The study of complex tissues — whether in the context of brain development, tumor progression, or organ-level disease — has long been constrained by a fundamental methodological tension. Three-dimensional imaging methods preserve the volumetric integrity of whole organs and large tissue blocks, but typically sacrifice molecular resolution. Two-dimensional multiplexed profiling techniques deliver rich molecular phenotyping at the single-cell level, but are limited to thin sections that capture only a sliver of tissue architecture. Neither approach alone is sufficient for truly comprehensive tissue analysis.
A new webinar, jointly presented by researchers from the Developmental Biology Institute of Marseille and Miltenyi Biotec, addresses this tension directly — presenting a workflow that links 3D whole-tissue imaging with high-plex 2D spatial proteomics to enable multiscale mapping of complex tissues in a single integrated pipeline.
About the Webinar
Title: Linking 2D and 3D Spatial Biology for Multiscale Mapping of Complex Tissues
Date: May 20, 2026
Time: 5:00 PM London (GMT+1)
Format: Virtual — Free registration required
The Core Challenge: Scale vs. Resolution in Tissue Analysis
Modern spatial biology has delivered remarkable advances in the ability to profile gene and protein expression at the single-cell level within tissue context. Technologies including multiplexed immunofluorescence, spatial transcriptomics, and cyclic immunostaining platforms enable researchers to simultaneously detect dozens to hundreds of molecular markers within tissue sections, building detailed molecular maps of individual cells and their immediate neighbors.
But these approaches are inherently limited to the two-dimensional plane of a tissue section — typically 5 to 20 micrometers thick. The spatial relationships that operate across hundreds of micrometers or millimeters — the organization of tumor invasion fronts across whole tissue lobes, the distribution of neural cell types across brain regions, the connectivity of vascular networks through organ parenchyma — are not captured by any individual section. Collecting serial sections to reconstruct three-dimensional structure is technically demanding, computationally intensive, and subject to registration artifacts that complicate the final reconstruction.
Light-sheet fluorescence microscopy addresses the volumetric imaging problem by enabling three-dimensional imaging of intact, optically cleared tissue samples — whole organs, large tumor blocks, or entire embryos — at cellular resolution throughout the full tissue volume. It reveals how structures are organized in three dimensions, where specific cell populations are located relative to each other across the full extent of the tissue, and which regions are architecturally distinct and therefore most informative for detailed molecular analysis.
The integration of these two approaches — using 3D light-sheet imaging to guide the selection of regions of interest (ROIs) for subsequent high-plex 2D profiling — is the conceptual core of the workflow this webinar will present.
The 3D–2D Workflow: How It Works
The workflow presented in this session represents a logical and technically coherent approach to combining the complementary strengths of volumetric imaging and high-plex spatial proteomics:
Step One: Whole-Tissue 3D Imaging with Light-Sheet Microscopy
The process begins with optical clearing of the intact tissue specimen — a chemical treatment that renders the tissue transparent by removing lipids and homogenizing the refractive index of the tissue components, allowing light to penetrate deeply without scattering. Once cleared, the specimen is imaged using light-sheet fluorescence microscopy, which illuminates a thin plane of tissue at a time and captures the emitted fluorescence with a camera oriented perpendicular to the illumination plane.
The result is a volumetric dataset that maps the three-dimensional structure of the tissue — including cell distribution, tissue architecture, vascular organization, and large-scale spatial domains — at resolution sufficient to identify individual cells and their positions throughout the full tissue volume. This three-dimensional map provides a global view of tissue organization that informs where the most biologically relevant or architecturally distinct regions are located.
Step Two: Light Sheet-Guided ROI Selection for 2D Sectioning
With the 3D volumetric map in hand, researchers can make informed, spatially guided decisions about where to section the tissue for subsequent 2D molecular profiling. Rather than selecting section planes arbitrarily or based on gross anatomical landmarks alone, the 3D imaging data allows the identification of specific ROIs that are most likely to capture the biological features of interest — a particular tumor invasion zone, a specific brain region, a vascular niche — with spatial precision that serial sectioning without 3D guidance cannot achieve.
This light sheet-guided sectioning approach fundamentally changes the information content of 2D profiling by ensuring that the sections analyzed represent biologically meaningful, spatially defined regions of the full tissue architecture rather than arbitrary planes through it.
Step Three: High-Plex Spatial Proteomics with MICS Technology
The selected tissue sections are then analyzed using Miltenyi Biotec’s MICS (Microfluidic Cell Sorting) high-plex spatial proteomics technology, which enables single-cell proteomic profiling of intact tissue sections across a large number of protein markers simultaneously. This multiplexed imaging approach builds on the spatial context established by 3D imaging, adding molecular identity — cell type, activation state, pathway activity, functional marker expression — to the architectural framework provided by the volumetric map.
The combination delivers what neither approach alone can: a dataset that is simultaneously three-dimensionally complete at the architectural scale and molecularly detailed at the single-cell scale.
Application in Glioblastoma Research
The webinar will present this workflow in the context of glioblastoma — one of the most aggressive and architecturally complex brain tumors, with a highly heterogeneous tumor microenvironment that has proven extraordinarily difficult to characterize using conventional profiling approaches.
Glioblastoma is characterized by regional heterogeneity at multiple spatial scales: different tumor zones — including the invasive edge, the hypoxic core, the perivascular niche, and the infiltration zone into normal brain parenchyma — have distinct cellular compositions, molecular phenotypes, and therapeutic vulnerabilities. Understanding how these zones are organized three-dimensionally within the tumor, and what their precise molecular characteristics are at the single-cell level, is fundamental to both scientific understanding and therapeutic strategy.
The 3D–2D workflow is particularly well-suited to this challenge because it allows the volumetric organization of the glioblastoma tumor — including the identification and spatial localization of distinct regional zones — to guide the selection of sections for high-plex molecular profiling. The result is spatial proteomic data that is anchored to a known three-dimensional context rather than floating in an uncertain relationship to the full tumor architecture.
Featured Speakers
Harold Cremer, Research Director, Developmental Biology Institute of Marseille
Harold Cremer brings deep expertise in three-dimensional imaging approaches applied to brain biology and development. As Research Director at the Developmental Biology Institute of Marseille — one of Europe’s leading centers for developmental and systems neuroscience — Cremer has extensive experience using volumetric imaging to study how neural cell populations are organized across the developing and adult brain. His contribution to this session will focus on how 3D imaging and spatial biology approaches can advance understanding of brain tumor development, drawing on his research experience with complex neural tissue architecture and its molecular underpinnings.
Kevin Bigott, MSc., Team Coordinator, R&D Neurobiology, Miltenyi Biotec
Kevin Bigott leads workflow development at Miltenyi Biotec’s R&D Neurobiology team, with a focus on the practical implementation of 3D tissue labeling, optical clearing, light-sheet imaging, and the integration of volumetric imaging data with downstream 2D spatial proteomics. His presentation will cover the technical workflow from tissue preparation through light sheet-guided sectioning to high-plex MICS profiling, grounding the conceptual framework in concrete experimental protocols and data. Bigott’s engineering perspective on the workflow complements Cremer’s biological perspective, together providing a complete view of how the 3D–2D pipeline functions in practice.
Key Scientific and Technical Takeaways
Attendees of this webinar will gain understanding of several areas that are at the frontier of spatial biology methodology:
- Optical clearing and light-sheet imaging fundamentals: How intact tissues can be rendered transparent and volumetrically imaged while preserving spatial integrity, and what the resulting datasets look like and contain.
- 3D-guided ROI selection: How volumetric imaging data can be used to make spatially informed decisions about where to section tissue for 2D profiling — a step that is often underappreciated but critical for the biological relevance of the resulting molecular data.
- High-plex MICS spatial proteomics: How single-cell proteomic profiling of tissue sections enables simultaneous characterization of cell type, phenotype, and molecular state across dozens of markers in intact tissue architecture.
- Multiscale data integration: How 3D volumetric and 2D molecular datasets from the same specimen can be conceptually and practically integrated to build a multiscale picture of tissue organization and molecular phenotype.
- Glioblastoma application: How this workflow reveals regional heterogeneity and molecular diversity within glioblastoma in ways that neither 3D imaging nor 2D profiling alone can achieve.
Who Should Attend
This webinar is highly relevant for researchers working across a range of disciplines and methodological backgrounds:
- Neuroscience and brain tumor researchers interested in applying spatial methods to understand the three-dimensional organization of brain tissue and glioblastoma architecture
- Spatial biology practitioners currently using 2D multiplexed imaging platforms who want to understand how 3D imaging can extend and contextualize their existing datasets
- Cancer biologists studying tumor microenvironment heterogeneity who need tools capable of capturing spatial organization across multiple scales simultaneously
- Imaging scientists and core facility directors evaluating next-generation spatial workflows for multi-user research environments
- Biotech and pharma translational teams working on therapeutic programs that require spatially resolved tissue-level evidence for biodistribution, efficacy, or safety characterization
The Broader Significance: Multiscale Tissue Biology
The workflow presented in this webinar represents a direction that spatial biology as a field is increasingly moving toward: the integration of complementary methods that operate at different spatial scales into coherent, multiscale analytical pipelines. As the questions being asked of tissue analysis become more sophisticated — spanning from the molecular state of individual cells to the large-scale architectural organization of whole organs — the tools required to answer them must similarly span multiple scales.
Light sheet-guided spatial proteomics is one concrete implementation of this multiscale ambition. By allowing whole-organ volumetric imaging to guide single-cell molecular profiling, it closes a methodological gap that has historically required researchers to choose between scale and resolution. The glioblastoma application presented in this session illustrates what becomes possible when that choice no longer needs to be made.