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Datasets:
MedOtter
/
NucMM-M

Tasks:
Image Segmentation
Modalities:
Text
Size:
n<1K
Tags:
medical-imaging
electron-microscopy
neuroscience
instance-segmentation
3d-segmentation
nucmm
License:
Dataset card Data Studio Files
xet
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The dataset generation failed
Error code:   DatasetGenerationError
Exception:    ArrowInvalid
Message:      Integer value 353 not in range: 0 to 255
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1816, in _prepare_split_single
                  for key, table in generator:
                                    ^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
                  for item in generator(*args, **kwargs):
                              ~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 91, in _generate_tables
                  yield Key(file_idx, batch_idx), cast_table_to_features(pa_table, self.info.features)
                                                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2276, in cast_table_to_features
                  arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
                            ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1852, in wrapper
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                                           ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2143, in cast_array_to_feature
                  return array_cast(
                      array,
                  ...<2 lines>...
                      allow_decimal_to_str=allow_decimal_to_str,
                  )
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1854, in wrapper
                  return func(array, *args, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1935, in array_cast
                  return pa_type.wrap_array(_c(array, pa_type.storage_type))
                                            ~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1854, in wrapper
                  return func(array, *args, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1970, in array_cast
                  return pa.ListArray.from_arrays(array_offsets, _c(array.values, pa_type.value_type))
                                                                 ~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1854, in wrapper
                  return func(array, *args, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1970, in array_cast
                  return pa.ListArray.from_arrays(array_offsets, _c(array.values, pa_type.value_type))
                                                                 ~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1854, in wrapper
                  return func(array, *args, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2006, in array_cast
                  return array.cast(pa_type)
                         ~~~~~~~~~~^^^^^^^^^
                File "pyarrow/array.pxi", line 1147, in pyarrow.lib.Array.cast
                File "/usr/local/lib/python3.14/site-packages/pyarrow/compute.py", line 412, in cast
                  return call_function("cast", [arr], options, memory_pool)
                File "pyarrow/_compute.pyx", line 604, in pyarrow._compute.call_function
                File "pyarrow/_compute.pyx", line 399, in pyarrow._compute.Function.call
                  result = GetResultValue(
                File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
                  return check_status(status)
                File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
                  raise convert_status(status)
              pyarrow.lib.ArrowInvalid: Integer value 353 not in range: 0 to 255
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1683, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1869, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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main
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End of preview.

NucMM-M Dataset (Mouse)

3D Neuronal Nuclei Segmentation in Mouse Brain Electron Microscopy.

Dataset Structure 

├── Image/
│   ├── train/
│   │   ├── img_000_200_200.h5
│   │   ├── img_000_604_576.h5
│   │   ├── img_508_200_576.h5
│   │   └── img_508_604_200.h5
│   └── val/
│       ├── img_000_200_576.h5
│       ├── img_000_604_200.h5
│       ├── img_508_200_200.h5
│       └── img_508_604_576.h5
└── Label/
    ├── train/
    │   └── seg_*.h5
    └── val/
        └── seg_*.h5

Label Information

  • Original: Instance segmentation (each nucleus has unique ID)
  • Classes: Background (0) + Nuclei instances (1, 2, 3, ...)

Related Datasets

Usage 

from huggingface_hub import hf_hub_download
import h5py

# Download a volume
local_path = hf_hub_download(
    repo_id="Angelou0516/NucMM-M",
    filename="Image/train/img_000_200_200.h5",
    repo_type="dataset"
)

# Load with h5py
with h5py.File(local_path, 'r') as f:
    volume = f[list(f.keys())[0]][:]
    print(volume.shape)  # (200, 200, 200)

Citation

If you use this dataset, please cite the NucMM paper:

@inproceedings{lin2021nucmm,
  title={NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale},
  author={Lin, Zudi and Wei, Donglai and Lichtman, Jeff and Bhanu, Bir and Bhattacharjee, Sumit and Bhavsar, Khushali and Bhosale, Pratik and Bhunre, Sandhya and others},
  booktitle={MICCAI},
  year={2021}
}
Downloads last month
53
Task:
3D Instance Segmentation of Neuronal Nuclei
Modality:
Electron Microscopy (EM)
Species:
Mouse
Volume Size:
200×200×200 voxels per sample
Format:
HDF5 (.h5)
Total file size:
39.9 MB