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An example application of DCE-MRI is early quantification of tumor response to therapy. The perfusion parameters are known to change in days/weeks while the commonly measured tumor size changes within months. Other applications include assessment of blood-brain-barrier opening in neurodegenerative diseases and diagnostics of ischemic diseases. DCE-MRI is an in vivo technique applicable both in patient diagnostics and animal experiments when developing new treatment strategies. It can be used repeatedly during patient or animal treatment to map the temporal development pattern of the disease and can give complex and specific information on the effect of the treatment.

DCE-MRI is still an experimental technique due to the complexity of the image processing chain (includes image registration, conversion to contrast-agent concentration, fitting a pharmacokinetic model) and high demands on MRI hardware. At ISI-MR core facility of the Institute of Scientific Instruments of the Czech Academy of Sciences, we have been developing an online DCE-MRI processing system, PerfLab, providing novel perfusion-analysis approaches based on our methodological research. Recently, PerfLab ranked 3rd in the OSIPI DCE challenge, organized by the international society ISMRM. In frame of CzBI, at ISI-MR facility we provide access to this online software system and the corresponding consultation and/or data-processing service, as well as access to own compressed-sensing DCE-MRI acquisition methods implemented at our small-animal MR scanner.

Services and equipment

MSC operates 7 microscopes: 2 advanced confocal microscopes – laser scanning and spinning disc, both offering super-resolution (SR) compatible with life-cell imaging; 2 laser scanning microscopes with two-photon excitation; 2 basic microscopes for routine wide-field and confocal imaging; and a light sheet microscope providing cellular resolution of cleared samples. We also provide support in data acquisition, analysis, and custom software development, using Matlab, Python, ImageJ, etc.

What makes us different?

The common techniques of fluorescent imaging are well accessible at most of the facilities within the CzBI. As a new member, we searched for the least covered fields where to specialize. We identified a lack of super-resolution methods compatible with life cell imaging. We offer two confocal microscopes with SR mode, that provide significant improvement in resolution while keeping a gentle dose of light and thus allow for long-term imaging of living cells. These SR techniques are derived from structured illumination microscopy, with the benefit of absolute simplicity of usage.

Figure 1A shows a series of SR images obtained from the same living neuron, that are transformed into a 3D model using a custom-made software. The image captures the dynamics of dendritic spinules over time. Note that the width of protrusions < 150 nm makes them practically invisible for regular confocal microscopes, while the changes over time would not be possible to capture with other SR techniques such as STORM or STED due to fixation or high phototoxicity.

The second field we specialize in is intra-vital microscopy, aa technique offering sub-cellular resolution within behaving animals, that has a history at IEM starting in 2010 with the first two-photon microscope and the first cranial window surgery. Today, we do routine two-photon functional imaging of awake mice through the cranial window using GCaMP calcium probe (Fig 1B).

We plan to open the intravital lab in a fully open-access mode like any other imaging technique. Users will be provided with on-site animal housing, surgery and imaging service, viral injections at the stereotactic device, and access to the advanced two-photon microscope, the Femtonics FEMTO3D Atlas. This microscope offers unparalleled speed and random-access 3D scanning allowing to study multi-layer interactions in real time.

Vision

Our vision is to offer easy access to state-of-the-art tools to support research excellence and to have fun while doing it 😊.

How to get in touch? Please visit our web or contact us directly via email:

https://www.iem.cas.cz/en/department/microscopy-unit/

stepan.kortus@iem.cas.cz

Štěpán Kortus, Ph.D.

The event took place on the 29th of June 2023 at the Krč campus near the IMG building and hosted about 50 participants who came to enjoy a lot of sun, networking and fun with us. The programme included a small competition for the best performance by a facility, in which EM CF IMG led by Vlada Filimonenko won. Another part of the official program was an announcement of 3 best microscopic Images of the Year competition, which received gold, silver and bronze awards, generously sponsored by Nikon in cooperation with CSMS.

Winners of Picture of the Year 2022/2023 competition:

Along with our congratulations to all winners, we see the event as a success and we will definitely repeat it again next year. Stay tuned.

This event will highlight how cutting-edge imaging technologies can support research into the structure and function of plants, shed light on plant health, resilience and adaptability, and help answer agroecology research questions. Applications of diverse imaging technologies and plant biology research contexts will be highlighted by two keynote speakers and presentations from users of the Euro-BioImaging services, showcasing the specific expertise available at the Euro-BioImaging Nodes. We will also provide information on funding opportunities to access Euro-BioImaging services for agroecology-related research projects.

Full program & registration

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