eminorhan/cellmap-2d

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), together with their corresponding labeled segmentation masks. The slices were prepared and pushed to the HF datasets Hub with this script.

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=400x400 at 0xFFFA15823BF0>,
'label': <PIL.PngImagePlugin.PngImageFile image mode=L size=400x400 at 0xFFFA15AE91F0>,
'crop_name': 'jrc_hela-2/recon-1/crop28',
'axis': 'z',
'slice': 352
}

where:

• image contains the actual 2D slice encoded as a PIL.Image object.
• label contains the labeled segmentation masks 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