Deep imaging by two-photon microscopy, reveals interplay between B cells and T cells (blue) with XCR1+ dendritic cells (green) in the spleen.

“The rapid advancement of our capacity to image immune cells in action deep within living tissues has already provided some amazing visual insights into immune cell behaviour. Future developments in microscopy and image processing promise truly spectacular viewing.”

In this theme, we are developing advanced surgical and engineering methods to enable imaging of live tissues, without disturbing their function, or of fixed tissues, where large volumes are imaged to gain tissue-wide views of immunity. This work is being combined with developing microscopes with increased capacity to image at high speeds deep within living animal tissues. We are also developing novel transgenic systems and cell labelling techniques to visualise multiple cell populations and structural features in living animals or animal tissues. Our work provides a highly visual, novel understanding of the biology of immune cells as they migrate, interact and function in their natural environment.



Our bodies are constantly at risk of attack by unseen microorganisms in the environment. To prevent potentially lethal infections, mammals have developed sophisticated immune systems comprising various cell types coordinated to work together to rapidly drive out invaders. Most immune responses start within lymph nodes – small glands with infection-fighting cells – or in the spleen. Both are organs located deep within the body and are challenging to visualise. To better understand immunity, we aim to observe the coordinated responses of immune cells deep within tissues. This will be achieved by creating tools to simultaneously monitor multiple populations of cells, improving microscopes for deeper penetration of vital organs, and by developing methodologies for labelling cells and structures within these tissues.

In 2020, Imaging CoE scientists successfully used intravital two-photon microscopy combined with tissue clearing to visualise B cell interactions with dendritic cells in lymph nodes and the spleen during the development of antibody responses. We also imaged DEC205 molecules expressed by these same dendritic cells using cryogenic electron microscopy (cryo-EM) to reveal how they interact and function on the cell surface. These studies revealed an important method of communication between immune cells essential for initiating immune responses.

Imaging CoE scientists reported their development of adaptive optics for video-rate aberration correction in two-photon microscopy, which allows high-speed imaging deep within tissues. This work greatly advances image resolution together with speed of image capture allowing clearer visualisation of fast-moving aspects of immunity.

In studies relating to the development of a malaria vaccination approach, imaging capacity developed by Centre scientists was used to visualise the immune cell involved in eliciting vaccine function. Natural killer T (NKT) cells were imaged deep in the liver under steady state conditions and then after vaccination to examine their recruitment to vaccination sites. In other studies, reorganisation of immune tissue architecture was revealed to affect generation of immunity after systemic inflammation, as seen after viral infection.

In this field, our scientists are working to solve major questions including: how immune cells interact with invading pathogens, how immune responses to infections begin, and how cells cooperate to fight microbes and cancer cells. By mapping the behaviour of various immune cell populations during the various phases of immunity, we have gained insights into the regulation of thiscomplex but vital system.


  1. Developed capacity to undertake deep two-photon imaging of brain, liver, skin, spleen and lymph nodes.
  2. Developed clearing techniques for spleen, liver and lymph nodes to enable whole organ or thick slice imaging leading to advances in understanding immune cell functions during immune responses.
  3. Developed immunohistocytometry approach to identify and map the location of multiple different cell types simultaneously in static images.
  4. Improved depth of intra-vital imaging by developing adaptive optics, rapid axial scanning and real-time image processing for 3D imaging deep in living tissues, e.g. spleen.
  5. Mathematically modelled immune surveillance of the liver, lymph nodes and spleen by identifying and measuring immune cells subset movement and function within these tissues, mapping tissue architecture and then modelling behaviour.