cp-bg-bench-anon/jump-cd

CP-BG-Bench JUMP CD: 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

import json, numpy as np, webdataset as wds

URLS = "https://huggingface.co/datasets/cp-bg-bench-anon/jump-cd/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.