Written by Karina Barreiro, PhD, Postdoctoral researcher at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland

From 14 to 17 October 2025, I attended the EMBL Conference’ Spatial biology: the melting pot’, co-organised by the EMBL and the European Society for Spatial Biology (ESSB). It was my first conference on spatial biology, and as I am just starting in the field, I did not have any results to submit an abstract. Thus, the virtual event was a great fit for me. The programme was remarkable, with outstanding speakers.

It was an excellent opportunity to learn about the latest technological and analytical advances, as well as how spatial omics is applied to the study of health and disease. It was an inspiring event that left me with ideas I am eager to test in my research project.  As an online participant, I couldn’t attend the poster sessions, but I think the mini talks were a great way to get snapshots of the selected poster presentations.

The conference started with an inspiring keynote lecture by Jeff Spraggins from Vanderbilt University on the spatial integration of multimodal molecular imaging data. Jeff showed examples of imaging mass spectrometry integration, e.g., with cyclic immunofluorescence microscopy and histochemistry.  Using the kidney as an example, he showed how multimodal integration is used to study lipid markers of kidney disease.

Session 1: Tumour microenvironment and cancer

Holger Heyn from the National Centre for Genomic Analysis opened the session by presenting three projects in which he uses technologies to profile millions of cells. One of the projects was STAMP – “Single-cell transcriptomics analysis and multimodal profiling through imaging”, which enables cost-efficient profiling of cells derived from many sources, e.g., tissues, cell cultures, and even nuclei extracted from FFPE samples.

Emine Kazanc from Bogazici University presented how spatial multi-omics 3D cartography can be applied to study tumour heterogeneity and predict therapeutic vulnerabilities in breast and ovarian cancer for personalised medicine.

Kristin Qian from Harvard Medical School presented results on spatial profiling of immune infiltration to advance therapeutic targeting and biomarker development in colorectal cancer and beyond.

Christian Schürch from University Hospital Tübingen presented the use of CODEX in hematopathology (examples include cutaneous T cell lymphoma and leukaemia) to study the tumour microenvironment and predict disease progression, outcomes, and therapy response.

Reema Baskar from the Genome Institute of Singapore showed that studying the extracellular milieu in colorectal cancer using spatial proteomics and transcriptomics, scRNAseq, and bulk RNA sequencing revealed axes of immunosuppression and inflammation.

Kristy Ou from EMBL Heidelberg showed how multimodal single-cell and spatial profiling can be used to identify early drivers of follicular lymphoma transformation.

Jasmine Plummer from St. Jude Children’s Research Hospital presented on integrating single-cell methods into spatial profiling of disease. During the presentation, Jasmine demonstrated tools such as QuantumCell (for cell-type matching), the Spatial Touchstone database, and SpatialQM (which can be run locally and supports the transfer of single-cell annotations). Dr Plummer also presented some results on prostate cancer using the new Illumina spatial sequencing platform.

Session 2: Spatial immunology

The session started with a presentation by Arutha Kulasinghe from The University of Queensland, who showed how spatial omics can be used to study the tumour microenvironment in lung, head and neck, skin, and other cancers, shedding light on differences between responders and non-responders to immune checkpoint inhibitors. Dr Kulasinghe also showed spatial profiling of proteins and RNA in Spanish flu lung archival tissue (stored for more than 100 years!).

Annika Raschdorf from University Hospital Schleswig-Holstein showed how spatial single-cell proteomics, transcriptomics, and other technologies can be used to study the mucosal humoral immunity in Crohn’s Disease.

Marc-Andrea Baertsch from Heidelberg University Hospital / German Cancer Research Center (DKFZ) showed how CODEX can be used to study the bone marrow microenvironment in multiple myeloma.

Anja Hauser from Charité – Universitätsmedizin / DRFZ presented results on applying spatial biology and light sheet microscopy to study bone regeneration in 3D.

Isaias Hernandez from Centre de Recherche des Cordeliers showed how spatial omics and non-spatial modalities were used to study the mechanism by which GABA promotes resistance to immunotherapy in patients with ccRCC and tertiary lymphoid structure-positive tumours.

The session ended with Konstantin Bräutigam from Institute of Cancer Research, UK presenting “Distinct spatial microenvironments and emergence of immune-cold niches during progression to colitis-associated colorectal cancer” Dr Bräutigam showed how using hematoxylin and eosin-stained slides (of samples taken every 2 cm across the colon) and RNA sequencing can be used to study changes on the tissue microenvironment in ulcerative colitis and how those changes give information on the prognosis.

Session 3: New advances in spatial biology

Session 3 started with a talk by Jiwoon Park from Weill Cornell Medicine, who presented the current status and future steps of the Spatial Atlas of Human Anatomy (SAHA).

Andy Fraser from the University of Toronto presented a method for measuring metabolites using DNA sequencing.

Sabrina Lewis from Heidelberg University Hospital presented a novel imaging and analysis pipeline, “LeGO-3D,” that combines lentiviral-based optical barcoding (LeGO) with whole-organ light-sheet microscopy and demonstrated its application to study metastatic breast cancer.

Rosalie Rietjens from Leiden University Medical Centre, The Netherlands, presented results from a study of kidney microenvironments using semi-quantitative spatial metabolomics and spatial transcriptomics to shed light on the progression to chronic kidney disease after acute kidney injury.

Adrien Hallou – University of Oxford – presented a new, exciting spatial mechanical-transcriptomics pipeline that enables the inference of mechanical forces at spatial resolution from a tissue slice analysed using spatial transcriptomics. Then, the two modalities can be used to study associations, e.g., between genes and cell mechanical force.

Barbara Treutlein from ETH Zurich presented the last talk of the session on mapping cell type diversity in the brain with spatial and single-cell technologies to study the emergence of neural cell types during development and to study injury and regeneration in established cell types. Dr Treutlein showed results from mapping cell types in the axolotl brain and from mapping cell and tissue morphodynamics in human neuron organoids.

Session 4: Data analysis for spatial biology

Johanna Klughammer from Ludwig-Maximilians-Universität München presented the TACCO framework for integrating multimodal data and demonstrated its use to study the tumour microenvironment in Metastatic breast cancer.

Erick Armingol from the Wellcome Sanger Institute presented “scCellFie”, which infers metabolic activities (short or long pathways) from single-cell and spatial transcriptomics.

Ekansh Chauhan from the Cancer Research UK Scotland Institute presented a computational framework to integrate tissue morphology and spatial transcriptomic data to study tumour microenvironments.

Julio Saez-Rodriguez from EMBL-EBI Hinxton gave an overview of resources and methods that combine multi-omic spatial data and single-cell data with biological knowledge (e.g., LIANA+) to study tissue biology, disease mechanisms, and more.

Ziqi Kang from The University of Helsinki presented “SPACEstat”, a framework for quantifying spatial organisation in the tumour microenvironment.

Sergio Marco Salas from the Helmholtz Centre Munich presented a framework for studying the biological relevance of RNAs that remain unassigned after cell segmentation.

Session 5: Subcellular spatial biology

Ralf Jungmann from the Max Planck Institute of Biochemistry presented “DNA-PAINT” and its latest technical advancement, “RESI,” for multiplex protein imaging using super-resolution microscopy.

Kotaro Tomuro from RIKEN / The University of Tokyo showed “APEX-Ribo-seq” for the study of translation at subcellular resolution.

Lucas Pelkmans from the University of Zurich presented Iterative Indirect Immunofluorescence Imaging (4i) for the study of subcellular and cellular states. The method achieves more than 100 plex proteins and is high-throughput and highly quantitative.

Britta Velten from Heidelberg University presented computational tools to analyse spatial omics data across resolutions and molecular layers. Some examples of such tools are MEFISTO, MOFA, and FISHfactor.

Session 6: Spatial pathology: New insights for disease

Nikolaus Rajewsky from the Max Delbrück Centre presented an excellent Keynote lecture showing how spatial omics can be used to predict disease trajectories and identify therapy targets. During this lecture, we also learnt about Open-ST, a scalable spatial sequencing method for subcellular resolution (2D and 3D), and MALVA, a “universal search index for single-cell and spatial sequencing technologies” that integrates data from various databases.

Miranda Orr from Washington University in St. Louis presented results from ultra-high-plex detection of RNA and proteins at subcellular resolution for the study of Alzheimer’s disease. Dr Orr presented the latest advances on spatial profiling of proteins using a 1000+ antibody panel.

Koen Rademaker from the Wellcome Sanger Institute demonstrated the use of spatial transcriptomics in mid-gestational brains to study autism-susceptibility genes in a spatial-temporal manner.

Anna Pascual Reguant from the Centro Nacional de Análisis Genómico showed how the combination of whole-transcriptome spatial molecular imaging, single-nucleus RNA sequencing, and digital histopathology can be used to study colorectal malignancy transformation.

Sandra de Haan from Leiden University Medical Centre presented how spatial transcriptomics was used to study inclusion body myositis and shed light on the link between inflammation and degeneration.

Sean Bendall from Stanford University, USA, gave the final presentation of the conference, “Massively multiplexed imaging of human neuropathology,” on the power of multiomic approaches to identify/predict tumour characteristics and outcomes/outcomes in glioma and Alzheimer’s disease.

In short, I think there is a really nice interplay among advances in technology, analytical tools, and database resources. Focusing on analytical advances, it was great to learn about pipelines developed to make the most of transcriptomic profiling, including, e.g., scCellfie and spatial mechano-transcriptomics, as well as tools to connect spatial omics with knowledge databases. I noticed that researchers are putting a lot of effort into compiling spatial omics data into databases (e.g., SAHA, HuBMAP, KPMP) and making the resources freely available to the public, which is fantastic. 

It has been insightful and inspiring to see how spatial omics approaches, alone or combined with other modalities, have been used to study diverse tissues in health and disease. I thank the EMBL dearly for giving me the opportunity to be an event reporter.

The EMBL Conference ‘Spatial biology: the melting pot’ took place between 14 – 17 October 2025 in Heidelberg, Germany, and virtually.

Read also about the #EMBLSpatialBiology poster prize winners and find out more about their research in another blog post from the meeting.

Did you know that you can become an event reporter and receive a conference fee waiver in exchange? Find out how to do that by visiting our Become an event reporter page.