Datasets:
File size: 5,399 Bytes
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"@context": {
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"cr": "http://mlcommons.org/croissant/",
"rai": "http://mlcommons.org/croissant/RAI/",
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"@type": "sc:Dataset",
"name": "cp-bg-bench-jump-sd",
"description": "CP-BG-Bench JUMP view SD (background-masked + density-augmented cell crop). Single-cell Cell Painting tiles from the JUMP-CP consortium, released as one of four paired views (C, S, CD, SD) for the CP-BG-Bench evaluation framework.",
"conformsTo": "http://mlcommons.org/croissant/1.0",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"url": "https://huggingface.co/datasets/anonymous/cp-bg-bench-jump",
"creator": {
"@type": "Organization",
"name": "anonymous"
},
"publisher": {
"@type": "Organization",
"name": "anonymous"
},
"citeAs": "Anonymous submission to NeurIPS 2026 Datasets & Benchmarks Track.",
"datePublished": "2026-05-05",
"version": "1.0.0",
"keywords": [
"Cell Painting",
"JUMP-CP",
"single-cell",
"microscopy",
"representation learning"
],
"rai:dataCollection": "Single-cell tiles were extracted from the JUMP-CP consortium image release (Chandrasekaran et al.). Cells were segmented at the FOV level, cropped at 150x150 px around the segmented centroid, and resized to 224x224. Per-FOV percentile normalisation was applied before quantisation to uint8.",
"rai:dataPreprocessingProtocol": "QC filters on (nuc_area, cyto_area, nuc_cyto_ratio) at percentiles [0.025, 0.975]. Per-(perturbation x experimental batch) cell cap of approximately 100 cells. Density-augmented views (CD, SD) encode per-cell local FOV density.",
"rai:dataUseCases": "Benchmarking representation learning models on single-cell morphology under perturbation; evaluating cell-vs-background contributions to learned representations.",
"rai:dataLimitations": "Cells from one cell line (U2OS), one assay (Cell Painting), one consortium (JUMP-CP). Channel order is the standard JUMP order and should be confirmed against the upstream pipeline before use. Quantisation to uint8 was applied during tile extraction.",
"rai:dataBiases": "Compound coverage follows the JUMP-CP Target2 + Compound plate design and is biased toward annotated chemical probes and drug-like molecules. Source (JUMP partner) is a known major covariate that should be controlled in evaluation.",
"rai:annotationsPerItem": "0",
"rai:personalSensitiveInformation": "None",
"distribution": [
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"@id": "cells",
"name": "cells",
"description": "One row per single-cell tile.",
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"name": "row_key",
"dataType": "sc:Text",
"description": "Stable per-cell identifier."
},
{
"@type": "cr:Field",
"@id": "cells/cell",
"name": "cell.bin",
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"description": "Raw uint8 bytes, shape (5, 224, 224), channel-first. View-specific image content."
},
{
"@type": "cr:Field",
"@id": "cells/mask",
"name": "mask.bin",
"dataType": "sc:ImageObject",
"description": "Raw uint8 bytes, shape (2, 224, 224), channel-first. Segmentation mask (nucleus, cell)."
},
{
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"@id": "cells/perturbation",
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"description": "Compound InChIKey."
},
{
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"@id": "cells/source",
"name": "source",
"dataType": "sc:Text",
"description": "JUMP partner identifier."
},
{
"@type": "cr:Field",
"@id": "cells/plate",
"name": "plate",
"dataType": "sc:Text",
"description": "JUMP plate identifier."
},
{
"@type": "cr:Field",
"@id": "cells/Metadata_PlateType",
"name": "Metadata_PlateType",
"dataType": "sc:Text",
"description": "TARGET2 or COMPOUND."
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]
}
]
} |