Article

SPARKLE: evidence-constrained correction of local RNA leakage in high-resolution spatial transcriptomics

2026-08-17

Abstract excerpt

High-resolution sequencing-based spatial transcriptomics, including Stereo-seq and Visium HD, aggregates dense capture units into cell-resolved expression matrices. During tissue processing and permeabilization, RNA released from source cells can spread to neighbouring capture locations, reducing cell-type specificity and biasing downstream analyses. Here we developed SPARKLE (Spatial Ambient RNA Kernel-based Leak...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: e91e4265-35eb-5812-8f29-38eb0d3929a2
DOI: 10.64898/2026.08.12.744394

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

SPARKLE: evidence-constrained correction of local RNA leakage in high-resolution spatial transcriptomicsDOI 10.64898/2026.08.12.744394Read

Validation of Morphology-Guided Computational Enhancement for Single-Cell Resolution Spatial TranscriptomicsSemantic proximity Read

STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial TranscriptomicsSemantic proximity Read

Exploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organizationSemantic proximity Read

SPOTlight: Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with Single-Cell TranscriptomesSemantic proximity Read

Mitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDeconSemantic proximity Read

Φ-Space ST: a platform-agnostic method to identify cell states in spatial transcriptomics studiesSemantic proximity Read

OmniCell: Unified Foundation Modelling of Single-Cell and Spatial Transcriptomics for Cellular and Molecular InsightsSemantic proximity Read

FlashDeconv reveals resolution horizons in atlas-scale spatial transcriptomicsSemantic proximity Read

Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics dataSemantic proximity Read

SNMF: Ultrafast, Spatially-Aware Deconvolution for Spatial TranscriptomicsSemantic proximity Read

Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics PlatformsSemantic proximity Read

Benchmarking ambient RNA removal across droplet and well-plate platforms reveals artificial count generation as a critical failure mode of scAR and CellClearSemantic proximity Read