# CosMx Spatial Molecular Imager

> **NIH NIH S10** · NORTHWESTERN UNIVERSITY · 2023 · $295,565

## Abstract

PROJECT SUMMARY
The CosMx Spatial Molecular Imaging Platform (CosMxTM SMI, NanoString, Seattle, WA) will allow a well-
funded group of biomedical scientists experienced in the application of single cell transcriptomic approaches
to human disease to perform combined spatial transcriptomics and proteomics at a cellular and subcellular
resolution using tissue samples collected at Northwestern University (NU) and within the greater Chicago
area. This is an integrated system with mature cyclic in situ hybridization chemistry, an ultra-high-resolution
imaging readout, and interactive data analysis and visualization software. The CosMx™ SMI platform
enables the simultaneous quantification and visualization of up to 1,000 RNA and 100 validated protein
analytes, allowing cell typing and discovery, neighborhood clustering, phenotyping of the tissue
microenvironment and differential expression analysis of cell types and subsets based on spatial location.
This disruptive technology will be applied to freshly isolated or paraffin-embedded-and-stored tissues
collected as part of clinical care or after causal genetic and pharmacologic interventions in murine models
of lung disease. In addition to their fundamental mechanistic work in cell and animal models of disease, the
Major Users in this application have pioneered the application of single cell RNA-sequencing approaches to
human disease, generating among the largest extant collaborative molecular atlases of human lung disease.
They will leverage this knowledge to optimize sample selection, probe design, and morphologic
measurements that will maximize the yield from the combined transcriptomic/proteomic and
spatial/morphological features of disease uniquely generated by the CosMx™ SMI platform. The machine
learning approaches they have developed to integrate single cell transcriptomic data from tens of
laboratories across hundreds of individuals and millions of cells will be foundational to analyzing data from
the The CosMx™ SMI platform and integrating them within this larger body of work. Thus, by providing this
instrument to these users, this Shared Instrument Proposal will accelerate the application of spatial
transcriptomics and proteomics to the study of human disease through innovations in clinical phenotyping,
sample collection and processing, imaging and cell biology, data science and a commitment to open access
data sharing. The CosMxTM SMI will be managed by the Metabolomics Developing Core Facility/Integrative
Genomics (MCF-IG) at Robert H. Lurie Cancer Center (RHLCCC) at NU, which supports all major and minor
users with LCMS based metabolomics and high throughput integrative genomics to enable integrated
analysis of genes and pathways through which metabolism contributes to disease. The core facility
physically resides within space provided by the Division of Pulmonary and Critical Care in the Department
of Medicine.

## Key facts

- **NIH application ID:** 10632423
- **Project number:** 1S10OD034357-01
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** Hiam Abdala-Valencia
- **Activity code:** S10 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $295,565
- **Award type:** 1
- **Project period:** 2023-05-01 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10632423

## Citation

> US National Institutes of Health, RePORTER application 10632423, CosMx Spatial Molecular Imager (1S10OD034357-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10632423. Licensed CC0.

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