Spatialomics
UMN Spatialomics Initiative
The University of Minnesota Spatialomics Initiative is a coordinated effort that aims to accelerate spatialomic research at the UMN by bringing together all of the relevant technical expertise in a single virtual location. The collection of resources on this site was established to help researchers probe spatial interactions at the level of genomics and proteomics.
For more information about all of the available spatialomic resources at the University of Minnesota, or to submit a project request, visit the UMN Spatialomics Initiative.
Spatialomic Technologies
GeoMx Digital Spatial Profiler
Technology 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.
Workflow
The GeoMx DSP Service is supported by the collaborative efforts of three core facilities at the University of Minnesota: UIC, CTSI Histology, and the UMGC.
- The Clinical and Translation Science Institute (CTSI) histology team provides optional assistance with tissue sectioning and mounting of FFPE or fresh frozen tissue.
- University Imaging Center (UIC) stains tissue slides with pre-mixed biological probes and fluorescently-labeled markers, works with investigators on ROI selection, and uses UV exposure to release DSP barcode tags from ROI. The UIC also provides consultation on the GeoMX DSP technology and assists with experimental design.
- UMN Genomics Center (UMGC) quantifies released tags on the nCounter or on an Illumina next-generation sequencer and counts are mapped back to tissue location to yield a digital profile.
The UIC and UMGC are neighboring facilities located at 1-220 and 1-210 Cancer & Cardiovascular Research Building (CCRB).
Pricing
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.
Data Delivery
More information on GeoMx DSP data delivery can be found on the UMGC's GeoMx DSP webpage under "Guidelines".
CosMx Spatial Molecular Imager
Technology 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.
Pricing
UIC CosMx SMI rates can be found on our rates page under the Spatialomic Services category.
Data Delivery
The UIC has three options for transferring data from the UIC to clients: 1) delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, 2) download with Globus or Box Secure Storage, or 3) shipment on an external hard drive. Data delivery will be discussed during the experimental design part of the project workflow.
1. MSI storage
UMN researchers will have their data delivered in the "data_delivery" folder in your group's folder on MSI's primary filesystem (home/GROUP/data_delivery/uic/cosmx_smi).
2. Globus and Box Secure Storage
Internal and External clients can use Globus or Box Secure Storage to download their data. These are the recommended method for external clients to download large datasets.
3. Hard drive
Clients may provide a hard drive to the UIC.
MIBI announcement 2/19/2025
On Friday February 14, 2025 we were notified by Ionpath that they have reached the end of their journey and the company would be closing effective immediately. While IonPath regrets they cannot continue to support any service or support efforts it has left us in a difficult situation. The bottom line is the UIC will be discontinuing to offer IonPath MIBI services. We are exploring options globally to complete ongoing projects.
What this means for you as a UIC IonPath MIBI customer:
- IonPath has announced that MIBItracker software will no longer be available after February 28, so all data should be downloaded and stored offline as soon as possible to prevent the potential loss of data. We are making efforts to back-up data, but each MIBI user should maintain their own copy.
- All current UIC MIBI projects will be completed.To our customers: we regret that we cannot continue to support your work. This happened with such suddenness that we had no time to communicate or prepare. We are working with third parties as we make every attempt to find you hardware and software support.
- Before February 28th, any currently planned MIBI projects with reagents on site can be run as long as the instrument and software remains operational. Effective immediately, no new MIBI projects will be accepted.
- The UIC does have other protein level spatialomic solutions (Bruker GeoMx and CosMx) in place and additional spatial approaches in the planning stages. We are happy to discuss options.
If you have any questions, please contact us at [email protected].
MIBIscope
Technology Overview
The MIBIscope System is a revolutionary imaging platform, enabling comprehensive phenotypic profiling and spatial analysis of the tissue microenvironment. The MIBIscope allows researchers to visualize over 40 markers simultaneously with higher sensitivity, resolution, and throughput than existing methods.
MIBI Technology is based on secondary ion mass spectrometry or SIMS. With SIMS, a primary ion beam is rastered across the surface of a sample, liberating reporter ions that are then simultaneously recorded on a pixel-by-pixel basis by Time-of-Flight detection. An ion beam, unlike a laser, enables resolution to be tuned over a broad range—in the case of the MIBIScope, from a few hundred nanometers to 1 micron. Once liberated, the reporter ions, or “secondary ions,” travel uninterrupted at supersonic speed from the sample to the detector, leading to fast acquisition and extraordinary sensitivity.