Notebooks ↔ figures / outputs

This table links each notebook to the main outputs used for the manuscript figures (and/or the figure files produced by the notebook). When figure panel IDs change during revision, update the “Manuscript figure(s)” column accordingly.

Notebook	What it does	Manuscript figure(s)	Key outputs (files)
nb_01_qc_cell_transcript_filtering.ipynb	QC summaries, library depth by condition, and technical replicate concordance; generates the labeled cell-type UMAP used throughout downstream analyses.	Fig. S6; Fig. S3; Fig. 2b	Supplementary_Table_QC_summary_publication.csv • library_depth_by_condition.pdf • qc_techrep_correlation_condition_day.pdf • umap_celltype_numbered.pdf
nb_02_compostion_analysis.ipynb	Global (whole-slide) immune/stromal composition comparisons across conditions and timepoints.	Fig. S3	stacked_celltype_day4.pdf • stacked_celltype_day8.pdf
nb_03_tumor_regions_compostion_analysis.ipynb	Core vs border tumor-region composition analysis using scCODA inputs.	Fig. 2d–g; Fig. S4a	scCODA region composition outputs (e.g., posterior/inference tables and core–border plots generated by the notebook).
nb_04_ligand_receptor_analysis.ipynb	Post-processing of ligand–receptor (LR) interaction scores; filters/ranks interactions for reporting.	Fig. 2h	all_lr_interactions_scores.csv • ligand_receptor_analysis_top50.csv
nb_05_Collagen_distance_bayes_model.ipynb	Bayesian modeling of collagen-distance / border–core contrasts and associated diagnostics.	Fig. 2i; Supp. Notes	model6_delta_ck_summary.csv • model_comparison_loo.csv • diagnostic PDFs (e.g., fig_ppc_model6.pdf, fig_trace_diagnostics.pdf)
nb_06_xenium_codex_alignment.ipynb	Xenium–CODEX alignment via interactive Napari landmark registration; produces aligned SpatialData objects for downstream spatial analyses/figures.	Fig. S4b	Corrected/registered .zarr objects (e.g., 05_spatialdata_zarr/slide_1_correction.zarr/) and alignment exports produced by the notebook.
nb_07_toxicology_compostion_analysis.ipynb	Tissue-wise immune composition + severity association analyses for toxicology.	Fig. 4a–d	toxicology_severity_correlation_all_tissues.csv (and associated tox composition plots/tables generated by the notebook).
nb_08_tcell_signature_gene_analysis.ipynb	T-cell signature / IFN-γ axis analysis (Poisson DGE posterior summaries; CD8 subset modeling).	Fig. 4g	fig4g_ifng_ifngr1_posterior_lnFC.csv • trace_cd8subsets_day4.pkl (posterior) and any figure panels exported by the notebook.