Intravital imaging laboratory

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The Intravital imaging laboratory is a part of the microscopy facility at IEM. It offers equipment and expertise needed for all stages of imaging experiments in living rodents.

The laboratory is equipped with several imaging systems, most importantly the Femtonics FEMTO3D Atlas two-photon microscope, that can be used for simultaneous imaging and photostimulation in living animals. The imaging services are supported by a BSL-2 certified surgical room and animal facility. The surgical room can be used for the preparatory procedures, such as viral injection or cranial window implantation.


Microscopy equipment

  • Femtonics FEMTO3D Atlas

    Upright two-photon microscope designed for in vivo imaging of small rodents


  • Olympus FV1200 MPE

    Multiphoton confocal microscope


  • Mesoscopic and intrinsic imaging setup

    Setup for mesoscopic imaging of living animals

    Restricted operation

Surgical and laboratory equipment

  • BSL-2 surgical room

    BSL-2 certified laboratory equipped for surgeries

    Restricted operation

Animal housing

  • BSL-2 animal facility

    Animal facility associated with the intravital imaging laboratory

    Restricted operation

Available experimental techniques

Cranial window implantation

Cranial window enables access to the brain for long-term in vivo imaging. Cranial window implantation is a surgical procedure, during which a part of the skull is removed and the exposed area is subsequently sealed with a glass coverslip. The coverslip is attached to the bone using dental cement. At the same time, a metal bar is attached to the bone to allow for fixation of the animal in the microscope during subsequent imaging.

The cranial window can be placed over an area of interest. The areas studied in the laboratory involve auditory cortex and inferior colliculus of a mouse.

Viral injection

Viral injection involves injecting a genetically modified virus to a selected part of the animal tissue. Viruses used in the lab are AAVs expressing GCaMP receptors and/or rhodopsins used for optogenetics.

Optogenetic modulation

Optogenetics is a method enabling targeted activation or inhibition of specific cell populations using light. The modulation is enabled by expressing light-gated ion channels in the cells of interests transduced via a viral vector. Therefore, the lasers in the microscope can be used both for optogenetic modulation and for subsequent recording of the signal.

Imaging can be also combined with chemogenetics. As with optogenetics, chemogenetics allows activating or inhibiting specific cell populations. However, the mode of activation is different and the effects are usually more long-lasting and slower to start. The receptors enabling chemogenetic modulation (DREADDs) are expressed in the populations of interest and can be activated using small, otherwise inert molecules, such as CNO. The expression of the receptors is enabled via viral vectors.

Laboratory access modes and requirements

If you are interested in utilizing the laboratory’s services, please contact the coordinator. We provide initial consultation and offer support with project planning, to decide how we can best accommodate to potential user’s experimental design.

Each project must be approved and must adhere to both Czech and European directives regarding animal experiments (European Communities council directive of 22nd of September 2010 (2010/63/EU)). We can offer further assistance in obtaining such permits if needed. Users are required to hold a valid animal handing license if they are to perform an experiment independently.

Users are able to select from one of the following options:

  1. Minimal support: Users will be given training of appropriate depth based on their individual experience in both surgical and imaging techniques. After the necessary training, users can carry out experiments on their own.
  2. Partial support:
    1. Users will be trained in surgical procedures to be able to prepare animals for live imaging on their own. Imaging and analysis will be carried out by our specialists.
    2. Users will be trained in imaging methods available in the laboratory to be able to perform live imaging on their own. Preparation of animals for the experiment will be carried out by our specialists.
  3. Full support: Our specialists will perform the experiments for users in full.

In some cases of long term or terminal imaging, it is possible to prepare animals in another facility before transporting them to ours.

The services are primarily tailored for rodent models. However, use of different model organisms, including fruit flies or zebrafish, may be feasible and can be explored through further discussion.



Surgery and microscopy specialist

Technical specialist