Spatial Informatics Hub
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.
Open-Source CosMx SMI Packages
This package offers superior accuracy and efficiency in cell typing for spatial single-cell transcriptomics that makes it an effective package to use with complex tissues.
InsituCor provides one answer to one of the biggest conundrums in CosMx analysis, “where do I look?”, by returning modules of spatially correlated genes.
AtoMx Custom Modules
The custom export modules are recommended if you wish to export data directly to your own AWS S3 bucket or if you wish to customize the export (e.g., edit the export script).
The CosMx SMI RNA QC Plot module reads in the output of the Quality Control (RNA) module from the AtoMx SIP cloud platform and creates flowcell-level summaries, including violin plots and a csv with the summarized QC data.
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.
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…
CosMx SMI Data Export
The CosMx DA Export module exports the TileDB array, Seurat object, and (optionally) raw, decoded files such as morphology images and per-FOV transcripts. Data is exported per-study.
The Flat File Export module exports flat files which are more readily used with open source tools utilizing functions like Seurat’s Load Nanostring. It does not include images, raw decoded data files, or data objects, and is intended to supplement the CosMx DA Export module. Data from a study is exported per flow cell.
DA Export Module
Resources: Vignette | Setup Instructions
Flat File Export Module
Resources: Vignette | Setup Instructions
AtoMx RNA QC Plot Custom Module
The CosMx SMI RNA QC Plot module reads in the output of the Quality Control (RNA) module from the AtoMx SIP cloud platform and creates flowcell-level summaries, including violin plots and a csv with the summarized QC data. To access the QC plots and results csv file, click the image icon on the successfully executed RNA QC Plot module in the Pipeline Structure panel.
Download
Resources: Setup Instructions
CosMx SMI InsituCor
One of the biggest conundrums in CosMx analysis is, “where do I look?” InsituCor provides one answer to this question, returning modules of spatially correlated genes. When genes are correlated across the space of a tissue, it suggests they regulate each other, or are jointly regulated by some underlying factor. We find that modules output by InsituCor are enriched for interesting biology worthy of precious human attention.
Download
Resources: Vignette Preprint Manuscript
Poster
Learn how the InSituCor algorithm discards trivial correlations, exposing gene sets worth attention, in the AACR 2024 poster, “InSituCor: Uncovering gene co-regulation networks in spatial transcriptomics data”
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
Resources: Vignette Preprint Manuscript