Task Zoo#

The datasets and configurations for which results are reported in the paper, per benchmark. Some models, for instance KRONOS, require distinct dataset configs to account for differences in standardization; for KRONOS, use configs/datasets/kronos/.

Cross-cohort Instance Segmentation#

See Cross-cohort Instance Segmentation for how to run it.

Dataset	Dataset config (VirTues)
cords2023cancer	`configs/datasets/virtues/cords2023cancer.yaml`
cords2024cancer	`configs/datasets/virtues/cords2024cancer.yaml`
danenberg2022breast	`configs/datasets/virtues/danenberg2022breast.yaml`
schulz2024immucan	`configs/datasets/virtues/schulz2024immucan.yaml`
moldoveanu2022spatially	`configs/datasets/virtues/moldoveanu2022spatially.yaml`
meyer2025stratification	`configs/datasets/virtues/meyer2025stratification.yaml`
lin2023highsubset	`configs/datasets/virtues/lin2023highsubset.yaml`
rigamonti2024integrating	`configs/datasets/virtues/rigamonti2024integrating.yaml`

In-cohort Cell Phenotyping#

See In-cohort Cell Phenotyping for how to run it.

Dataset	Dataset config (VirTues)	Benchmark config
cords2023cancer	`configs/datasets/virtues/cords2023cancer.yaml`	`configs/benchmarks/cell_probe/cords2023cancer.yaml`
cords2024cancer	`configs/datasets/virtues/cords2024cancer.yaml`	`configs/benchmarks/cell_probe/cords2024cancer.yaml`
danenberg2022breast	`configs/datasets/virtues/danenberg2022breast.yaml`	`configs/benchmarks/cell_probe/danenberg2022breast.yaml`
hoch2022multiplexed	`configs/datasets/virtues/hoch2022multiplexed.yaml`	`configs/benchmarks/cell_probe/hoch2022multiplexed.yaml`
lin2023highsubset	`configs/datasets/virtues/lin2023highsubset.yaml`	`configs/benchmarks/cell_probe/lin2023highsubset.yaml`
meyer2025stratification	`configs/datasets/virtues/meyer2025stratification.yaml`	`configs/benchmarks/cell_probe/meyer2025stratification.yaml`
moldoveanu2022spatially	`configs/datasets/virtues/moldoveanu2022spatially.yaml`	`configs/benchmarks/cell_probe/moldoveanu2022spatially.yaml`
rigamonti2024integrating	`configs/datasets/virtues/rigamonti2024integrating.yaml`	`configs/benchmarks/cell_probe/rigamonti2024integrating.yaml`
schulz2024immucan	`configs/datasets/virtues/schulz2024immucan.yaml`	`configs/benchmarks/cell_probe/schulz2024immucan.yaml`
wang2023spatial	`configs/datasets/virtues/wang2023spatial.yaml`	`configs/benchmarks/cell_probe/wang2023spatial.yaml`

Cross-cohort Cell Annotation#

See Cross-cohort Cell Annotation for how to run it.

Dataset	Dataset config (VirTues)	Benchmark config
cords2023cancer	`configs/datasets/virtues/cords2023cancer.yaml`	`configs/benchmarks/cell_annotation/cords2023cancer.yaml`
cords2024cancer	`configs/datasets/virtues/cords2024cancer.yaml`	`configs/benchmarks/cell_annotation/cords2024cancer.yaml`
danenberg2022breast	`configs/datasets/virtues/danenberg2022breast.yaml`	`configs/benchmarks/cell_annotation/danenberg2022breast.yaml`
schulz2024immucan	`configs/datasets/virtues/schulz2024immucan.yaml`	`configs/benchmarks/cell_annotation/schulz2024immucan.yaml`
moldoveanu2022spatially	`configs/datasets/virtues/moldoveanu2022spatially.yaml`	`configs/benchmarks/cell_annotation/moldoveanu2022spatially.yaml`
meyer2025stratification	`configs/datasets/virtues/meyer2025stratification.yaml`	`configs/benchmarks/cell_annotation/meyer2025stratification.yaml`
lin2023highsubset	`configs/datasets/virtues/lin2023highsubset.yaml`	`configs/benchmarks/cell_annotation/lin2023highsubset.yaml`
rigamonti2024integrating	`configs/datasets/virtues/rigamonti2024integrating.yaml`	`configs/benchmarks/cell_annotation/rigamonti2024integrating.yaml`

Tissue-level Prediction#

See Tissue-level Prediction for how to run it.

Dataset	Dataset config (VirTues)	Benchmark config
cords2024cancer	`configs/datasets/virtues/cords2024cancer.yaml`	`configs/benchmarks/tissue_level/cords2024cancer.yaml`
danenberg2022breast	`configs/datasets/virtues/danenberg2022breast.yaml`	`configs/benchmarks/tissue_level/danenberg2022breast.yaml`
fischer2023multiplex	`configs/datasets/virtues/fischer2023multiplex.yaml`	`configs/benchmarks/tissue_level/fischer2023multiplex.yaml`
hoch2022multiplexed	`configs/datasets/virtues/hoch2022multiplexed.yaml`	`configs/benchmarks/tissue_level/hoch2022multiplexed.yaml`
meyer2025stratification	`configs/datasets/virtues/meyer2025stratification.yaml`	`configs/benchmarks/tissue_level/meyer2025stratification.yaml`
wang2023spatial	`configs/datasets/virtues/wang2023spatial.yaml`	`configs/benchmarks/tissue_level/wang2023spatial.yaml`

H&E-to-MPX Virtual Staining#

See H&E-to-MPX Virtual Staining for how to run it.

Dataset	Dataset config
lin2023high	`configs/datasets/he_staining/lin2023high.yaml`
hickey2023organization	`configs/datasets/he_staining/hickey2023organization.yaml`
schurch2020coordinated	`configs/datasets/he_staining/schurch2020coordinated.yaml`
phillips2021immune	`configs/datasets/he_staining/phillips2021immune.yaml`

MPX-to-MPX Virtual Staining#

See MPX-to-MPX Virtual Staining for how to run it.

Dataset	Dataset config (VirTues)
cords2024cancer	`configs/datasets/virtues/cords2024cancer.yaml`
schulz2024immucan	`configs/datasets/virtues/schulz2024immucan.yaml`
rigamonti2024integrating	`configs/datasets/virtues/rigamonti2024integrating.yaml`
danenberg2022breast	`configs/datasets/virtues/danenberg2022breast.yaml`