Spatial Biology
Spatial Biology: Mapping Life in Its Context
Spatial proteomics is revolutionizing biomedical research by providing unprecedented insights into how proteins are organized and function within their native tissue environment. Recognized as Nature Methods' 2024 Method of the Year, spatial proteomics combines high-resolution imaging with molecular profiling to reveal where proteins are located in tissues and how they contribute to health and disease. This spatially resolved protein information is crucial for understanding complex biological processes such as cancer development, immune responses, and tissue organization ultimately advancing the discovery of more precise therapies.
Biological function is fundamentally spatial from the organization of molecules within single cells to the structural complexity of entire tissues and organs. Understanding these spatial relationships is key to advancing research in fields like oncology, immunology, and neuroscience. Spatial biology bridges molecular profiling with imaging technologies to map cellular and molecular interactions within intact tissues, offering a deeper understanding of disease mechanisms and tissue function. While conventional methods like RNA sequencing or mass spectrometry provide valuable information on gene or protein expression, they often lack spatial context. Microscopy closes this gap, enabling high-resolution, single-cell analysis directly within tissue samples. Recent advances in light microscopy particularly multiplexed imaging, now allow simultaneous visualization of dozens of biomarkers, transforming how we explore biological complexity. At the Center for Microscopy and Image Analysis (ZMB) of the University of Zurich, we provide access to advanced imaging platforms and the expertise required to support your spatial biology and spatial proteomics research. Our services cover the full workflow from experimental design and sample preparation to imaging, image processing, and data analysis. We also collaborate closely with other technology platforms likeFunctional Genomics Center Zurich at UZH to ensure you find the most suitable tools for your specific spatial omics project. As spatial biology and proteomics continue to evolve, integrating high-end imaging with molecular technologies will be essential to unraveling the complexity of biological systems. Our facility is here to support you at every stage of your project, helping you advance your research and translate spatial insights into biological understanding.
Available instruments
Currently we offer different instruments that are suitable for Spatial biology / Multiplexing workflows:
| Instrument | Omics type | Number of targets | Spatial resolution |
| Lunaphore COMET | Proteomics: SeqIF™ Transcriptomics: RNAscope™ |
20-40 + codetection 9-12 RNA | 2D, cellular |
| ZEISS LSM 980 Airyscan2 + Automated Perfusion System | Proteomics: IBEX, CODEX, 4i |
10-60 (depending on protocol used) | 3D, subcellular |
| ZEISS ELYRA 7 + Automated Perfusion System | Proteomics: IBEX, CODEX, 4i |
10-60 (depending on protocol used) | 3D, super-resolution |
Spinning Disk Nikon CrestOptics X-Light V3 + Automated Perfusion System |
Proteomics: IBEX, CODEX, 4i |
10-60 (depending on protocol used) | 3D, subcellular |
| Leica Stellaris SpectraPlex | Proteomics: SpectraPlex™ |
8-15+ | 3D, subcellular |
| ZEISS LSM 980 Airyscan2 | Proteomics: Spectral-Multiplexing™ |
7-11 | 3D, subcellular |
| Akoya Vectra Polaris | Proteomics: Opal™ Reagents |
8 + DAPI | 2D, cellular |
Spatial biology technologies: an overview
| Technology | Description |
| Iterative Indirect Immunofluorescence Imaging (4i) | Iterative Indirect Immunofluorescence Imaging (4i) is a technique that enables the visualization of multiple proteins within a single tissue sample. It involves cycles of indirect immunofluorescence staining, imaging, and antibody removal. After imaging, antibodies are gently eluted using mild conditions that preserve sample integrity. This process allows for the sequential detection of numerous proteins without degrading the tissue. 4i utilizes standard, commercially available primary and secondary antibodies, eliminating the need for custom labeling. |
| iterative Bleaching Extends Multiplexity (IBEX) | IBEX is a high-content imaging technique that enables visualization of over 65 biomarkers within a single tissue sample. This method involves repeated cycles of antibody labeling, imaging, and chemical bleaching. After each imaging round, fluorophores are chemically bleached, effectively removing their signals while preserving tissue integrity. This process allows for subsequent rounds of staining without spectral overlap. IBEX is compatible with a wide range of commercially available antibodies and fluorophores, making it versatile for various research applications. |
| Co-Detection by Indexing (CODEX) | CODEX is a high-parameter imaging technology that enables simultaneous visualization of up to 60 biomarkers within a single tissue sample. This method utilizes antibodies conjugated to unique DNA oligonucleotides, which bind to their target antigens in the tissue. Fluorescently labeled complementary DNA probes are then introduced in cycles to hybridize with these oligonucleotides, allowing for the sequential imaging of multiple markers. After each imaging cycle, the fluorescent probes are removed, and new probes are applied, facilitating extensive multiplexing without compromising tissue integrity. Compatible with formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues. |
| Sequential Immunofluorescence (seqIF) | seqIF is a fully automated imaging technique that enables the detection of multiple protein biomarkers within a single tissue sample. This method involves iterative cycles of staining with non-conjugated primary antibodies, imaging, and gentle elution of antibodies, preserving tissue integrity throughout the process. Each cycle allows for the detection of different antigens, facilitating high-plex spatial proteomics analysis. |
| Lieca SpectraPlex | SpectraPlex is an advanced confocal imaging workflow on the Leica STELLARIS platform that enables simultaneous visualization of up to 15 biomarkers in a single acquisition. This method relies on antibodies directly conjugated to spectrally distinct fluorophores, combined with spectral and fluorescence lifetime-based unmixing to separate overlapping signals. Reference spectra are acquired from partially stained control samples to build an unmixing matrix, minimizing the need for extensive single-stain controls. SpectraPlex allows high-plex imaging in 3D without repeated staining cycles, making it ideal for complex tissues such as FFPE sections, organoids, or fresh-frozen samples. |
| ZEISS Spectral Multiplex | Spectral Multiplex is an advanced confocal imaging method available on ZEISS LSM systems that enables simultaneous visualization of over 10 fluorescent markers in a single acquisition. The system captures the full emission spectrum of each pixel using a multi-channel detector array, generating a so-called lambda stack. Using pre-recorded reference spectra or automatically extracted spectral fingerprints, overlapping fluorescence signals are computationally separated through linear unmixing. Autofluorescence can be treated as an independent signal source and removed during processing. Spectral Multiplex allows for flexible, high-content imaging of complex samples, including live cells, organoids, and tissue sections, without requiring repeated staining or sequential imaging cycles. |
| Akoya Vectra Polaris | Akoya Vectra Polaris / PhenoImager HT is a slide scanning platform that enables the simultaneous detection of up to 8 biomarkers within a single tissue section. The system uses Opal fluorophores, which are covalently deposited at the antigen site, resulting in bright, photostable signals. Biomarker panels containing DAPI, Opal 480, Opal 520, Opal 570, Opal 620, Opal 690, and Opal 780 can be imaged using standard filter sets without multispectral acquisition, allowing significantly faster scanning. Panels including additional fluorophores such as Opal 540 or Opal 650 require multispectral imaging with linear unmixing to accurately resolve overlapping signals. The method is compatible with FFPE and fresh-frozen tissues. |
Other technologies available at UZH/ETH Zurich
If you are interested in spacial analysis of higher plex targets or of the whole transcriptome please check the available technologies offered by the FGCZ Spatial Transcriptomics.