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ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Royal Inst Technol KTH, Sch Biotechnol, Div Gene Technol, Sci Life Lab, SE-10691 Solna, Sweden..
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2018 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 11, p. 1966-1968Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2018. Vol. 34, no 11, p. 1966-1968
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Chemical Sciences
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URN: urn:nbn:se:kth:diva-230824DOI: 10.1093/bioinformatics/bty030ISI: 000434108800031PubMedID: 29360929Scopus ID: 2-s2.0-85048044897OAI: oai:DiVA.org:kth-230824DiVA, id: diva2:1220762
Note

QC 20180619

Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2018-06-19Bibliographically approved

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Navarro, Jose FernandezBergenstrahle, LudvigStahl, Patrik L.Lundeberg, Joakim
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Gene TechnologyScience for Life Laboratory, SciLifeLab
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