Spatial Imaging Mass Cytometry and Transcriptomics – SIMCaT

The SIMCaT platform (Spatial Imaging Mass Cytometry and Transcriptomics), based at the Institut de Recherche en Cancérologie de Montpellier (IRCM), is a state‑of‑the‑art spatial biology facility dedicated to tissue analysis at single‑cell resolution. It was the first site in France to implement the Hyperion imaging mass cytometry system and now brings together three cutting‑edge instruments: the Helios XT mass cytometer, the Hyperion XTi imaging system (Standard BioTools) and the Xenium in situ platform (10x Genomics).​

Available technologies include: the Helios XT, a mass cytometer dedicated to high‑dimensional proteomic profiling of cells in suspension; the Hyperion XTi, an imaging mass cytometry system that generates spatial protein maps at single‑cell level on tissue sections; and Xenium (10x Genomics), an in situ spatial transcriptomics platform capable of measuring the expression of thousands of genes directly within the tissue architecture.​

By combining Helios and Hyperion, SIMCaT performs highly multiplexed spatial proteomics on both cell suspensions and tissue sections, using metal‑tagged antibodies detected by mass spectrometry, thereby avoiding the usual constraints of fluorescence such as autofluorescence and spectral overlap. The platform offers complex panels (up to 50 parameters) and an extensive library of validated antibodies for mouse and human samples, enabling in‑depth exploration of immune and metabolic compartments within tissues.​

With the recent acquisition of Xenium, SIMCaT has expanded into in situ spatial transcriptomics, providing single‑cell gene expression maps directly in tissue sections. The combined proteomic–transcriptomic workflow delivers an integrated view of the tumour microenvironment, ideally suited to translational research projects in oncology.​

A unique end‑to‑end service underpins these technologies. Rather than limiting its role to data acquisition, SIMCaT acts as a genuine partner throughout the project lifecycle:

• Design phase – joint project definition, strategic advice on experimental design, and optimisation of marker panels in line with the scientific questions.

• Execution phase – experimental set‑up, high‑dimensional data acquisition and rigorous quality control at each step.

• Analysis phase – advanced bioinformatics pipelines, integration of spatial proteomic and transcriptomic datasets generated on the platform, and support with biological interpretation of the results.

• Dissemination phase – input for manuscript writing, preparation of conference materials and contribution to funding applications.​

A strong R&D activity underlies the platform, allowing continuous optimisation and in‑house validation of antibody panels and protocols, ensuring robust results tailored to the needs of each project. In the longer term, SIMCaT aims to shape an innovative spatial biology offering by actively developing new mass‑imaging panels, designing dedicated bioinformatics pipelines, and integrating emerging technologies (including Xenium, Helios XT, Hyperion XTi and new spatial transcriptomics platforms), while contributing to methodological standards and best practices for high‑content spatial analysis.​

The SIMCaT platform is supported by funding from the Région Occitanie and the European Union, which have played a key role in the deployment of this unique infrastructure.