embryos  (Jackson Laboratory)

Journal: Nucleic Acids Research

Article Title: Benchmarking sketching methods on spatial transcriptomics data

doi: 10.1093/nar/gkag434

Figure Lengend Snippet: Overall sketching performance for 0.10 sampling fraction across datasets. ( A ) Spatial scatter plots of real datasets colored by cell type or cluster label. ( B ) Heatmap of rank-sums for each method aggregated by metric across all real world datasets. Low rank indicates best performance for that metric. ( C ) Spatial scatter plots of simulated Visium HD-like and Xenium like datasets. ( D ) Heatmap of rank-sums for each method aggregated by metric across all simulated datasets. Low rank indicates best performance for that metric.

Article Snippet: Mouse embryo: We downloaded the whole mouse embryo Visium HD dataset from the publicly available datasets on the 10x website https://www.10xgenomics.com/datasets/visium-hd-three-prime-mouse-embryo-fresh-frozen (last accessed date: 12 February 2025).

Techniques: Sampling

Journal: Nucleic Acids Research

Article Title: Benchmarking sketching methods on spatial transcriptomics data

doi: 10.1093/nar/gkag434

Figure Lengend Snippet: Retained cell type/cluster label proportions at 0.10 sketching fraction for ( A ) Merfish mouse ovary; ( B ) Merfish sagittal mouse brain; ( C ) Xenium human breast cancer; ( D ) Xenium human lung; ( E ) Xenium whole mouse pup; ( F ) Visium HD coronal mouse brain; ( G ) Visium HD mouse embryo; ( H ) Visium HD ovarian cancer.

Article Snippet: Mouse embryo: We downloaded the whole mouse embryo Visium HD dataset from the publicly available datasets on the 10x website https://www.10xgenomics.com/datasets/visium-hd-three-prime-mouse-embryo-fresh-frozen (last accessed date: 12 February 2025).

Techniques:

Journal: Nucleic Acids Research

Article Title: Benchmarking sketching methods on spatial transcriptomics data

doi: 10.1093/nar/gkag434

Figure Lengend Snippet: Quantification of transcriptomic and coordinate Hausdorff distance at 0.10 sampling fraction for real datasets. ( A ) Quantification of imaging based (Merfish, Xenium) dataset’s Hausdorff distances. ( B ) Quntification of sequencing/spot based (Visium HD) dataset’s Hausdorff distances. Each boxplot represents one sketching method, with individual points corresponding to results from 10 independent runs with different random seeds.

Article Snippet: Mouse embryo: We downloaded the whole mouse embryo Visium HD dataset from the publicly available datasets on the 10x website https://www.10xgenomics.com/datasets/visium-hd-three-prime-mouse-embryo-fresh-frozen (last accessed date: 12 February 2025).

Techniques: Sampling, Imaging, Sequencing