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bioRxiv · 10.1101/2024.06.19.599766

Bin2cell reconstructs cells from high resolution Visium HD data

Polanski, K.·Bartolome-Casado, R.·Sarropoulos, I.·Xu, C.·England, N.·Jahnsen, F. L.·Teichmann, S. A.·Yayon, N.
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Abstract

SummaryVisium 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 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 m bins on mouse brain and human colorectal cancer data. Availability and ImplementationBin2cell 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 Contactny1@sanger.ac.uk, st9@sanger.ac.uk Supplementary informationSupplementary data are available online.

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Polanski, K., Bartolome-Casado, R., Sarropoulos, I., Xu, C., England, N., Jahnsen, F. L., Teichmann, S. A., Yayon, N.. 2024-06-22. Bin2cell reconstructs cells from high resolution Visium HD data. https://doi.org/10.1101/2024.06.19.599766

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