CP3D Analytical results and intermediate data for 3D Cell Painting in HepG2 spheroids (v1.0.0)

Complementary data supporting the manuscript:Iáñez I, et al. "3D Cell Painting in HepG2 spheroids for phenotypic drug discovery."Communications Biology (2026). This deposit contains the analytical outputs and intermediate datagenerated by the CP3D pipeline for the paper submission version v1.0.0. Contents (see included README.md for details): DATA- data/raw/ Raw CellProfiler feature tables per replicate plate (C2386R1-R4, C2387R1-R4, C2388R1-R4)- data/processed/ Per-compound consensus profiles in the CellProfiler feature space- data/embeddings/ DINOv2 embeddings (4 x 384-dim per-channel plus 1,536-dim integrated) for all 735 compounds- data/annotated/ Annotated compound library (SMILES, InChIKey, target, MoA, is_hit_3D flag) RESULTS- results/integrated_hits/ Final 25 3D hits cross-plate (Table 1 source)- results/hits_summary/ Hit summary tables- results/multi_rep/ Per-compound replicate correlation tables- results/medina_2d_vs_3d/ Paired 2D vs 3D analysis (Figure 3)- results/hsp90_chemotype/ HSP90 ansamycin cluster and distance heatmap (Figure 4)- results/hsp90_vs_stk24/ HSP90 vs STK24 comparison (Figure 4)- results/dinov2_analysis/ Mantel test, per-channel HSP90 test, UMAP (Figure 5)- results/multivariate/ PCA, t-SNE, UMAP validation outputs- results/chemical_diversity/ Tanimoto similarities and Murcko scaffolds (Supp. Fig. S10)- results/enrichment/ Fisher target enrichment (Benjamini-Hochberg FDR)- results/qc/ QC artefacts: Echo dispensation maps, DMSO MAD distributions (Supp. Figs. S1, S2)- results/norm/ Normalisation diagnostics (Supp. Fig. S3) Every table here is regenerable from the raw imaging data using the CP3Dpipeline. The deposit is provided to guarantee long-term availability of theexact numerical outputs supporting the manuscript figures and statistics. The complete raw imaging data (four-channel maximum-intensity projectionsand confocal z-stacks) is available from the corresponding author uponreasonable request. A representative subset of imaging data will bedeposited separately on Zenodo.