README.md

metadata

pretty_name: Pan-Multiplex (Pan-M) dataset
tags:
  - multiplexed imaging
  - digital pathology
license: cc-by-sa-4.0
task_categories:
  - image-segmentation

Pan-Multiplex (Pan-M) dataset

This dataset was to train the Nimbus model for the publication "Improving cell phenotyping by factoring in spatial marker expression patterns with Nimbus". The dataset contains multiplexed images from different modalities, tissues and protein marker panels. It was constructed by semi-automatic pipeline, where the cell types assigned by the authors of the original studies that published the data, where mapped back to their expected marker activity. More details to the construction of the dataset can be found in the paper. The dataset consists of five subsets named codex_colon,mibi_breast,mibi_decidua,vectra_colon,vectra_pancreas, each in an individual folder. After unzipping, the data should be stored in the following folder structure to use the code provided for training and inference. To construct the binary segmentation maps used for training, you can use the code in segmentation_data_prep.py and simple_data_prep.py in the training repository.

.
├── data
│   ├── codex_colon
│   ├── vectra_colon
│   ├── vectra_pancreas
│   ├── mibi_decidua
│   ├── mibi_breast
│   ├── experimental_results.csv
│   ├── gt_pred_ie_consolidated.csv

When using the dataset please cite

@article{rum2024nimbus,
  title={Improving cell phenotyping by factoring in spatial marker expression patterns with Nimbus},
  author={Rumberger, J. Lorenz and Greenwald, Noah F. and Ranek, Jolene and Boonrat, Potchara and Walker, Cameron and Franzen, Jannik and Varra, Sricharan Reddy and Kong, Alex and Sowers, Cami and Liu, Candace C. and Averbukh, Inna and Piyadasa, Hadeesha and Vanguri, Rami and Nederlof, Iris and Wang, Xuefei Julie and Van Valen, David and Kok, Marleen and Hollman, Travis and Kainmueller, Dagmar and Angelo, Michael},
  journal={bioRxiv},
  pages={2024--05},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}
@article{greenbaum2023spatially,
  title={A spatially resolved timeline of the human maternal--fetal interface},
  author={Greenbaum, Shirley and Averbukh, Inna and Soon, Erin and Rizzuto, Gabrielle and Baranski, Alex and Greenwald, Noah F and Kagel, Adam and Bosse, Marc and Jaswa, Eleni G and Khair, Zumana and others},
  journal={Nature},
  volume={619},
  number={7970},
  pages={595--605},
  year={2023},
  publisher={Nature Publishing Group UK London}
}
@article{hickey2023organization,
  title={Organization of the human intestine at single-cell resolution},
  author={Hickey, John W and Becker, Winston R and Nevins, Stephanie A and Horning, Aaron and Perez, Almudena Espin and Zhu, Chenchen and Zhu, Bokai and Wei, Bei and Chiu, Roxanne and Chen, Derek C and others},
  journal={Nature},
  volume={619},
  number={7970},
  pages={572--584},
  year={2023},
  publisher={Nature Publishing Group UK London}
}