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Emulated-Inc
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sci-cell-cycle-3d-dapi-new-microscope

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The dataset generation failed

Error code:   DatasetGenerationError
Exception:    TypeError
Message:      int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1531, in _prepare_split_single
                  for key, record 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/webdataset/webdataset.py", line 127, in _generate_examples
                  for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
                                              ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
                  for filename, f in tar_iterator:
                                     ^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
                  for x in self.generator(*self.args):
                           ~~~~~~~~~~~~~~^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1400, in _iter_from_urlpath
                  with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
                       ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 977, in xopen
                  file_obj = fs.open(paths[0], mode)
                File "<string>", line 3, in open
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
                  return self._mock_call(*args, **kwargs)
                         ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
                  return self._execute_mock_call(*args, **kwargs)
                         ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
                  result = effect(*args, **kwargs)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
                  tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
                                                               ~~~^^^^^^^^
              TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
              
              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 1393, 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 1571, 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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	widefield/images/06a84ccb	hf://datasets/Emulated-Inc/sci-cell-cycle-3d-dapi-new-microscope@f31f2a490a55939bda238fe490f7e90c78e1a5a2/widefield.tar
	widefield/images/06ab3dc4	hf://datasets/Emulated-Inc/sci-cell-cycle-3d-dapi-new-microscope@f31f2a490a55939bda238fe490f7e90c78e1a5a2/widefield.tar
	widefield/images/06b34539	hf://datasets/Emulated-Inc/sci-cell-cycle-3d-dapi-new-microscope@f31f2a490a55939bda238fe490f7e90c78e1a5a2/widefield.tar
	widefield/images/06b96f02	hf://datasets/Emulated-Inc/sci-cell-cycle-3d-dapi-new-microscope@f31f2a490a55939bda238fe490f7e90c78e1a5a2/widefield.tar
	widefield/images/06c88dd0	hf://datasets/Emulated-Inc/sci-cell-cycle-3d-dapi-new-microscope@f31f2a490a55939bda238fe490f7e90c78e1a5a2/widefield.tar
	widefield/images/06d035ac	hf://datasets/Emulated-Inc/sci-cell-cycle-3d-dapi-new-microscope@f31f2a490a55939bda238fe490f7e90c78e1a5a2/widefield.tar

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Widefield 3D DAPI nuclei with G1 / S/G2 labels

widefield.tar holds 4,074 single-nucleus crops of fixed Fucci2a mouse 3T3 fibroblasts stained with DAPI, imaged on a widefield epifluorescence microscope with a 40x objective (voxels 0.188 x 0.188 x 0.5 micrometres), each labelled G1 or S/G2 from the Fucci2a reporter.

widefield/images/<id>.tif: DAPI counts, uint16, planes x rows x columns, the nucleus's bounding box padded by 1 micrometre (clipped at the tile), zlib-compressed TIFF with the voxel size in its metadata.
widefield/masks/<id>.tif: uint8, 1 on the nucleus's voxels.
widefield/labels.csv: id,phase,field (field is the tile of the source acquisition).

Source and licence

Derived from BioImage Archive S-BIAD1752 (https://doi.org/10.6019/S-BIAD1752), "Predicting cell cycle stage from 3D single-cell nuclear stained images", by Gang Li, Eva K. Nichols, Valentino E. Browning, Nicolas J. Longhi, Madison Sanchez-Forman, Conor K. Camplisson, Brian J. Beliveau and William S. Noble, licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). Paper: Li, Nichols et al., Life Science Alliance (2025), doi 10.26508/lsa.202403067.

Changes: the DAPI channel of the 40x tiles (tile_N.tif) was cropped around each nucleus labelled in GT_labels_40x_with_source_file.tsv, with the nucleus's own mask cut from the deposited filtered segmentation; intensities are unchanged; nuclei were renamed to random ids. This dataset is released under CC BY 4.0.

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Total file size:

885 MB