Spatial Biology
Spatial Biology: Mapping Life in Its Context
Biological function is inherently spatial, from the arrangement of molecules within cells to the organization of tissues in health and disease. Spatial biology integrates imaging, transcriptomics, and proteomics to map cellular interactions within their native environment, offering deeper insights into fields such as cancer research and immunology. Traditional molecular techniques, like RNA sequencing and mass spectrometry, provide essential data but lack spatial resolution. Microscopy bridges this gap by enabling single-cell analysis within intact tissues, revealing protein distribution and cellular dynamics. Advances in light microscopy now support multiplexed imaging, allowing researchers to visualize multiple biomarkers simultaneously. We provide systems now automate this process, enhancing accuracy and efficiency. As spatial biology continues to evolve, integrating cutting-edge imaging with molecular profiling will be key to uncovering complex biological processes. Our core facility provides the expertise and technology to support these advancements. At the Center for Microscopy and Image analysis we provide user support for all phases of your spatial biology-multiplexing project : from experimental design, sample preparation to imaging and processing of the resulting data. We also closely collaborate with the other technology platforms at the University of Zurich and will support you in finding the best technology that fits your spatial-omic research.
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 |
| Akoya Vectra Polaris | Proteomics: Opal™ Reagents | 9 | 2D, cellular |
| MDImageXpress | Proteomics: IBEX, CODEX, 4i | 10-60 | 3D, subcellular |
| ZEISS LSM 980 Airyscan2 + Automated Perfusion System | Proteomics: IBEX, CODEX, 4i | 10-60 | 3D, subcellular |
| ZEISS ELYRA 7 + Automated Perfusion System | Proteomics:IBEX, CODEX, 4i | 10-60 | 3D, super-resolution |
Spinning Disk Nikon CrestOptics X-Light V3 + Automated Perfusion System |
Proteomics: IBEX, CODEX, 4i | 10-60 | 3D, subcellular |
| Leica Stellaris (comming soon) | Proteomics: SpectraPlex 3D | 15+ | 3D, subcellular |
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. |
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.