Bin2cell reconstructs cells from high resolution Visium HD data
Preprint
Abstract
Summary: Visium HD by 10X Genomics is the first commercially available platform capable of capturing full scale transcriptomic data paired with a reference morphology image from archived FFPE blocks at sub-cellular resolution. However, aggregation of capture regions to single cells poses challenges. Bin2cell reconstructs cells from the highest resolution data (2 μ m bins) by leveraging morphology image segmentation and gene expression information. It is compatible with established Python single cell and spatial transcriptomics software, and operates efficiently in a matter of minutes without requiring a GPU. We demonstrate improvements in downstream analysis when using the reconstructed cells over default 8 μ m bins on mouse brain and human colorectal cancer data. Availability and Implementation: Bin2cell is available at https://github.com/Teichlab/bin2cell , along with documentation and usage examples, and can be installed from pip. Probe design functionality is available at https://github.com/Teichlab/gene2probe Contact: ny1@sanger.ac.uk , st9@sanger.ac.uk Supplementary information: Supplementary data are available online.Keywords
All Related Versions
- Published version: Bioinformatics, 40 (9).
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