SpotSweeper

SpotSweeper provides spatially-aware quality control methods for identifying local outliers and regional artifacts in spot-based spatial transcriptomics such as 10x Visium.

Key Features:

• Spot-level QC: Calculates local nearest-neighbors mean and variance of standard QC metrics including library size, unique genes, and mitochondrial percentage to identify outlier spots relative to their local neighborhood.
• Artifact-level QC: Uses multiscale methods to detect large regional technical artifacts unique to spatially-resolved transcriptomics.
• Spatially-aware evaluation: Evaluates quality of individual spots relative to their local neighborhood to minimize bias due to biological heterogeneity.

Scientific Applications:

• Spatial transcriptomics quality control: Identifies systematically low quality Visium barcodes/spots that are confounded by spatial biology and inappropriate for snRNA-seq-derived QC approaches.
• Regional artifact detection: Accurately identifies distinct types of histological tissue artifacts unique to spatially-resolved transcriptomics.
• Downstream analysis improvement: Removal of low-quality spots and artifacts results in improved clustering and marker gene detection for spatial domains.

Methodology:

SpotSweeper calculates local nearest-neighbors mean and variance of standard QC metrics and uses multiscale methods to detect regional artifacts.