<frozen codecs>", line 325, in decode
              UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 78: invalid start byte

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Info

Subset of the MedMNIST+ OrganMNIST3D dataset containing only the organ classes bladder and femur-right, prepared for use with the AUTOENCODIX Imagix3D tutorial. The complete MedMNIST dataset collections can be found here.

OrganMNIST3D is a three-dimensional biomedical image classification dataset derived from abdominal CT scans. The MedMNIST+ version provides the volumes at a spatial resolution of 64 × 64 × 64 voxels.

For this tutorial dataset, only samples belonging to the bladder and right-femur classes were retained. The volumes were converted from its original .npz file format to compressed NIfTI files (.nii.gz).

345 images (174 bladder, 171 femur-right) with a spatial size of 64 × 64 × 64 voxels.
organmnist3d_images.zip: compressed archive containing the individual volumes in NIfTI format (.nii.gz).
organmnist3d_mappings.csv: comma-separated annotation file containing the sample identifiers, paths to the corresponding NIfTI files, and organ-class labels.

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The files can be downloaded from Hugging Face using huggingface_hub:

from huggingface_hub import hf_hub_download
import zipfile

mapping_path = hf_hub_download(
repo_id="autoencodix/OrganMNIST3D-subsample",
repo_type="dataset",
filename="organmnist3d_mappings.csv",
)

zip_path = hf_hub_download(
repo_id="autoencodix/OrganMNIST3D-subsample",
repo_type="dataset",
filename="organmnist3d_images.zip",
)

with zipfile.ZipFile(zip_path) as zf:
zf.extractall("data/images/")

License

Original dataset licensed under Creative Commons Attribution 4.0 International (CC BY 4.0), see: https://medmnist.com/. The Apache-2.0 license associated with the MedMNIST project applies to the MedMNIST software code, see: https://github.com/MedMNIST/MedMNIST/.

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