Збережено в:
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| Формат: | Recurso digital |
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| Опубліковано: |
Zenodo
2026
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| Онлайн доступ: | https://doi.org/10.5281/zenodo.19684403 |
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Зміст:
- <h2>Analysis Code — Rose et al. (2026)</h2> <p>This release contains the analysis scripts used to reproduce all figures and metrics in:</p> <blockquote> <p><strong>CRISP enables comparisons of image-based spatial transcriptomic segmentation quality across ten organs</strong> Rose et al. (2026). <em>bioRxiv.</em> https://doi.org/10.64898/2026.04.16.718947</p> </blockquote> <h3>What's included</h3> <ul> <li><strong><code>clustering/</code></strong> — Orchestration and scoring pipeline (Seurat loading, QC, CRISP scoring, silhouette metrics) across 10 tissues × 6 segmentation algorithms</li> <li><strong><code>figures/</code></strong> — Figure generation scripts and Quarto documents for all main and supplementary figures</li> <li><strong><code>sensitivity/</code></strong> — Simulation-based validation and downsampling stability analyses</li> </ul> <h3>Figure coverage</h3> <p>| Figures | Script | |---|---| | Fig 2 | <code>sensitivity/01_threshold_sensitivity.R</code> | | Fig 3 | <code>sensitivity/04_marker_prevalence.R</code> | | Fig 4a,c,d; Fig 6; Fig 7; Supp 2-3 | <code>figures/combined_seg_metrics_vis_clean.qmd</code> | | Fig 4b | <code>figures/cell_area_histograms.R</code> | | Fig 5a-d | <code>figures/segmentation_comparison.qmd</code> | | Fig 5e; Supp 4 | <code>figures/seg_viz.qmd</code> |</p> <h3>Dependencies</h3> <p>R ≥ 4.5.0, Seurat ≥ 5.4.0, crispRSeg (<a href="https://github.com/santangelo-lab/CRISP">santangelo-lab/CRISP</a>), Quarto ≥ 1.4</p>