---
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](https://cellmapchallenge.janelia.org/). 
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):
```python
ds = load_dataset("eminorhan/cellmap-2d", split='train')
```
and then inspect the first data row:
```python
>>> 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](https://www.openorganelle.org/) data portal [released](https://www.openorganelle.org/faq#sharing) under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/deed.en) 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](https://www.nature.com/articles/s41586-021-03977-3)


```
@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](https://janelia.figshare.com/collections/CellMap_2024_Segmentation_Challenge/7456966)