PT  - JOURNAL ARTICLE
AU  - Giovanni Palla
AU  - Hannah Spitzer
AU  - Michal Klein
AU  - David Fischer
AU  - Anna Christina Schaar
AU  - Louis Benedikt Kuemmerle
AU  - Sergei Rybakov
AU  - Ignacio L. Ibarra
AU  - Olle Holmberg
AU  - Isaac Virshup
AU  - Mohammad Lotfollahi
AU  - Sabrina Richter
AU  - Fabian J. Theis
TI  - Squidpy: a scalable framework for spatial single cell analysis
AID  - 10.1101/2021.02.19.431994
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.02.19.431994
4099  - http://biorxiv.org/content/early/2021/04/29/2021.02.19.431994.short
4100  - http://biorxiv.org/content/early/2021/04/29/2021.02.19.431994.full
AB  - Spatial omics data are advancing the study of tissue organization and cellular communication at an unprecedented scale. Here, we present Squidpy, a Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins. Squidpy provides both infrastructure and numerous analysis methods that allow to efficiently store, manipulate and interactively visualize spatial omics data.Competing Interest StatementF.J.T. reports receiving consulting fees from Roche Diagnostics GmbH and Cellarity Inc., and ownership interest in Cellarity, Inc. and Dermagnostix