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. 2018 Jun 1;34(11):1966-1968.
doi: 10.1093/bioinformatics/bty030.

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

Kim Wong  1 , José Fernández Navarro  1 , Ludvig Bergenstråhle  1 , Patrik L Ståhl  1 , Joakim Lundeberg  1
Affiliations

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

Kim Wong et al. Bioinformatics. .

Abstract

Motiviation: Spatial Transcriptomics (ST) is a method which combines high resolution tissue imaging with high troughput transcriptome sequencing data. This data must be aligned with the images for correct visualization, a process that involves several manual steps.

Results: Here we present ST Spot Detector, a web tool that automates and facilitates this alignment through a user friendly interface.

Contact: jose.fernandez.navarro@scilifelab.se.

Supplementary information: Supplementary data are available at Bioinformatics online.

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