MULTI-SPACE is an interinstitutional technology platform housing state-of-the art instrumentations, currently mainly located at both the EMBL Heidelberg and BioQuant of Heidelberg University. The platform leverages the individual strengths of the Alliance institutions and benefits from the advanced complementary expertise and technologies already available. MULTI-SPACE is designed to jointly establish the latest spatially-resolved omics-technologies and data analysis methods for all partner institutions and to make them widely accessible.

Quantitative molecular analyses of tissue using spatially-resolved Multi-Omics-techniques provide completely new insights into cellular functions in health and disease, and into the cellular response to environmental influences and drug treatment. The challenging technical requirements for providing spatially-resolved omics-technologies, however, cannot be met by a single institution. A concerted effort is needed to integrate the diverse omics methods with high-resolution multimode imaging to address cellular heterogeneity for basic research questions + personalized disease therapies. This will not only enable novel holistic analyses but also the further development of cutting-edge technologies. To fill this gap, MULTI-SPACE has been established.

The technology hub currently makes the following instrumentation, technologies, computational analysis, and application to biomedical questions available to all scientists at Alliance institutions:

Image credit: Ghasemi et al,


MULTI-SPACE provides assisted access to commercial as well as custom-made instrumentation for quantitative and molecular analysis methods that utilize spatially resolved multi-omics techniques with single-cell resolution, including data management and analysis support.


Quantitative and genome-scale multiplexed imaging technique for identifying nucleic acids in their native tissue environment with resolution scaling from subcellular to tissue scale using MERFISH technology.

GeoMx® Digital Spatial Profiler

Spatial multiomic platform for analysis of FFPE and fresh frozen tissue sections, non-destructive profile expression of RNA and protein with an automated and scalable workflow that integrates with standard histology staining.

Visium slides

For sequencing-based mapping of the whole transcriptome within the tissue context in FFPE or fresh frozen samples using spotted barcodes with a diameter of 55 µm.


Hyperplex assay using a sequential immunofluorescence (seqIF™) approach, where 40 protein markers per automated run can be detected in FFPE tissue samples.

Hybridization-based in situ sequencing (ISS)

Transcriptome analysis in tissues and cell lines with padlock probes coupled to rolling circle amplification for detection by hybridization-based in situ combinatorial barcoding on different fluorescence microscopy systems.


Single-molecule FISH approach to visualize the whole transcriptome. Low-cost DIY protocols for sample preparation, up to 10,000 RNAs per cell, software for probe design, and protocol for probe production.

Microscopy unit: 8-band excitation (DAPI – NIR), highly sensitive camera (~95% QE), Andor Sona CMOS detector, hardware AF, 20x-60x ir imaging

Illumina MiniSeq sequencing, for Seq-Scope

MULTI-SPACE data server to download data generated at BioQuant hub. Data transfer across institutions: SDS@hd storage and DKFZ

Lambda Vector workstation with 64 and 24 cores, for Image analysis

Slide-Seq, is a method that transfers RNA from fresh tissue sections onto a surface covered in DNA-barcoded beads with known positions. This allows the spatial locations of the RNA to be inferred by sequencing.

Seq-Scope, is a spatial barcoding technology using an Illumina sequencing-by-synthesis platform to achieve sub-micron resolution spatial transcriptomics, enabling the visualization of transcriptomic heterogeneity at the cellular and subcellular level in various tissues.

Imaging Mass Spectrometry

Custom Cartana/PadFISH microscope

Robotic microscope for FISH applications with sample alteration capabilities involving pipetting and microfluidic flushing.

PhenoCycler-Fusion System from Akoya Biosciences

How to get started

If you are interested in utilizing our services, please contact us directly. We can discuss the various methodologies that are available for your project and determine the best technology to meet your specific needs. Each methodology has its own advantages, schedule a meeting to discuss your project and we will help you choose the most suitable technology for the successful completion of your project.


  • First contact: send a short research plan: multi-space[at]
  • Research plan: Meet the experts, discuss the plan, choose techniques and kits to be purchased, plan budget, book machines, timelines
  • Request Trainer
  • Sample submission: following guidelines
  • Lab work: measurements, method development or pilot assay
  • Analysis results: readout sent out, book analysis workstation, get data analysis support.


Natalia Gabrielli, PhD

Project Coordinator
Centre for Organismal Studies
Heidelberg University
Im Neuenheimer Feld 230 (INF 230)
69120 Heidelberg

Phone: +49 6221 54 5673