---
license: cc0-1.0
pretty_name: "CP-BG-Bench JUMP SD (background-masked + density-augmented cell crop)"
size_categories:
- 100K<n<1M
task_categories:
- image-feature-extraction
tags:
- cell-painting
- microscopy
- single-cell
- jump-cp
configs:
- config_name: default
  data_files:
  - split: train
    path: data/shard-*.tar
---

# CP-BG-Bench JUMP SD: background-masked + density-augmented cell crop

Single-cell tiles from JUMP-CP, packaged for the CP-BG-Bench evaluation.
This is one of four row-aligned views of the same 645,390 cells:

| view | repo | cell.bin content |
|---|---|---|
| C  | `cp-bg-bench-anon/jump-c`  | raw 5-channel crop |
| S  | `cp-bg-bench-anon/jump-s`  | background-masked crop |
| CD | `cp-bg-bench-anon/jump-cd` | density-augmented crop |
| SD | `cp-bg-bench-anon/jump-sd` | background-masked + density-augmented |

All four share `row_key`. Join on it to combine views.

## Loading

```python
import json, numpy as np, webdataset as wds

URLS = "https://huggingface.co/datasets/cp-bg-bench-anon/jump-sd/resolve/main/data/shard-{{00000..00042}}.tar"

def decode(s):
    cell = np.frombuffer(s["cell.bin"], dtype=np.uint8).reshape(5, 224, 224)
    mask = np.frombuffer(s["mask.bin"], dtype=np.uint8).reshape(2, 224, 224)
    return cell, mask, json.loads(s["json"])

ds = wds.WebDataset(URLS, shardshuffle=True).shuffle(2000).map(decode)
```

## Per-cell payload

| file | shape | dtype |
|---|---|---|
| `<key>.cell.bin` | (5, 224, 224) | uint8 |
| `<key>.mask.bin` | (2, 224, 224) | uint8 |
| `<key>.json`     | -             | json  |

`cell.bin` and `mask.bin` are raw bytes. Channel order is in `channels.json`.

### Image channels (cell.bin)

| 0 | 1 | 2 | 3 | 4 |
|---|---|---|---|---|
| DNA (Hoechst) | AGP (Phalloidin+WGA) | ER (ConA) | Mito (MitoTracker DR) | RNA (SYTO 14) |

This order differs from JUMP-CP v2 `[DNA, ER, RNA, AGP, Mito]` and Recursion
`[DNA, ER, AGP, RNA, Mito, ...]`. Cross-dataset code must remap by name.

### Mask channels (mask.bin)

| 0 | 1 |
|---|---|
| nucleus | cell |

Binary uint8 in {0, 255}. Identical across all four views.

### JSON metadata

| field | dtype | example |
|---|---|---|
| `row_key` | str | `source_4__20210922_Run1__BR00121430__J18__1__27` |
| `source` | str | `source_4` |
| `batch`  | str | `source_4` |
| `plate`  | str | `BR00121430` |
| `well`   | str | `J18` |
| `tile`   | str | `1` |
| `id_local` | int | `27` |
| `perturbation` | str | `IAZDPXIOMUYVGZ-UHFFFAOYSA-N` |
| `Metadata_InChIKey` | str | `IAZDPXIOMUYVGZ-UHFFFAOYSA-N` |
| `Metadata_PlateType` | str | `COMPOUND` or `TARGET2` |
| `nuc_area`, `cyto_area` | int | nuclear / cytoplasm pixel counts |
| `nuc_cyto_ratio` | float | derived |
| `n_cells_in_fov`, `n_cells_scaled` | int, float | local density |

`metadata.parquet` mirrors the JSON fields and adds `shard_index` and
`key_in_shard` for direct cell lookup.

## Stats

645,390 cells, 43 shards, 10 sources, 900 plates,
1467 compounds. Plate library: COMPOUND 445,968 cells, TARGET2 199,422 cells.
Held-out evaluation batch: `source_4` (21,177 cells).

## License

CC0 1.0. Anonymous NeurIPS 2026 Datasets and Benchmarks submission; citation
on acceptance.