Datasets:

eminorhan
/

cellmap-2d

configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train-*
dataset_info:
  features:
    - name: image
      dtype: image
    - name: crop_name
      dtype: string
    - name: axis
      dtype: string
    - name: slice
      dtype: int32
  splits:
    - name: train
      num_bytes: 54704214286
      num_examples: 238805
  download_size: 54701266342
  dataset_size: 54704214286
license: cc-by-4.0

CellMap 2D

This dataset contains all 2D slices from the EM volumes used in the CellMap segmentation challenge. The dataset contains all x, y, z slices obtained from a total of 289 3D EM volume crops (the crops come from 22 different samples). The slices are in their native resolution (no resizing).

You can load the dataset as follows (non-streaming mode):

ds = load_dataset("eminorhan/cellmap-2d", split='train')

and then inspect the first data row:

>>> print(ds[0])
>>> {
'image': <PIL.PngImagePlugin.PngImageFile image mode=L size=300x300 at 0xFFF93926C850>,
'crop_name': 'jrc_mus-kidney/recon-1/crop129',
'axis': 'z',
'slice': 0
}

where:

image contains the actual 2D slice encoded as a PIL.Image object.
crop_name is an identifier string indicating the sample and crop names the slice comes from.
axis indicates the axis along which the slice was taken (x, y, or z).
slice is the slice index along the axis.

Please note that the dataset rows are pre-shuffled to make the shards roughly uniform in size.

License: The data originally come from HHMI Janelia's OpenOrganelle data portal released under the CC-BY-4.0 license.

Citation: If you use these data, please cite the following papers:

@article{heinrich2021whole,
  title={Whole-cell organelle segmentation in volume electron microscopy},
  author={Heinrich, Larissa and Bennett, Davis and Ackerman, David and Park, Woohyun and Bogovic, John and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Xu, C Shan and others},
  journal={Nature},
  volume={599},
  number={7883},
  pages={141--146},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

Paper link

@misc{CellMap2024,
  title={CellMap 2024 Segmentation Challenge},
  author={{CellMap Project Team} and Ackerman, David and Ahrens, Misha B. and Aso, Yoshinori and Avetissian, Emma and Bennett, Davis and others},
  year={2024},
  publisher={Janelia Research Campus},
  doi={10.25378/janelia.c.7456966},
}

Paper link