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A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data

View ORCID ProfileAlma Andersson, View ORCID ProfileŽaneta Andrusivová, View ORCID ProfilePaulo Czarnewski, Xiaofei Li, View ORCID ProfileErik Sundström, View ORCID ProfileJoakim Lundeberg
doi: https://doi.org/10.1101/2021.11.11.468178
Alma Andersson
1Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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Žaneta Andrusivová
1Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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Paulo Czarnewski
1Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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Xiaofei Li
2Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
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Erik Sundström
2Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
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Joakim Lundeberg
1Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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  • For correspondence: joakim.lundeberg@scilifelab.se
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1 Abstract

The increasing amount of spatial transcriptomics data prompts for means to amalgamate observations from distinct experiments, especially attractive is to cast quantities from different sources into a common coordinate frame-work (CCF) to relate signals across space. We here present a method that enables transfer of information from multiple samples to a reference representing a CCF, and show its utility by analyzing an assortment of real and synthetic data sets.

Competing Interest Statement

A.A., Z.A. and J.L. are scientific advisors for 10x Genomics Inc., providing spatially barcoded slides. The remaining authors declare no competing interests.

Footnotes

  • https://github.com/almaan/eggplant

  • https://doi.org/10.5281/zenodo.5659093

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 13, 2021.
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A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data
Alma Andersson, Žaneta Andrusivová, Paulo Czarnewski, Xiaofei Li, Erik Sundström, Joakim Lundeberg
bioRxiv 2021.11.11.468178; doi: https://doi.org/10.1101/2021.11.11.468178
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A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data
Alma Andersson, Žaneta Andrusivová, Paulo Czarnewski, Xiaofei Li, Erik Sundström, Joakim Lundeberg
bioRxiv 2021.11.11.468178; doi: https://doi.org/10.1101/2021.11.11.468178

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