| --- |
| license: mit |
| task_categories: |
| - image-classification |
| - feature-extraction |
| tags: |
| - biology |
| - microscopy |
| - CRISPR |
| - evaluation |
| - benchmark |
| size_categories: |
| - 1M<n<10M |
| --- |
| |
| # OPS-Eval: Leakage-Resistant Evaluation for Optical Pooled Screens |
|
|
| Benchmark artifacts for evaluating representation learning on pooled CRISPR |
| microscopy data. This dataset accompanies a submission to the NeurIPS 2026 |
| Evaluations and Datasets Track. |
|
|
| ## Contents |
|
|
| | Directory/File | Description | Size | |
| |----------------|-------------|------| |
| | `montages/` | Per-gene montage images (4 channels x 2 phases, ~10 PNGs per gene) | ~66 GB | |
| | `cell_embeddings/` | Pre-extracted 512-dim cell embeddings per sgRNA (.npz) | ~15 GB | |
| | `splits_v1.json` | Gene-disjoint train/val/test split (3,628 / 694 / 1,000 genes) | 1.4 MB | |
| | `splits_v1_random.json` | Random image-level split (comparison, demonstrates leakage) | 1.4 MB | |
| | `splits_v1_sgrna_disjoint.json` | Guide-disjoint split (comparison) | 1.3 MB | |
| | `gene_metadata.parquet` | Per-gene metadata: cluster labels, mitotic index, guide count, 98-dim features | 1.9 MB | |
| | `sgrna_metadata.parquet` | Per-sgRNA metadata | 48 KB | |
| | `leakage_audit_v1.json` | Formal verification of zero gene overlap across splits | 99 KB | |
| | `manifest_v1.json` | SHA-256 checksums for all montage images | 4 KB | |
| | `external_gene_pairs_v1.json` | STRING + CORUM gene relationships for co-functional retrieval | 14 MB | |
| | `results/` | All experiment results (baseline ladder, ablations, split sensitivity) | 2.4 MB | |
| | `idr0071/` | External validation on independent idr0071 dataset (A549 cells) | 7.4 MB | |
| | `cellpaint_posh/` | Cell Painting POSH replication: features (`.pq`) and sgRNA library (`.csv`) | 1.5 GB | |
|
|
| ## Montage Image Structure |
|
|
| Each gene directory contains ~10 PNG files following the naming convention: |
| ``` |
| {GENE}.{phase}-montage-{channel}.png |
| ``` |
|
|
| - **Phases:** `interphase`, `mitotic` |
| - **Channels:** 0=DNA/DAPI, 1=Tubulin, 2=gH2AX, 3=Actin, 4=Label (segmentation mask) |
| - **Dimensions:** ~2700x2000 px per montage |
| - **Band structure:** 5 horizontal bands per montage (sgRNA 1-4 + non-targeting control), each containing ~100 tiled single-cell crops at ~100x100 px |
|
|
| Total: 5,322 genes, ~53,000 montage images, ~2.1M single cells. |
|
|
| ## Cell Embeddings |
|
|
| Pre-extracted 512-dimensional cell-level embeddings (float16) from a frozen ResNet-18 encoder. |
| One `.npz` file per gene, with keys corresponding to individual sgRNAs. |
|
|
| ## Quick Start |
|
|
| ```python |
| from huggingface_hub import hf_hub_download, snapshot_download |
| import json |
| |
| # Download just the splits |
| path = hf_hub_download("cspeters119/ops-eval", "splits_v1.json", repo_type="dataset") |
| splits = json.load(open(path)) |
| print(f"Loaded splits for {len(splits)} genes") |
| |
| # Download a single gene's montages |
| snapshot_download("cspeters119/ops-eval", repo_type="dataset", |
| allow_patterns="montages/AAAS/*") |
| |
| # Download everything (warning: ~85 GB) |
| snapshot_download("cspeters119/ops-eval", repo_type="dataset") |
| ``` |
|
|
| ## Code |
|
|
| See the supplementary material for evaluation code, |
| baseline implementations, and one-command reproduction harness |
| (`bash scripts/run_all.sh --tiny`). |
|
|
| ## License |
|
|
| MIT |
|
|
