Initial release

LICENSE

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+CC0 1.0 Universal
+
+The person who associated a work with this deed has dedicated the work to the
+public domain by waiving all of his or her rights to the work worldwide under
+copyright law, including all related and neighboring rights, to the extent
+allowed by law.
+
+Full text: https://creativecommons.org/publicdomain/zero/1.0/legalcode

README.md

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----
-license: cc0-1.0
----
+---
+license: cc0-1.0
+pretty_name: "CP-BG-Bench JUMP C (raw cell crop)"
+size_categories:
+- 100K<n<1M
+task_categories:
+- image-feature-extraction
+tags:
+- cell-painting
+- microscopy
+- representation-learning
+- single-cell
+- biology
+- jump-cp
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path: data/shard-*.tar
+---
+
+# CP-BG-Bench: JUMP view C (raw cell crop)
+
+This dataset is one of four paired views of the same single-cell tiles from
+the JUMP-CP Cell Painting consortium, prepared for the CP-BG-Bench evaluation
+framework.
+
+The four views — C (raw crop), S (background-masked crop), CD (density-augmented),
+SD (background-masked + density-augmented) — are released as separate
+repositories. They are **row-aligned**: each `row_key` exists in all four
+views and refers to the same underlying cell. Each view ships the same
+schema (cell + mask + metadata); only the `cell.bin` content differs.
+
+This repository contains view **C**: raw cell crop.
+
+## Format
+
+WebDataset tar shards. Each cell occupies one sample with four files sharing a
+key:
+
+- `{key}.cell.bin` — raw uint8 bytes, shape `(5, 224, 224)`, channel-first.
+  View-specific image content (raw / background-masked / density-augmented).
+- `{key}.mask.bin` — raw uint8 bytes, shape `(2, 224, 224)`, channel-first.
+  Segmentation mask (`[nucleus, cell]`); identical across all four views.
+- `{key}.json` — per-cell metadata (see below).
+
+Note: the binary blobs are **raw bytes**, not PNG/NPY. Decode with:
+
+```python
+import numpy as np
+cell = np.frombuffer(cell_bytes, dtype=np.uint8).reshape((5, 224, 224))
+mask = np.frombuffer(mask_bytes, dtype=np.uint8).reshape((2, 224, 224))
+```
+
+## Channels
+
+The 5 channels are stored in this order:
+
+| index | label | stain |
+|---|---|---|
+| 0 | DNA  | Hoechst 33342 |
+| 1 | AGP  | Phalloidin + WGA |
+| 2 | ER   | Concanavalin A |
+| 3 | Mito | MitoTracker Deep Red |
+| 4 | RNA  | SYTO 14 |
+
+> **Note: this on-disk order is `[DNA, AGP, ER, Mito, RNA]`, which differs
+> from both the JUMP-CP v2 publication order `[DNA, ER, RNA, AGP, Mito]` and
+> the Recursion RxRx order `[DNA, ER, AGP, RNA, Mito, ...]`.** Code that
+> assumes a particular order without checking will feed the wrong stain to
+> downstream channel slots. A machine-readable `channels.json` is provided at
+> the repo root; please use it. The CP-BG-Bench framework resolves channels
+> by name and is robust to per-dataset reorderings.
+
+
+The 2 mask channels are stored in this order:
+
+| index | label | description |
+|---|---|---|
+| 0 | nucleus | binary nucleus segmentation mask |
+| 1 | cell    | binary whole-cell segmentation mask |
+
+Masks are uint8 with values in `{0, 255}` (or another non-zero label).
+A machine-readable `channels.json` is provided at the repo root.
+
+
+## Metadata fields
+
+Each `.json` sidecar contains:
+
+| Field | Type | Description |
+|---|---|---|
+| `row_key` | str | Stable cell identifier (`source__date_run__plate__well__tile__id`) |
+| `source` | str | JUMP partner code (e.g. `source_4`) |
+| `batch` | str | Batch identifier (= `source` for JUMP-CP) |
+| `plate` | str | JUMP plate identifier |
+| `well` | str | Well coordinate (e.g. `B02`) |
+| `tile` | str | Site index within well |
+| `id_local` | int | Per-tile cell index |
+| `perturbation` | str | Compound InChIKey (= `Metadata_InChIKey`) |
+| `Metadata_InChIKey` | str | Public PubChem-derivable compound ID |
+| `Metadata_PlateType` | str | `TARGET2` or `COMPOUND` |
+| `nuc_area`, `cyto_area`, `nuc_cyto_ratio` | num | Single-cell QC features |
+| `n_cells_in_fov`, `n_cells_scaled` | num | Local density features |
+
+A flat `metadata.parquet` covering all rows (with `shard_index` and
+`key_in_shard` columns) is provided at the repo root for fast subsetting
+without scanning the tar shards.
+
+## Statistics
+
+- Total cells: 645,390
+- Shards: 43
+- Approximate shard size: ~5.3 GB
+- Plate types: COMPOUND: 445,968, TARGET2: 199,422
+- Sources (JUMP partners): 10
+- Plates: 900
+- Unique perturbations (InChIKeys): 1467
+
+## Splits
+
+A natural held-out batch is `source_4` (21,177 cells), used in the
+CP-BG-Bench cross-batch retrieval evaluation. Filter with:
+
+```python
+ds = ds.filter(lambda r: r["source"] == "source_4")
+```
+
+## Pairing across views
+
+The four CP-BG-Bench JUMP repos share `row_key` exactly. To use a paired
+dataloader, load all four and join on `row_key` (the `metadata.parquet` files
+make this cheap):
+
+- `<anon-org>/jump-c-target2`  (this view: C)
+- `<anon-org>/jump-s-target2`
+- `<anon-org>/jump-cd-target2`
+- `<anon-org>/jump-sd-target2`
+
+## Shard ordering
+
+- Rows are written in the order they appear in the source HF Datasets
+  directory. Shuffle at load time (PyTorch `DataLoader(shuffle=True)` or
+  `webdataset.WebDataset(...).shuffle(N)`); shards are not pre-shuffled.
+- `(shard_index, key_in_shard)` for every row is in `metadata.parquet`.
+
+## License
+
+CC0 1.0 Universal. Underlying JUMP-CP data is released by the JUMP-Cell
+Painting consortium under CC0 1.0.
+
+## Citation
+
+Anonymous submission to NeurIPS 2026 Datasets & Benchmarks Track.
+
+For the underlying JUMP-CP data, please cite the JUMP-CP consortium release.

channels.json

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+{
+  "view": "C",
+  "view_description": "raw cell crop",
+  "files": {
+    "cell.bin": {
+      "channels": [
+        "DNA",
+        "AGP",
+        "ER",
+        "Mito",
+        "RNA"
+      ],
+      "stains": {
+        "DNA": "Hoechst 33342",
+        "AGP": "Phalloidin + WGA",
+        "ER": "Concanavalin A",
+        "Mito": "MitoTracker Deep Red",
+        "RNA": "SYTO 14"
+      },
+      "shape": [
+        5,
+        224,
+        224
+      ],
+      "dtype": "uint8",
+      "layout": "channel-first (C, H, W)",
+      "encoding": "raw bytes; np.frombuffer(blob, dtype=np.uint8).reshape(5, 224, 224)"
+    },
+    "mask.bin": {
+      "channels": [
+        "nucleus",
+        "cell"
+      ],
+      "shape": [
+        2,
+        224,
+        224
+      ],
+      "dtype": "uint8",
+      "layout": "channel-first (C, H, W)",
+      "encoding": "raw bytes; np.frombuffer(blob, dtype=np.uint8).reshape(2, 224, 224)"
+    }
+  },
+  "notes": [
+    "On-disk channel order [DNA, AGP, ER, Mito, RNA] differs from the JUMP-CP v2 publication order [DNA, ER, RNA, AGP, Mito] and from the Recursion RxRx order [DNA, ER, AGP, RNA, Mito, ...].",
+    "Loaders must remap by name, not by index, when combining JUMP with other Cell Painting datasets.",
+    "Mask channels are [nucleus, cell] \u2014 both binary uint8."
+  ]
+}

croissant.json

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+{
+  "@context": {
+    "@language": "en",
+    "@vocab": "https://schema.org/",
+    "cr": "http://mlcommons.org/croissant/",
+    "rai": "http://mlcommons.org/croissant/RAI/",
+    "data": {
+      "@id": "cr:data",
+      "@type": "@json"
+    },
+    "dct": "http://purl.org/dc/terms/",
+    "examples": {
+      "@id": "cr:examples",
+      "@type": "@json"
+    },
+    "extract": "cr:extract",
+    "field": "cr:field",
+    "fileObject": "cr:fileObject",
+    "fileSet": "cr:fileSet",
+    "format": "cr:format",
+    "includes": "cr:includes",
+    "isLiveDataset": "cr:isLiveDataset",
+    "jsonPath": "cr:jsonPath",
+    "key": "cr:key",
+    "md5": "cr:md5",
+    "parentField": "cr:parentField",
+    "path": "cr:path",
+    "recordSet": "cr:recordSet",
+    "references": "cr:references",
+    "regex": "cr:regex",
+    "repeated": "cr:repeated",
+    "replace": "cr:replace",
+    "sc": "https://schema.org/",
+    "separator": "cr:separator",
+    "source": "cr:source",
+    "subField": "cr:subField",
+    "transform": "cr:transform"
+  },
+  "@type": "sc:Dataset",
+  "name": "cp-bg-bench-jump-c",
+  "description": "CP-BG-Bench JUMP view C (raw 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": [
+    {
+      "@type": "cr:FileSet",
+      "@id": "shards",
+      "name": "shards",
+      "description": "WebDataset tar shards.",
+      "containedIn": {
+        "@id": "https://huggingface.co/datasets/anonymous/cp-bg-bench-jump"
+      },
+      "encodingFormat": "application/x-tar",
+      "includes": "data/shard-*.tar"
+    }
+  ],
+  "recordSet": [
+    {
+      "@type": "cr:RecordSet",
+      "@id": "cells",
+      "name": "cells",
+      "description": "One row per single-cell tile.",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "cells/row_key",
+          "name": "row_key",
+          "dataType": "sc:Text",
+          "description": "Stable per-cell identifier."
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "cells/cell",
+          "name": "cell.bin",
+          "dataType": "sc:ImageObject",
+          "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)."
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "cells/perturbation",
+          "name": "perturbation",
+          "dataType": "sc:Text",
+          "description": "Compound InChIKey."
+        },
+        {
+          "@type": "cr:Field",
+          "@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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