Speakers
Description
The Spatial Transcriptomics as Images Project (STIM) is a framework for storing, interactively viewing & 3D-aligning, as well as rendering sequence-based spatial transcriptomics data (e.g. Slide-Seq), which builds on the powerful libraries Imglib2, N5, BigDataViewer and Fiji (https://github.com/PreibischLab/STIM). In contrast to the ""classical"" sequence analysis space, STIM relies on scalable, tried-and-tested image processing solutions to work with spatial sequencing data by treating the data as an image consisting of irregularly-spaced, high-dimensional (each gene is treated as a channel) pixels/measurements.
In the workshop we will teach how to import, view, align the data using command line tools and Fiji as well as interactive tools that build on BigDataViewer. We will start with a small toy dataset and show how to work with larger data.
| Target audience | Intermediate users, Advanced users |
|---|---|
| Keywords | spatial transcriptomics, registration, rendering, BigDataViewer, ImgLib2, Fiji |
