Spatialomics

Overview

The Lunaphore COMET platform is an advanced, fully automated system that integrates liquid handling with high-resolution microscope imaging for sequential, multiplex immunofluorescence staining. Designed for use with standard glass slides and off-the-shelf antibodies, the COMET enables up to 20 distinct staining conditions in a single run, including mono-stains and dual-plexes. Its microfluidic technology ensures minimal reagent use and optimized biochemistry. With a four-slide capacity, the system can achieve up to 40-plex imaging per cycle. Post-run, slides remain compatible for further COMET processing or downstream applications like H&E, sequencing, or in situ hybridization, due to its gentle elution buffer and low-temperature protocol.

Key Features:

• Adaptable panel development using unlabeled antibodies: Researchers can leverage readily available, off-the-shelf primary antibodies without the need for conjugation or barcording, enabling rapid assay setup and flexibility in experimental design.
• Advanced multiplexing: The COMET system enables highly multiplexed spatial analysis, allowing for the simultaneous detection of up to 40 distinct markers on a single tissue slide in ony fully automated run.
• Multiplex staining enables the creation of cell-by-cell map to decipher complext interactions: The detection and quantification of multiple proteins allows researchers to study not only morphological changes due to pathological or therapeutic conditions, but also to characterize phenotypes at single cell level, and examine cell distance as well as measure cell density in a specific area.
• Streamline imaging and analysis: The COMET combines an automated scanner with a high-resolution microscope to deliver subscellular detail. It outputs data in OME-TIFF format that is compatible with leading spatial biology analysis platforms like HORIZON, QuPath, and HALO.

To support the launch of the Lunaphore COMET spatialomic platform at the University of Minnesota, Bio-Techne and supporting R&D Systems are partnering with the University Imaging Centers (UIC) to provide researchers with access to antibodies at no cost to use in their experiments on the COMET.

This promotion is offered to researchers conducting experiments on the Lunaphore COMET system, and will remain available until credit funds are exhausted, or until the end of March 2026.

This is a unique opportunity to try out the new COMET platform without additional antibody costs.

Program Details:

• Antibodies must be requested by researchers ready to start their COMET projects; requests for future or potential studies will not be approved.
• Researchers may request up to $1,000 in antibody support for active COMET experiments. Based on the selected antibodies, this amount will typically cover the cost of antibodies for lower-plex studies involving approximately 1–5 markers.
• Supported antibodies must be selected from the approved inventory list designated for the credit program.
• The UIC will procure the antibodies requested through this program. Any leftover antibodies acquired through this program will be retained by the UIC and made available to all COMET user projects at no additional cost, while supplies last.
• Researchers are responsible for all other applicable COMET spatialomic service costs.

Antibodies:

• COMET validated mIF Antibodies from R&D Systems and Novus Biologicals
• Bio-Techne validated immunofluorescence antibodies

Ready to start your COMET project? 
Get started by submitting a project intake form on the UMN Spatial Initiative website. After receiving your request, a member of the UIC Spatialomics team will reach out to schedule a time to discuss your project.

Lunaphore COMET rates can be found on our rates page.

Given the considerable variability in experimental parameters and their influence on overall project costs, UIC staff and vendor representatives will work closely with you to determine the final pricing.

The  following files are delivered when your project is completed:

• Run report PDFs: documentation of the imaging and cycling parameters used to generate each imaging dataset.
• OME-TIFF images: stitched multi-channel images containing all captured image layers for a slide, including protein/nuclear stains, autofluorescence, post-elution signal, and negative controls. A single OME-TIFF image is generated for each capture area, regardless of its size (5.6 x 5.6 mm, 9.0 x 9.0 mm, or 12.5 x 12.5 mm) and the number of imaging cycles. Images may be opened and processed with HORIZON and/or other OME-compatible software.
• Run reports and OME-TIFF files may be provided for each protocol run in a project irrespective of the protocol type – titration, positioning, seqIF, etc.

UMN users: deliverables are copied to your group’s data_delivery folder on the MSI Tier1 file system

Non-UMN users: The UIC offers external data delivery options through Globus, Box Secure Storage, and physical drives. Alternative delivery mechanisms can be discussed during project intake

For more information on data transfer methods and delivery, visit our Data Transfer & Resources page.

Overview

Bruker's GeoMx Digital Spatial Profiler (DSP) combines standard immunofluorescence techniques with digital optical barcoding technology to perform highly multiplexed, spatially resolved profiling experiments. In a single reaction, the DSP technology performs whole slide imaging with up to four fluorescent stains to capture tissue morphology and select regions of interest for high plex profiling. The DSP chemistry enables spatially resolved high plex profiling of RNA and protein targets on just two serial sample sections, with no-destructive tissue processing.

• Minimum sample: protein or RNA analysis from formalin-fixed paraffin-embedded (FFPE) or fresh-frozen section

• Morphological context: whole-slide 4 color imaging to guide profiling

• Digital quantitation: up to 6 logs (base 10) dynamic range

• Preserve precious samples with non-destructive processing

The GeoMx DSP is designed to fit into a range of research and plex needs, including applications in oncology, immunology, neuroscience, and developmental biology. For more information on available RNA and protein assays, as well as the Whole Transcriptome Atlas, visit Bruker's website. 

Key Features

• Quickly resolve tissue heterogeneity and the complexity of microenvironments: The GeoMx Digital Spatial Profiler (DSP) is a highly flexible and robust spatial multiomic platform for analysis of FFPE and fresh frozen tissue sections. GeoMx is the only spatial biology platform that non-destructively profiles expression of RNA and protein from distinct tissue compartments and cell populations with an automated and scalable workflow that integrates with standard histology staining.
• GeoMx RNA assays allow you to profile the whole transcriptome: GeoMx RNA Assays are pre-validated and modular to provide flexibility and support a range of research needs. Available content covers immunology, immuno-oncology, neurodegeneration, and neuroinflammation with a rapidly growing pipeline.
• High-plex Spatial Proteomics: GeoMx Protein Assays enable quantitative, spatial analysis of up to 570+ proteins, vastly expanding the number of markers you can profile from a single tissue section compared to traditional immunohistochemical methods. All assays are validated for use in multiplex.
• Stain whole slides with assay probes and up to four fluorescent markers and then image them on the instrument: Choose which regions to profile and segment each region using qualified and verified morphology markers, decide which regions of the tissue you want to profile, and using masking, optionally profile two or more tissue compartments or cell types in each region. Quantify RNA and protein expression levels with direct, digital counting of barcodes using the UMGC nCounter or Illumina sequencing platforms.

Project costs for GeoMx DSP include services from multiple core facilities. Each core will provide an independent estimate and invoice for their portion of the service. The UIC and UMGC provide general pricing information on their websites. 

• UIC Rates
• UMGC GeoMx DSP pricing
• CTSI Histology Services

Given the considerable variability in experimental parameters and their influence on overall project costs, core staff and vendor representatives will work closely with you to determine the final pricing.

The following files are delivered when your project is completed:

• Fastq files - some data repositories require uploading the fastq files for GeoMx projects, so be sure to download a copy when they are made available to you
• DCC count zip file
• LabWorksheet.txt and Config.ini
• ROI Report image export - A zip file for each slide containing a separate image of every ROI and every segment within that ROI, as well as an HTML summary of those images and a rendered scan image (full-color publication-quality image)
• Geomxqc.html summary report

GeoMx project data will be maintained on the GeoMx instrument for 1 year, after which it may be archived. Be sure to download all experimental data and securely store it on a local filesystem.

UMN users: deliverables are copied to your group's data_delivery folder on the MSI Tier1 file system

Non-UMN users: a delivery email will provide instructions for downloading the deliverables from our download website

For more information on data transfer methods and delivery, visit our Data Transfer & Resources page.

Overview

The CosMx Spatial Molecular Imager (SMI) is a high-plex in situ analysis platform providing spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes.

CosMx Spatial Molecular Imager is a robust spatial single-cell imaging platform for:

• Minimum sample: protein or RNA analysis from formalin-fixed paraffin-embedded (FFPE) or fresh-frozen section
• Defining cell types, cell states, tissue microenvironment phenotypes, and gene expression networks
• Understanding biological process controlled by ligand-receptor interactions
• Quantifying change in gene expression based on treatment and identify single-cell subcellular biomarkers
• Preserve precious samples with non-destructive processing

The CosMx SMI is designed to fit into a range of research and plex needs, including applications in oncology, neuroscience, infectious disease, immunology, and developmental biology. For more information on available RNA and protein assays, as well as available panels, visit Bruker's website. 

Key Features

• Multi-modal cell segmentation process provides accurate cell boundaries detection: CosMx cell segmentation uses cell membrane and morphology marker protein images, machine-learning augmented cell segmentation algorithm and transcript-based segmentation refinement to achieve precise single-cell segmentation in morphologically intact tissue.
• High-Plex Single-Cell Spatial: RNA assays enable high-plex analysis of up to 6000 genes at cellular and sub-cellular levels. RNA assays are designed to provide robust cell typing, cell-cell interaction analysis, and more in a wide range of human and mouse tissues and disease states. Assays are designed to provide a wealth of genomic breadth with ultra-high-plex RNA panels that can provide high numbers of genes detected per sample. Profile expression of highly curated targets at subcellular resolution and customize some assays with your own targets. Panels: Human Whole Transcriptome, Human 6K Discovery, Universal Cell Characterization, Mouse Neuroscience, Human Immuno-Oncology.
• High Resolution Spatial Proteomic Analysis: Protein assays enable high-plex analysis of up to 64 proteins with spatial context at single-cell resolution. Protein assays provide unbiased spatial proteomic analysis of tissue sections to expand the number of markers you can profile compared to traditional immunohistochemical and immunofluorescent methods. All protein assays are validated for use in multiplex. Panels: Mouse Neuroscience, Human Immuno-Oncology.
• Analyze and visualize CosMx spatial data with flexibility:  From AtoMx, the UIC exports CosMx data (counts matrices, cell metadata, decoded transcript information, and image files) in formats readable by a variety of open-source tools, allowing researchers to develop fully custom analysis pipelines using their own preferred workflows. CosMx target decoding and segmentation are completed in the AtoMx Spatial Informatics Platform. Here, researchers can visualize spatial data using image overlays of morphology markers, decoded transcripts, and segmentation masks.

CosMx SMI rates can be found on our rates page.

Given the considerable variability in experimental parameters and their influence on overall project costs, UIC staff and vendor representatives will work closely with you to determine the final pricing.

The following files are delivered when your project is completed:

Flat CSV files:

• Counts matrix (exprMat_file.csv.gz): matrix of target counts per cell (RNA) or target mean fluorescence intensity per cell (Protein)
• Cell metadata (metadata_file.csv.gz): various information associated with the CosMx run, which may include cell locations, cell areas / aspect ratios, marker intensity, etc.
• Transcripts (tx_file.csv.gz): tabulated transcript information, including local and global transcript pixel location, decoded target, compartment, and cell/FOV of origin. Large data. RNA assays only.
• Polygons (polygons.csv.gz): local and global coordinates of polygons outlining
• FOV positions (fov_positions_file.csv.gz): coordinates (in pixels and mm) of FOV centers.

Seurat Objects (Large Data)

• RDS file: file format readable by the Seurat package or other R-based open-source tools.
  • The provided Seurat object, by default, does not include transcript coordinates or polygon coordinates (large data). This information can be wrapped into the Seurat object on request.

FOV Image files

• Cell Labels TIFF: image indicating cell assignments of each pixel.
• Compartment Labels TIFF: image indicating compartment assignment (nucleus, cytoplasm) of each pixel.
• Cell Overlays JPG: image of segmentation outline overlays on DAPI nuclear stain.
• 2D Morphology TIFF: 5-channel raw images of FOV morphology stains.
• A python script and instructions will be provided that use the 2DMorphology TIFFs to create a composite image.

UMN users: deliverables are copied to your group's data_delivery folder on the MSI Tier1 file system

Non-UMN users: The UIC offers external data delivery options through Globus, Box Secure Storage, and physical drives. Alternative delivery mechanisms can be discussed during project intake

For more information on data transfer methods and delivery, visit our Data Transfer & Resources page.