JLrumberger/Pan-Multiplex-Gold-Standard

Pan-Multiplex-Gold-Standard dataset

This dataset was constructed to test the Nimbus model for the publication "Automated classification of cellular expression in multiplexed imaging data with Nimbus". The dataset contains multiplexed images from different modalities, tissues and protein marker panels. It was constructed by 4 expert annotators, who proofread ~1.1M annotations which served as the gold-standard for assesing the algorithm. More details on 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. The labels have the following meaning (0: marker negative, 1: marker positive, 2: ambiguous, 3: ambiguous)

The MIBI Breast dataset is currently not available. The original study where this dataset comes from is still under review. Once the study is published, the dataset will be available here.

When using the dataset please cite

@article{rum2024nimbus,
  title={Automated classification of cellular expression in multiplexed imaging data with Nimbus},
  author={Rumberger, J. Lorenz and Greenwald, Noah F. and Ranek, Jolene S. and Boonrat, Potchara and Walker, Cameron and Franzen, Jannik and Varra, Sricharan Reddy and Kong, Alex and Sowers, Cameron 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 J. and Kainmueller, Dagmar and Angelo, Michael},
  journal={bioRxiv},
  pages={2024--05},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}