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

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Gene Expression Profiling / methods*
  • Humans
  • Image Interpretation, Computer-Assisted / methods*
  • Internet
  • Plants
  • Sequence Analysis, RNA / methods
  • Software*
  • Spatial Analysis