Reproducibility

Three notebooks under analysis/data/plots/ reproduce the paper figures from cached metric CSVs. No model is retrained.

Setting (Fig 1c)	Notebook
End-to-end reconstruction (PCA / AE / scVI / nlscVI / mlscVI)	analysis/data/plots/fig2_clean.ipynb
Foundation-model reconstruction (frozen FM + decoder)	analysis/data/plots/fig3_clean.ipynb
Latent-shift reconstruction (CellFlow + STATE)	analysis/data/plots/fig4_clean.ipynb

Cached artefacts

The metric CSVs and lookup tables consumed by the biological metrics are hosted at huggingface.co/datasets/theislab/ReconEval. Download them into analysis/frozen/ before running the notebooks. The notebooks use paths relative to analysis/data/plots/ (../frozen/ and ../figs/<fig>/), so run them from that directory.

Funky-map helper

The plotting helper that produces the rank-percentile funky map (the Fig 3 summary) is available as sc_reconstruction.metrics.funky_heatmap(). The analysis notebooks keep their own variants for paper-specific styling, but library users can produce the same layout with one call on the score DataFrame.