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Datasets:
nabil-m
/
bcss

Tasks:
Image Segmentation
Modalities:
Image
Languages:
English
Size:
n<1K
License:
Dataset card Data Studio Files
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Dataset Preview
The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed
Error code:   DatasetGenerationError
Exception:    TypeError
Message:      Mask must be a pyarrow.Array of type boolean
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1586, in _prepare_split_single
                  writer.write(example, key)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 553, in write
                  self.write_examples_on_file()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 511, in write_examples_on_file
                  self.write_batch(batch_examples=batch_examples)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 631, in write_batch
                  self.write_table(pa_table, writer_batch_size)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 646, in write_table
                  pa_table = embed_table_storage(pa_table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2248, in embed_table_storage
                  arrays = [
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2249, in <listcomp>
                  embed_array_storage(table[name], feature, token_per_repo_id=token_per_repo_id)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in wrapper
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in <listcomp>
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2124, in embed_array_storage
                  return feature.embed_storage(array, token_per_repo_id=token_per_repo_id)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/features/image.py", line 292, in embed_storage
                  storage = pa.StructArray.from_arrays([bytes_array, path_array], ["bytes", "path"], mask=bytes_array.is_null())
                File "pyarrow/array.pxi", line 3257, in pyarrow.lib.StructArray.from_arrays
                File "pyarrow/array.pxi", line 3697, in pyarrow.lib.c_mask_inverted_from_obj
              TypeError: Mask must be a pyarrow.Array of type boolean
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1595, in _prepare_split_single
                  num_examples, num_bytes = writer.finalize()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 658, in finalize
                  self.write_examples_on_file()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 511, in write_examples_on_file
                  self.write_batch(batch_examples=batch_examples)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 631, in write_batch
                  self.write_table(pa_table, writer_batch_size)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 646, in write_table
                  pa_table = embed_table_storage(pa_table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2248, in embed_table_storage
                  arrays = [
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2249, in <listcomp>
                  embed_array_storage(table[name], feature, token_per_repo_id=token_per_repo_id)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in wrapper
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in <listcomp>
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2124, in embed_array_storage
                  return feature.embed_storage(array, token_per_repo_id=token_per_repo_id)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/features/image.py", line 292, in embed_storage
                  storage = pa.StructArray.from_arrays([bytes_array, path_array], ["bytes", "path"], mask=bytes_array.is_null())
                File "pyarrow/array.pxi", line 3257, in pyarrow.lib.StructArray.from_arrays
                File "pyarrow/array.pxi", line 3697, in pyarrow.lib.c_mask_inverted_from_obj
              TypeError: Mask must be a pyarrow.Array of type boolean
              
              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 1456, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1055, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 894, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1609, in _download_and_prepare
                  super()._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 970, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1447, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1604, 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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End of preview.

BCSS Dataset (Hugging Face Mirror)

This is a re-hosted copy of the Breast Cancer Semantic Segmentation (BCSS) dataset, made available on Hugging Face so that others can more easily download the data to their local environment. This exists thanks to the generous authors, who so kindly licensed the dataset under a CC0 1.0 Universal (CC0 1.0) license, allowing redistribution.

Sources

Original Paper Link: https://academic.oup.com/bioinformatics/article/35/18/3461/5307750?login=false

Original Github Repo: https://github.com/PathologyDataScience/BCSS?tab=readme-ov-file

Google Drive (Original Data): https://drive.google.com/drive/folders/1zqbdkQF8i5cEmZOGmbdQm-EP8dRYtvss

License

This dataset is licensed under CC0 1.0 Universal (CC0 1.0).

Citation

Mohamed Amgad, Habiba Elfandy, Hagar Hussein, Lamees A Atteya, Mai A T Elsebaie, Lamia S Abo Elnasr, Rokia A Sakr, Hazem S E Salem, Ahmed F Ismail, Anas M Saad, Joumana Ahmed, Maha A T Elsebaie, Mustafijur Rahman, Inas A Ruhban, Nada M Elgazar, Yahya Alagha, Mohamed H Osman, Ahmed M Alhusseiny, Mariam M Khalaf, Abo-Alela F Younes, Ali Abdulkarim, Duaa M Younes, Ahmed M Gadallah, Ahmad M Elkashash, Salma Y Fala, Basma M Zaki, Jonathan Beezley, Deepak R Chittajallu, David Manthey, David A Gutman, Lee A D Cooper, Structured crowdsourcing enables convolutional segmentation of histology images, Bioinformatics, Volume 35, Issue 18, September 2019, Pages 3461–3467, https://doi.org/10.1093/bioinformatics/btz083

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