Neuro Imaging: microscopy and macroscopy

The Antwerp Training Platform will cover the imaging facilities hosted by Partner 8 which are related to neuro macroscopy (microMRI) and neuro microscopy (fluorescence, confocal, Two photon, FRET/FRAP techniques, life cell imaging (Ca++-imaging))
They are directed towards:

  • Phenotyping neurodegenerative diseases by MRI (experimental)
  • Imaging neuronal networks by MRI (experimental)
  • Imaging brain activity (experimental)
  • In vivo tract tracing (experimental)
  • Fluorescence, Confocal, Two photon, FRET/FRAP techniques, life cell imaging (Ca++-imaging) of neurons


  1. To obtain both insight and experience in different MRI techniques using animals and microMRI instrumentation
  2. To learn what information (anatomical, physiological, cellular, molecular) these images provide
  3. Insight and experience in the required image and data processing techniques to process the data
  4. To obtain both insight and experience in CT using animals and microCT instrumentation
  5. To learn what information these images can provide
  6. Insight and experience in the required image and data processing techniques to process the data
  7. Getting insight and practical experience in modern microscopical imaging techniques
  8. Getting insight and practical experience in neuro applications of these microscopical techniques

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Description of the work:

a) Available training infrastructure

  • Macroscopy:
    The University of Antwerp can provide training access to a 7T microMRI systems and one in vivo microCT system (SkyScan, Belgium) for experimental in vivo small animal work (rats and mice). The Antwerp platform will also be a demonstration site for the SMEs MRRS and SkyScan which might get involved in the DiMI network along the line. The SME’s will ensure the state of the art condition of the platform in terms of providing the latest soft and hardware release in collaboration with the platform.

  • Microscopy:
    We can provide training in all microscopical techniques, starting from classical light microscopy, confocal microscopy, two-photon microscopy, life cell imaging, protein trafficking, fret/frap techniques, stereological and morphometric techniques to classical TEM and SEM including ultracryomicrotomy

b) Specific training packages

  • MRI training:

    The training is considered as an integrated practical course in which different aspects of animal neurobiology, relevant for DiMI, are tackled using different MRI techniques. The students will be allowed to perform experiments, involving animal handling, MR imaging, image and data processing. They will end up with a set of data drawn from the MRI experiments.

    1. General theoretical course on MRI and introduction to instrumentation (2 days, including 1 day on the instrument)
    2. Training on animal handling, restraining, catheterization, contrast applications, stereotactical injections, physiological monitoring and this for any MRI and CT setup (1 day, 0.5 days on the instrument)
    3. In depth training in different current MRI applications and the customized image processing relevant for the EMIL network (1.5 day per application, including theoretical background, instrument practice, processing of the obtained images).
    4. Perfusion-weighted MRI to measure Cerebral Blood Flow, angiography, functional MRI, diffusion weighted MRI, contrast applications in MRI including manganese enhanced MRI (total 7. 5 days)
  • microCT training:
    Theoretical and practical course on basics of CT and introduction to the use / and use of the microCT instrument (2 days)
  • Image Processing training:
    Matlab, practical training (2 days)
  • Microscopy training:
    1. Basic introduction in microscopical techniques (2 days)
    2. Hands on conventional light microscopy (including phase-contrast/DIC/Dark-field) and electron microscopy (SEM+TEM) (1day)
    3. Hands on fluorescence microscopy (0.5 days)
    4. Hands on confocal microscopy (1 day)
    5. Hands on Two photon microscopy (1 day)
    6. Hands on FRET/FRAP techniques + life cell imaging (Ca++-imaging) (1 day)

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 People involved in training:

  • MRI: Prof. A. Van der Linden, Dr. Marleen Verhoye (physicist), Ing. Johan van Audekerke, last years PhD student (Greet Vanhoutte), last years PhD student (Nadja Van Camp)
  • MicroCT: Prof. N. De Clerck, Dr. Andrea Postnov (physicist)
  • Image processing: Prof. Paul Schuenders, Dr. Jan Sijbers (physicist), Dr. Steve De Backer (physicist)
  • Microscopy: Prof. Dr. J.-P Timmermans, Prof. Dr. D. Adriaensen, Prof. Dr. F. Van Meir, Dr. L. Van Nassauw (zoologist), Dr. I. Brouns (Biomedical scientist)

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