What is SSAM-lite?

SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. It provides the functionality of SSAMs most popular and widely used features in a graphical user interface with a few functions added for convenience and ease of use. It neither requires specialised computational experts nor hardware to handle and process data and thus can be run on a modest laptop.

The SSAM framework allows for cell segmentation-free identification of cell-types by integrating prior knowledge of cell type-specific gene signatures with data from a variety of spatial in situ transcriptomics techniques.

Citations

Sebastian Tiesmeyer, Shashwat Sahay, Niklas Müller-Bötticher, Roland Eils, Sebastian D. Mackowiak, Naveed Ishaque. 2021. “SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data” Frontiers Genetics. doi: 10.3389/fgene.2022.785877 bioRxiv. doi: 10.1101/2021.09.29.462194

Contents:

• What is SSAM-lite?
• quickstart / tl;dr
  • Test data
  • Open SSAM-lite
  • My first analysis
• Installation
  • Requirements
  • SSAM-lite
  • SSAM-lite-server
• Usage
  • Test Data
  • Open SSAM-lite
  • Navigation
  • Data
  • Parameters
  • Analysis
  • Save results
• Local or Server?
  • SSAM-lite (local)
  • SSAM-lite-server