Spatial Informatics Hub

Extract valuable insights from your spatial data

Spatial Biology Informatics play a crucial role in advancing our understanding of data from spatial biology platforms.

By developing the computational tools, we are able to extract valuable insights from the wealth of spatially resolved biological data generated by modern technologies. ​

Our experts in Spatial Informatics here at NanoString have designed and implemented methodologies that can handle the unique challenges posed by spatial data, such as the need to account for tissue heterogeneity, spatial interactions, cell typing, and accurate localization of biological molecules. These methods enable scientists like yourself to uncover spatial patterns, identify novel cell types and functionalities, discover molecular interactions, and gain a deeper understanding of how biology functions within its spatial context. Welcome to the Spatial Informatics Hub: home of all things Spatial Informatics.​

Open-Source Tools for Spatial Biology

Open-source software tools play a vital role in advancing biological discovery by providing researchers with access to the latest technologies (or “latest from NSTG”) at NanoString by promoting collaboration & transparency, improving reproducibility, and encouraging innovation. By making open-source packages freely available to all researchers, we make sure everyone has access to the latest tools and technologies to carry out research. We’re dedicated to help accelerate our researchers time to discovery​.

The latest open-source packages for CosMx™ SMI and GeoMx® DSP are featured here, with even more available on GeoScript Hub for GeoMx DSP data analysis. Explore the packages below to see our latest releases.​

Featured CosMx Packages
Featured GeoMx Packages
Prebuilt Solutions

Open-Source CosMx SMI Packages

This module offers superior accuracy and efficiency in cell typing for spatial single-cell transcriptomics that makes it an effective package to use with complex tissues.

The CosMx SMI data export module copies data from the AtoMx SIP cloud platform to a user-specified AWS S3 bucket. From there, users can further move or manage their data. Files that can be exported include Seurat data object, TileDB arrays, and raw files. ​

This export module generates the five flat files needed to follow the Seurat data analysis vignette. These files are saved to a user-specified AWS S3 bucket. The flat files include count matrix, cell metadata, transcript coordinates, cell polygons, and FOV positions. These files can be downloaded separately.

Open-Source GeoMx Packages

This package overlays gene counts, segment annotations, pathway scores, cell type proportions, among other annotations on GeoMx images.

The Labeled Volcano Plot DSP DA script creates publication-ready labeled volcano plots based on the
researchers’ input and statistical study results. The script also creates a table of tagged genes.

v1.3 updated October 2022 This script was designed for data from GeoMx high-plex RNA assays, such as the Cancer Transcriptome Atlas and Whole Transcriptome Atlas.

This script was designed for data from GeoMx DSP NGS assays (Whole Transcriptome Atlas or Cancer Transcriptome Atlas) with TCR Profiling Add-on.

More on the GeoScript Hub »

Prebuilt Solutions

Prebuilt Informatics Solutions

Designed with researchers of all backgrounds in mind, we’ve built AtoMx™ SIP to simplify spatial bioinformatics and data management to allow data analysis and visualization anytime, anywhere. ​

AtoMx SIP is a no-code informatics solution that allows researchers to analyze spatial multiomics data with NanoString developed best in class analysis modules and provides the flexibility to allow researchers with computational backgrounds to create custom analysis pipelines and scripts. Let us simplify your spatial informatics and data infrastructure so that you can focus on your research.​

For current GeoMx DSP users who prefer to analyze their GeoMx DSP data on-instrument, DSPDA (DSP Data Analysis Suite), offers researchers the ability to use pre​…

Learn About AtoMx Learn about GeoMx Analysis

CosMx SMI Data Export

The CosMx SMI data export module copies data from the AtoMx SIP cloud platform to a user-specified AWS S3 bucket. From there, users can further move or manage their data. Files that can be exported include Seurat data object, TileDB arrays, and raw files. ​

Download

CosMx SMI Flat File Export

The CosMx SMI flat file export module generates the five flat files needed to follow the Seurat data analysis vignette. These files are saved to a user-specified AWS S3 bucket. The flat files include count matrix, cell metadata, transcript coordinates, cell polygons, and FOV positions. These files can be downloaded separately. ​

CosMx SMI InsituType

This module offers superior accuracy and efficiency in cell typing for spatial single-cell transcriptomics that makes it an effective package to use with complex tissues. ​

Download
Download