Flanders Bioimaging Imaging Node

Flanders BioImaging is a multi-sited, multi-modality Node that offers a full and complementary portfolio of biological and biomedical imaging techniques and expertise, at scales ranging from the molecular all the way up to human/clinical imaging (“molecule to man”). The node comprises 9 separate imaging facilities spread across 5 sites, all situated within a 70km radius. Whilst each facility is well equipped for imaging in either the biological or biomedical domain, our strategy is to specialise in the particular spearpoint techniques as detailed in the section below.

The Flanders Bioimaging Node itself is funded by the FWO International Research Infrastructure program, in co-ordination with the Department of Economy, Science and Innovation (EWI), whilst the combined available imaging infrastructure from the constituent sites represents more than €50mi investment.

Specialties and expertise of the Node

Flanders Bioimaging aims to help develop projects for a wide range of users from academia and industry to understand disease at the molecular, cellular, organ and organism levels, and to help develop and validate biomarker tools to help guide drug development and precision medicine. Whilst our sites have broad expertise, there is an especial focus on the oncology and neurodegenerative disease settings. 

Our strategy is to focus on providing access to the leading applications (‘spearpoints’) that have been developed at each site – each spearpoint is described below.


●      Translation of novel CNS tracers

The Molecular Imaging and Research Clinic at KU Leuven (MIRaCLe) is well established in the validation and application of novel PET biomarkers to clinical populations for improved diagnosis and precision medicine for central nervous system (CNS) disease and especially neurodegeneration. The MIRaCLe platform focuses on translating novel PET candidates to first in human studies, including full quantitation and methodology development, as well as employing established markers for receptor occupancy studies in response to novel drugs in clinical populations, via interface with the UZL Clinical Trial unit.


●      GMP production of nanobody theranostics

The In vivo Cellular and Molecular Imaging (ICMI) core facility at the VUB specialises in the development of new Nanobody-based (Nb) optical and nuclear diagnostic imaging probes and therapeutics for oncology and immuno-oncology in particular. Importantly, ICMI provides a GMP production platform for such Nb diagnostics & therapeutics, that includes selection of production vectors for (GMP-grade) Nanobody productions; Nanobody fermentation and purification protocols with qualification of in-process controls (IPCs) and analytical tests for follow-up and release; GLPgrade Nanobody batch production for in vivo PET imaging proof of concept studies and to support toxicity and stability studies and finally production of GMP-grade Nanobody batch that can be used for clinical translation.



●      Multi-modality image-guided radiotherapy

CORE ARTH (Animal facilities Radiological Techniques & Histology) Infinity at the University of Gent houses the SmART+ system for small animal irradiation, a unique system in Europe that combines multiple imaging modalities to allow the determination of biological target volumes (BTVs) for radiotherapy planning using non-uniform dose delivery protocols for automated nonhomogeneous doses.

In addition the facility has established pipelines for the integration of PET and MRI biomarkers to inform such higher dose delivery with the goal of targeting the more malignant or more radiation-resistant tumour areas. This comprehensive imaging biomarker platform also allows the monitoring of combination radio/chemotherapy responses and thus the validation of predictive imaging biomarkers.


●      PET and High-field MRI characterisation of CNS disease models and therapy response

The in vivo small animal imaging facilities of the University of Antwerp consist of the Molecular Imaging Centre Antwerp and the Bio-Imaging Lab (MICA-BIL), and provides a battery of early biomarkers to evaluate neurodegenerative diseases, cancer as well as treatment response in a range of preclinical disease models. MICA-BIL makes use of PET biomarkers for the visualisation of proteinopathies, neuro-inflammation and presynaptic receptor density and combines functional connectivity and activity, structural integrity and connectivity from MRI. Fully optimised scan protocols and processing pipelines are available, including multi-modality integration to both increase predictive power and better discriminate underlying disease mechanisms and enable the early evaluation of potential treatments.


o   Enteric Nervous System Imaging:

The Cell & Tissue Imaging Cluster (CIC) at KU Leuven integrates live fluorescence (single, two- and recently 3-photon), lattice light sheet and second and third harmonic imaging to provide multiplex real-time structural and physiological information on the enteric nervous system (ENS). The CIC is able to offer advanced (neuro)physiological imaging experimental setups involving (for example) the perfusion of drugs or electrical stimulation on widefield (incl. with high frame rate cameras), confocal, 2|3-photon, Abberior STED and Lattice Light sheet microscopes. Full protocols for physiological measurements in a range of sample types (including organs, tissue slices and organoids) on multiphoton/STED/LLS microscopes are available and extendable to allow pharmacological/electrical interventions at defined and accurate (ms) timepoints, with full analysis pipelines for the extraction and interpretation of valid physiological information from non-linear, superresolution and high-rate/noisy imaging data.

  • Correlative Light/Electron Microscopy:

The Biological Imaging Core (BIC) at the Vlaams Instituut voor Biotechnology (VIB) houses a Zeiss Elyra 7-Structured Illumination Microscope (SIM)² equipped with the LSM980 two-photon module to enable accurate correlation of super-resolution light microscopy with EM data. This allows defined region study at resolutions ranging from 60nm (SIM²) to <20nm (PALM/d STORM) to nanometre ultrastructure via SEM, with Focused Ion Beam SEM (FIB-SEM) available to allow applications under cryo conditions. This dynamic 3D/4D super-resolution microscopy platform closes the resolution gap between LM and EM, expanding in situ structural analysis, and enables the correlation of protein clusters/complexes with morphological domains in organelles and tissues. Imaging neurodegenerative processes at the level of organelles and identifying the initial stages of protein/peptide aggregation, transmission and organellar involvement is a key focus, with the aim to better understand neurodegenerative mechanism(s) and identify novel targets for early diagnosis and therapy.

  • Pharmacokinetic Imaging:

The Gent Light Microscopy Core (GLiM; has expertise in pharmacokinetic imaging, i.e. the study of the physicochemical properties of single molecules and nanoparticles in biological systems. This technique makes use of advanced imaging (Fluorescence Recovery after Photobleaching, FRAP; Fluorescence Correlation Spectroscopy, FCS; Single Particle Tracking, SPT) with major applications in the study of drug delivery and nanoparticle therapy (nanomedicines) in a range of biological systems. GLiM also has unique and complementary expertise in the intracellular delivery of compounds, including labels for microscopy or preclinical imaging of cells, via ‘photoporation’ (valorized at GU via the formation of the spin-off Trince). A major focus is the development of techniques to elucidate nanoparticle transport mechanisms in spheroids and patient-derived tissue fragments with the goal of informing the development of a range of nanomedicines, with special focus on improved therapeutic efficacy for the treatment of cancer. Different pharmacological and biomechanical manipulations to enhance nanoparticle transport can also be studied and developed using these model systems and readouts.

  • Dynamic Optical Microscopy:

The Advanced Optical Microscopy Centre (AOMC) at the University of Hasselt has unique expertise in studying molecular dynamics via Förster resonance energy transfer (FRET) and image correlation spectroscopy (ICS), two powerful fluorescence methods especially suited to study the dynamics of live biological processes, enabling 'fluorescence-based dynamic structural biology’ investigations from the single-molecule scale via e.g. super-resolution, TIRF and confocal microscopes all the way to the organoid, organs and model organism length scale via state-of-the-art light-sheet microscopy. A particular focus is the application of FRET/ICS procedures to enable dynamic optical imaging in large multicellular assemblies and thus create a framework for super-resolved multidimensional correlation imaging (ICS) methods, furthermore to map viscosity/viscoelastic properties of/ diffusive heterogeneity within biomolecular assemblies below the 200-nm optical diffraction limit. Multiplex FRET combining space-and-time-resolved data recording is available to characterise heterogenous biological environments.


  • Systems microscopy: 

The Antwerp Centre for Advanced Microscopy (ACAM; develops data-driven microscopy approaches, based on a diversity of imaging technologies (incl. electron microscopy, high-throughput screening, live cell and light sheet microscopy) to gain insight in and expose novel therapeutic targets for human age-related diseases. ACAM has established end-to-end pipelines to query among others, oxidative stress and mitochondrial defects in human patient cells, synaptic connectivity in primary or iPSC-derived neurons, and DNA damage in cancer cells. High-end super-resolution and expansion microscopy in combination with cyclic staining is optimized for molecular-level investigations, while deep learning-enhanced image recognition enables cell type and state recognition in more complex, physiologically relevant biological specimens such as mixed cell cultures. A systematic workflow based on tissue clearing and light sheet microscopy allows cellular phenotyping of intact tissue mimics such as cerebral organoids and whole organs such as mouse brain. Thus, together our imaging expertise allows quantitative investigation of pathological defects across scales.

Additional services offered by the Node

  • Full project support, experimental design, user training
  • Wide range of disease models
  • Large animal scanning (mini-pigs)
  • BSL2 animal facility
  • SPF facility for high-field MRI imaging
  • Autoradiography of ex-vivo tissue with a wide range of isotopes
  • Laser microdissection and photoablation
  • Support for patient and subject recruitment for clinical studies
  • Support for obtaining preclinical and clinical ethical permission
  • Full clinical and preclinical quantitation for PET studies
  • Image processing and data analysis for all spearpoint technologies
  • Data storage and support for metadata definitions/implementation

Instrument Highlights

Clinical PET imaging: 

Two PET/CT scanners (GE Discovery MI, Siemens TruePoint), a simultaneous 3T PET/MRI (GE Healthcare Signa), four SPECT/CT scanners (Symbia Intevo Bold, GE Discovery NM530s CZT, GE Discovery MI, Siemens Symbia). A wide range of 11C, 18F, 15O and 13N tracers are available for clinical research use from the associated on-site GMP production facility.

●      Glucose metabolism/[18F]FDG

●      Pre-synaptic density (SV2A)/ [18F]SynVesT-1/[11C]UCB-J

●      Dopamine transporter (DAT)/ [18F]PE2I

●      Tau/ [18F]MK6240

●      Neuroendocrine tumours/[18F]NOTA-Octreotide

●      Neuroinflammation (Translocator protein, TSPO)/[18F]DPA-714

●      mGluR5/[18F]FPEB

●      Beta-amyloid in ALZ/[11C]PiB

●      Biomolecular labelling/[18F], [89Zr], [111In], [99mTc]


Preclinical Multimodality imaging: 

Our core facilities at the Universities of Gent and Antwerp, KU Leuven and the Vrije Universiteit Brussel host a wide range of preclinical instrumentation.

PET/SPECT/CT scanners: Dual Siemens Inveon, Dual Molecubes β-cubes (high-throughput PET-CT) are available at the Molecular Imaging Core Antwerp (MICA) and the Molecular Imaging Research and Clinic Leuven (MIRaCLe) whilst CORE ARTH Infinity houses β- and X cubes . SPECT and CT are available at these three sites and the In Vivo Cellular and Molecular Biology (ICMI) at the VUB (γ- and X-cubes, MiLabs VECTor+). MICA, MIRaCLE, CORE ARTH Infinity and ICMI all have facilities for the onsite synthesis of a range of radiotracers.


●      Glucose metabolism/[18F]FDG

●      Pre-synaptic density (SV2A)/ [18F]SynVesT-1

●      Dopamine DReceptors (D1R)/ [11C]SCH23390

●      Dopamine D2/3 Receptors (D2/3R)/ [11C]Raclopride

●      Phosphodiesterase 10A (PDE10a)/ [18F]MNI-659

●      Neuroinflammation (Translocator protein, TSPO) / [18F]PBR111 and [18F]DPA-714

●      mGluR5/[11C]ABP688/[18F]FPEB

●      mHTT using [11C]CHDI-180R/[18F]CHDI-650

●      Beta-amyloid using [18F]AV-45/[11C]PiB

●      Biomolecular labelling/[18F], [111In], [99mTc], [68Ga/67Ga], [64Cu]

●      LAT transport/[18F]FET

●      Prostate specific membrane antigen/[18F]-PSMA-11

●      Tumoural Lipogenesis/[18F]-Choline


Commercially available alpha/beta isotopes can be used for therapeutic biomolecule production at MIRaCLe and ICMI.

High-field preclinical MRI: the Biological Imaging Lab at the University of Antwerp hosts two Bruker 7T preclinical MRI instruments and one Bruker 9.4T high-field MRI (with cryo-coil), with a wide range of available sequences:

●      Structure analysis (volumetric and morphometry)

●      Microstructural MRI (diffusion tensor, kurtosis, and fixel-based)

●      Brain functional connectivity (Functional connectivity, CAPs and QPPs)

●      Brain functional activity (stimulus-based and pharmaco-based fMRI)

●      Susceptibility weighted Imaging (SWI and QSM)

●      Cerebral Blood perfusion (CBF) and volume (CBV) using ASL

●      Brain clearance (invasive and non-invasive glymphatic clearance)

●      Manganese enhanced MRI (MEMRI)

●      Magnetic resonance spectroscopy (MRS)

●      Metabolic rate of O2 consumption; 31P MRS for energy metabolism

●      Fluor-MRI; Magnetization transfer / Glutamate CEST


Optical Imaging: Bioluminescence is available at multiple sites (Perkin Elmer IVIS Lumina LT at CORE ARTH Infinity, Biospace PhotonImager at MICA-BIL and ICMI). Intravital microscopy is available at ICMI (Leica Stellaris DIVE Dual Intravital Microscope)

Radiotherapy delivery: The CORE ARTH Infinity core facility at the University of Gent hosts a SmART+ (Precision X-ray) platform for laboratory animal radiation research, enabling researchers to plan high-precision multimodal image-guided radiotherapy on laboratory animals using PET/MRI/BLI/CT (including longitudinal follow-up for therapy evaluation).

Imaging modalities can be integrated at all sites, with a wide range of in-vivo and ex-vivo assays available, especially in the CNS and oncology domains.

Biological imaging:   

The core facilities at the Universities of Gent, Antwerp and Hasselt along with KU Leuven and the VIB host a comprehensive imaging park for biological imaging and microscopy.

Light Microscopy:

●      Deconvolution Widefield Microscopy (DWM)

●      Laser Scanning Confocal Microscopy (LSCM/CLSM)

●      Spinning Disk Confocal Microscopy (SDCM)

●      Multiphoton Microscopy

Functional imaging and specialised methodologies

●      High throughput microscopy/high content screening (HTM/HCS)

●      Fluorescence Resonance Energy Transfer (FRET)

●      Fluorescence Recovery After Photobleaching (FRAP)

●      Fluorescence-Lifetime Imaging Microscopy (FLIM)

●      Multicolor Fluorescence Correlation Spectroscopy (FCS)

●      Multicolor  Image Correlation Spectroscopy (ICS)

●      Intravital Microscopy (IVM)

●      Anisotropy/Polarization Microscopy

●      Single Particle Tracking (SPT)


Super-Resolution Microscopy:

●      Structured Illumination Microscopy (SIM)

●      Image Scanning Microscopy (ISM)

●      Single Molecule Localisation Microscopy (SMLM)

●      Stimulated Emission Depletion Microscopy (STED).

●      Total Internal Reflection Fluorescence Microscopy (TIRF)

Mesoscopic Imaging:

●      Light-sheet mesoscopic imaging/ Selective Plane Illumination Microscopy (SPIM or dSLSM)

●      Optical Projection Tomography (OPT)

Label-free Imaging:

●      Second/Third Harmonic Generation (SHG/THG)


Electron Microscopy:

●      TEM of chemically fixed samples

●      EM tomography

●      Serial blockface SEM

●      Focus Ion Beam SEM

●      Immuno-gold EM on thawed cryo-section (Tokuyasu Method)

●      Immuno-gold EM on resin sections

●      Genetic encoded EM probes (e.g. APEX)

●      Pre-embed CLEM

●      Post-embed CLEM

●      Immunolabelling on immobilized particles

●      SEM (topography)

Multimodal Correlative Microscopy:

●      Pre-embed CLEM

●      Post-embed CLEM

●      Live-cell CLEM


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