Add dataset card

README.md

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+---
+license: cc-by-nc-4.0
+pretty_name: Z-Screen Source Data (June 2026 Release)
+tags:
+  - drug-discovery
+  - single-cell
+  - transcriptomics
+  - high-content-imaging
+  - cheminformatics
+  - perturbation
+size_categories:
+  - 100K<n<1M
+---
+
+# Z-Screen Source Data (June 2026 Release)
+
+This deposit contains the curated public source-data layers for the Z-Screen platform, a
+modality-agnostic single-nanowell drug-discovery screen that couples transcriptomic counts,
+imaging morphology embeddings, and compound chemistry across a shared public compound identifier.
+
+Each row of the primary data represents a single **nanowell** (90 microns diameter by 120 microns
+tall, holding approximately 2 to 10 cells), not a single cell.
+
+- **Nanowells profiled:** 768,162 across 49 devices (numbered 0 to 48)
+- **Genes measured:** 46,944 (transcriptomic counts)
+- **Cell lines / clone variants:** 6 (HEK293, HEK293-clone, A549, H1650, THP1, AEC7)
+- **Libraries:** 14 (named-control compounds, OBOC combinatorial libraries, control beads)
+- **Unique compounds / precursors:** 142,227 (78 named controls, 142,149 OBOC building blocks, plus controls)
+
+The primary tables are joined 1-to-1 across `counts.h5ad`, `MasterFile.parquet`, and the chemistry
+layer on the nanowell axis, and share a `public_compound_id` key that links biology to chemistry.
+
+## Contents
+
+```
+raw_counts_data/               Raw transcriptomic counts + master well table
+normalized_image_embeddings/   Normalized morphology features + biomarker intensities
+chemical_features/             Public compound / building-block chemistry features
+active_seq_same_well/          Same-well RNA + imaging calibration layer (ActiveSeq)
+external_reference/            External benchmark atlases (ranked gene lists) + gene sets
+README.md                      This file
+MANIFEST.csv                   Per-file SHA256, size, and parquet row/column counts
+```
+
+### `raw_counts_data/` (~3.9 GB)
+
+| File | Shape | Description |
+|---|---|---|
+| `counts.h5ad` | 768,162 wells x 46,944 genes | Raw transcriptomic counts (AnnData / HDF5). |
+| `MasterFile.parquet` | 768,162 x 274 | Master per-well table (well/device/library/compound/QC metadata), 1-to-1 with `counts.h5ad`. |
+| `data_shape_summary.md` | - | Human-readable data map (devices, cell lines, libraries, nomenclature). |
+| `data_shape_visualization.html` | - | Interactive overview of dataset structure. |
+
+### `normalized_image_embeddings/` (~6 MB)
+
+| File | Shape | Description |
+|---|---|---|
+| `normalized_image_embeddings.parquet` | 21,795 x 39 | Compound-level normalized morphology (image) features, keyed by `public_compound_id`. |
+| `biomarker_intensity_layer.parquet` | 18,942 x 11 | Protein/cellular-state marker intensities (BRD4, p21/CDKN1A, DAPI, actin, ConA, p62/SQSTM1). |
+
+### `chemical_features/` (~295 MB)
+
+| File | Shape | Description |
+|---|---|---|
+| `compound_chemistry_feature_master.parquet` | 144,645 x 961 | Compound + building-block chemistry, keyed by `public_compound_id`. Formula/InChIKey where available, plus Chemeleon and ChemBERTa embeddings (whole-molecule and per-building-block BB0 to BB4). |
+
+### `active_seq_same_well/` (~440 MB)
+
+The public layer supporting the claim that RNA and morphology were measured from the **same
+physical nanowell**. The primary deliverable is self-contained; the remaining files are the full
+pre-join latent spaces so the same-well matching can be reproduced from scratch.
+
+| File | Shape | Role |
+|---|---|---|
+| `joined_same_well_data_with_public_compound_id.parquet` | 18,727 x 550 | **Primary deliverable.** Matched same-well rows carrying 32 RNA latent dims (`D00`-`D31`), 448 image latent dims (`img_lat_*`), well geometry, RNA QC, and public compound mapping. |
+| `activeseq_control_name_public_compound_map.parquet` | 36 x 7 | Control-name to `public_compound_id` mapping (35 named compounds, 2 ActiveSeq devices). |
+| `imaging_lats.parquet` | 126,662 x 451 | Full imaging-patch latent space (pre-join). |
+| `rnaseq_lats.parquet` | 61,101 x 33 | Full RNA-cell latent space (pre-join). |
+| `assay_well_dataframe.parquet` | 126,662 x 35 | Imaging-patch geometry / detection metadata. |
+| `rnaseq_obs.parquet` | 61,101 x 27 | RNA-cell observation metadata / QC. |
+| `matches_table.parquet` | 20,222 x 8 | Imaging-to-RNA well matches used to build the joined table. |
+
+> Note: the redundant `joined_same_well_data.parquet` (a strict subset of the
+> `_with_public_compound_id` table, differing only by a pandas index column) is intentionally
+> excluded from this deposit.
+
+### `external_reference/` (~182 MB)
+
+Clean, reusable external-benchmark surface. The core assets are the **ranked gene-list signature
+tables** (`*_rank_signatures_top_genes.parquet`) plus their metadata, catalogs, provenance, and
+gene sets.
+
+| Atlas | Key ranked-gene-list table |
+|---|---|
+| Replogle 2022 K562 genome-wide CRISPR KO | `crispr_perturbation_atlases/replogle_2022_k562_gwps/replogle_rank_signatures_top_genes.parquet` |
+| Replogle 2022 RPE1 CRISPR KO | `crispr_perturbation_atlases/replogle_2022_rpe1/rpe1_rank_signatures_top_genes.parquet` |
+| Norman & Weissman 2019 K562 CRISPRa | `crispr_perturbation_atlases/norman_weissman_2019_k562_crispra/norman_rank_signatures_top_genes.parquet` |
+| Selected THP1 scPerturb CRISPR | `crispr_perturbation_atlases/scperturb_thp1_selected/scperturb_rank_signatures_top_genes.parquet` |
+| LINCS L1000 compound signatures | `compound_atlases/lincs_l1000/processed/lincs_l1000_rank_signatures_top_genes.parquet` |
+| Tahoe-100M | `compound_atlases/tahoe_100m/` (metadata + capmatinib slice) |
+| Control transcriptome expansion (2026-05-25) | `compound_atlases/control_transcriptome_expansion_20260525/` |
+
+Also included: `benchmark_outputs/` (prior LINCS vs Z-Screen overlap/correlation outputs),
+`catalog/` (dataset catalog, file manifest with hashes, provenance), `gene_sets/` (Enrichr KEGG /
+Hallmark / Reactome GMTs, disease-reversal and aging signature JSONs), and the provenance/fetch
+scripts documenting how the tables were produced.
+
+> Curation note: the raw external `.h5ad` matrices (`scperturb_downloads/`, ~6.3 GB) are **not**
+> bundled here. They are publicly re-downloadable from scPerturb's own Zenodo record; see
+> `crispr_perturbation_atlases/scperturb_thp1_selected/source_manifest/` and
+> `external_reference/fetch_zenodo.py` for retrieval. Only the processed rank-signature tables are
+> included, so downstream comparisons do not require rebuilding them.
+
+## Loading
+
+Parquet (Python):
+
+```python
+import pandas as pd
+master = pd.read_parquet("raw_counts_data/MasterFile.parquet")
+chem   = pd.read_parquet("chemical_features/compound_chemistry_feature_master.parquet")
+# link biology to chemistry on the shared key
+merged = master.merge(chem, on="public_compound_id", how="left")
+```
+
+Counts (AnnData):
+
+```python
+import anndata as ad
+adata = ad.read_h5ad("raw_counts_data/counts.h5ad")   # 768,162 obs (nanowells) x 46,944 vars (genes)
+```
+
+## Integrity
+
+`MANIFEST.csv` lists every file with its SHA256 checksum, byte size, and (for parquet) row and
+column counts. Verify a download with, for example, `sha256sum -c` after reformatting, or by
+recomputing hashes and comparing against the manifest.
+
+## Excluded from this release
+
+The following were deliberately left out of the deposit: the `Manuscripts_June2026` folder, the
+`zscreen_v2` / `v3` / `v4` working directories, the raw external `scperturb_downloads/` H5AD
+matrices, and the redundant `active_seq_same_well/joined_same_well_data.parquet`.
+
+## License and citation
+
+License: **CC BY-NC 4.0** (Creative Commons Attribution-NonCommercial 4.0 International).
+You may share and adapt the data with attribution, for non-commercial purposes only.
+Please cite the associated Z-Screen manuscript and this dataset DOI.