Datasets:

esholmess
/

CRC-ICM_HE-Subset

Error code:   DatasetGenerationError
Exception:    UnicodeDecodeError
Message:      'utf-8' codec can't decode byte 0xff in position 0: invalid start byte
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1855, in _prepare_split_single
                  for _, table in generator:
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/csv/csv.py", line 188, in _generate_tables
                  csv_file_reader = pd.read_csv(file, iterator=True, dtype=dtype, **self.config.pd_read_csv_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/streaming.py", line 75, in wrapper
                  return function(*args, download_config=download_config, **kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/utils/file_utils.py", line 1213, in xpandas_read_csv
                  return pd.read_csv(xopen(filepath_or_buffer, "rb", download_config=download_config), **kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
                  return _read(filepath_or_buffer, kwds)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read
                  parser = TextFileReader(filepath_or_buffer, **kwds)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
                  self._engine = self._make_engine(f, self.engine)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
                  return mapping[engine](f, **self.options)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
                  self._reader = parsers.TextReader(src, **kwds)
                File "parsers.pyx", line 574, in pandas._libs.parsers.TextReader.__cinit__
                File "parsers.pyx", line 663, in pandas._libs.parsers.TextReader._get_header
                File "parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
                File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
                File "parsers.pyx", line 2053, in pandas._libs.parsers.raise_parser_error
              UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte
              
              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 1436, 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 1053, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 925, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1001, 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 1742, 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 1898, 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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image_name;label string
9212046_HE_20x_CT.jpg;0
9212046_HE_20x_IM.jpg;0
92290_HE_20x_CT.jpg;0
92290_HE_20x_IM.jpg;0
92625_HE_20x_CT.jpg;0
92625_HE_20x_IM.jpg;0
92658_HE_20x_CT.jpg;0
92658_HE_20x_IM.jpg;0
929082_HE_20x_CT.jpg;0
929082_HE_20x_IM.jpg;0
929116_HE_20x_CT.jpg;0
929116_HE_20x_IM.jpg;0
929329_HE_20x_CT.jpg;0
929329_HE_20x_IM.jpg;0
92952_HE_20x_CT.jpg;1
92952_HE_20x_IM.jpg;1
929602_HE_20x_CT.jpg;0
929602_HE_20x_IM.jpg;0
929718_HE_20x_CT.jpg;0
929718_HE_20x_IM.jpg;0
929850_HE_20x_CT.jpg;0
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9310335_HE_20x_CT.jpg;0
9310335_HE_20x_IM.jpg;0
9310352_HE_20x_CT.jpg;0
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9310390_HE_20x_CT.jpg;0
9310390_HE_20x_IM.jpg;0
9310656_HE_20x_CT.jpg;0
9310656_HE_20x_IM.jpg;0
9310667_HE_CT_20x_02.jpg;1
9310667_HE_IM_20x_01.jpg;1
9310808_HE_20x_CT.jpg;1
9310808_HE_20x_IM.jpg;1
9310823_HE_20x_CT.jpg;0
9310823_HE_20x_IM.jpg;0
9312132_HE_20x_CT.jpg;0
9312132_HE_20x_IM.jpg;0
9312315_HE_20x_CT.jpg;1
9312315_HE_20x_IM.jpg;1
9312903_HE_20x_CT.jpg;1
9312903_HE_20x_IM.jpg;1
9314077_HE_20x_CT.jpg;0
9314077_HE_20x_IM.jpg;0
9314763_HE_20x_CT.jpg;0
9314763_HE_20x_IM.jpg;0
9314906_HE_20x_CT.jpg;0
9314906_HE_20x_IM.jpg;0
932497_HE_20x_CT.jpg;0
932497_HE_20x_IM.jpg;0
932540_HE_20x_CT.jpg;2
932540_HE_20x_IM.jpg;2
933512_HE_20x_CT.jpg;0
933512_HE_20x_IM.jpg;0
935656_HE_20x_CT.jpg;0
935656_HE_20x_IM.jpg;0
937208_HE_20x_CT.jpg;0
937208_HE_20x_IM.jpg;0
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938684_HE_20x_CT.jpg;0
938684_HE_20x_IM.jpg;0
941017_HE_20x_CT.jpg;0
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9410255_HE_20x_CT.jpg;0
9410255_HE_20x_IM.jpg;0
9410306_HE_20x_CT.jpg;1
9410306_HE_20x_IM.jpg;1
9410433_HE_20x_CT.jpg;0
9410433_HE_20x_IM.jpg;0
9410475_HE_20x_CT.jpg;0
9410475_HE_20x_IM.jpg;0
9410675_HE_20x_CT.jpg;0
9410675_HE_20x_IM.jpg;0
94109_HE_20x_CT.jpg;0
94109_HE_20x_IM.jpg;0
9411135_HE_20x_CT.jpg;0
9411135_HE_20x_IM.jpg;0
9411329_HE_20x_01.jpg;1
9411329_HE_20x_02.jpg;1
9411547_HE_20x_CT.jpg;0
9411547_HE_20x_IM.jpg;0
9411570_HE_20x_CT.jpg;0
9411570_HE_20x_IM.jpg;0
9411618_HE_20x_CT.jpg;0
9411618_HE_20x_IM.jpg;0
9411750_HE_20x_CT.jpg;0
9411750_HE_20x_IM.jpg;0
9412328_HE_20x_CT.jpg;0
9412328_HE_20x_IM.jpg;0
9412651_HE_20x_CT.jpg;0
9412651_HE_20x_IM.jpg;0
9413147_HE_20x_CT.jpg;0
9413147_HE_20x_IM.jpg;0
9413283_HE_20x_CT.jpg;0
9413283_HE_20x_IM.jpg;0
9413294_HE_20x_CT.jpg;0
9413294_HE_20x_IM.jpg;0
9413383_HE_20x_CT.jpg;0
9413383_HE_20x_IM.jpg;0

End of preview.

CRC-ICM-H&E Subset – Colorectal Cancer Immune Cell Markers (H&E Images Only)

This dataset is a filtered version of the CRC-ICM-v1 dataset from Mendeley Data, containing only Hematoxylin & Eosin (H&E) stained histopathology images.

Dataset Summary

Source: CRC-ICM-v1 (Mendeley Data)
Content: H&E-stained colorectal cancer tissue images
Format: .jpg images and a metadata file (data.csv)
Image Types: CT (central tumor), IM (invasive margin)
Magnification: 20x

The images are suitable for tasks such as:

Cancer tissue classification
Segmentation
Pretraining on medical image datasets

File Structure

only_he_images/: Contains all the .jpg H&E images.
data.csv: Metadata file with information on image names and annotations.

Source and License

Wang, Y. (2024), Colorectal Cancer Immune Cell Markers Dataset v1 (CRC-ICM-v1), Mendeley Data, V2, https://doi.org/10.17632/h3fhg9zr47.2
License: CC BY 4.0

This subset was prepared by esholmess and is published under the same license with attribution to the original authors.

Modifications

Extracted only H&E images from the original dataset
Metadata renamed as data.csv

Example Usage

from datasets import load_dataset

dataset = load_dataset("esholmess/crc-icm-he-subset")

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