TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data

Abstract

Abstract Motivation Visual assessment of scanned tissue samples and associated molecular markers, such as gene expression, requires easy interactive inspection at multiple resolutions. This requires smart handling of image pyramids and efficient distribution of different types of data across several levels of detail. Results We present TissUUmaps, enabling fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used both as a web service or locally in any computer, and regions of interest as well as local statistics can be extracted and shared among users. Availability and implementation TissUUmaps is available on github at github.com/wahlby-lab/TissUUmaps. Several demos and video tutorials are available at http://tissuumaps.research.it.uu.se/howto.html. Supplementary information Supplementary data are available at Bioinformatics online.