CM4AI-DREAM training data

CM4AI-DREAM provides fluorescence microscopy training data for machine learning (ML) model training, such as development of generative ML tools that simulate protein staining. Reference marker staining images (DNA, Microtubules, ER), cell-line information, target protein identifiers and protein sequences provide context for the observed protein stain.

The HPA images have been derived from Human Protein Atlas version 25. The KOLF images were generated by the Cell Maps for Artificial Intelligence (CM4AI) project in KOLF2.1J human induced pluripotent stem cells. Each image is a 512 × 512 pixel crop centered on a target cell, spanning approximately 48.2 × 48.2 μm (0.0942 μm per pixel). Crops can also contain neighboring cells.

Protein sequences come from Ensembl release 109.

Release contents

HPA-train_v1.0/
  LICENSE.txt
  hpa_train_manifest.csv.gz
  tars/
    CAB00/ ... CAB08/
    HPA00/ ... HPA07/
KOLF-train_v1.0/
  LICENSE.txt
  kolf_train_manifest.csv.gz
  tars/
    CAB07/ CAB08/
    HPA00/ ... HPA07/

Download

Download the dataset with the Hugging Face CLI:

hf download LundbergLab/CM4AI-DREAM --repo-type dataset --local-dir CM4AI-DREAM

To download one component:

hf download LundbergLab/CM4AI-DREAM --repo-type dataset \
  --include 'KOLF-train_v1.0/**' --local-dir CM4AI-DREAM

Manifest and archive format

Each compressed CSV manifest has one row per cell. TAR archives group the corresponding image files and protein sequences. The manifests use the following columns:

Column	Contents
image_key	Cell-image identifier
antibody_id	Antibody identifier
ensembl_protein_id	Ensembl protein identifier
ensembl_gene_id	Ensembl gene identifier
gene_name	Gene name
cell_line	Cell-line name
locations	Supplied localization annotation; may be empty
fov_key	Field-of-view identifier
tar_file	TAR basename
protein_path	Protein-stain PNG member path inside the TAR
nucleus_path	Nucleus-stain PNG member path inside the TAR
microtubules_path	Microtubule-stain PNG member path inside the TAR
er_path	Endoplasmic-reticulum-stain PNG member path inside the TAR
mask_path	Mask PNG member path inside the TAR
sequence_path	Protein sequence member path inside the TAR

Resolve tar_file within the same release's tars/ subdirectories. The other path columns refer to members inside that archive, rather than standalone repository files.

For example, inspect a row and open its protein image without extracting a whole archive:

import csv
import gzip
import io
from pathlib import Path
import tarfile
from PIL import Image

release = Path("CM4AI-DREAM/KOLF-train_v1.0")
with gzip.open(release / "kolf_train_manifest.csv.gz", "rt", newline="") as stream:
    row = next(csv.DictReader(stream))

matches = list((release / "tars").glob("*/" + row["tar_file"]))
if len(matches) != 1:
    raise RuntimeError("Download the matching TAR archive for this row first")
with tarfile.open(matches[0], "r:") as archive:
    member = archive.extractfile(row["protein_path"])
    if member is None:
        raise RuntimeError("Protein image is missing from the archive")
    image = Image.open(io.BytesIO(member.read()))
    image.load()
print(row["gene_name"], row["cell_line"], image.size)

Cells from the same field of view or acquisition can share biological and technical variation. Localization annotations provide context and should not be treated as independently verified localization ground truth for every cell.

Licensing and attribution

The image and annotation licenses specify Creative Commons Attribution 4.0 International (CC BY 4.0), with different source attributions. Read the original HPA license and KOLF license and retain the appropriate attributions. See the root license note for a summary.

Please cite the underlying sources listed in those notices:

• Thul PJ et al. A subcellular map of the human proteome. Science 356, eaal3321 (2017). DOI: 10.1126/science.aal3321
• Clark T et al. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv 2024.05.21.589311 (2024). DOI: 10.1101/2024.05.21.589311

Maintainer

Published by the Lundberg Lab for the CM4AI-DREAM challenge. Report dataset questions through this repository's Community tab.