Project directors

• Dr. Santiago F. Gonzalez is a group leader at the Institute for Research in Biomedicine (IRB, Bellinzona, Switzerland). Dr. Gonzalez has extensive experience in the field of imaging. During his postdoctoral research at Harvard University, he received complete training for the use of state-of-the-art imaging techniques, including MP-IVM. After establishing his own group in Switzerland, he has completed, with support from the Swiss National Science Foundation, the installation of a state-of-the-art MP-IVM facility at the IRB.
• Prof. Dr. Rolf Krause is the director of the Euler institute and a professor with a chair in Advanced Scientific Computing at USI, Lugano - Switzerland.
  His research focuses on numerical simulation and mathematical modelling in scientific computing and computational sciences, leading the research group "High Performance Methods for Numerical Simulation in Science, Medicine and Engineering". He is also co-director of the recently installed Center for Computational Medicine in Cardiology - CCMC.
• Dr. Diego Ulisse Pizzagalli leads the Digital Pathophysiology Lab at the Euler institute, USI. His research is at the intersection of Computational Sciences and Biomedicine. In his doctoral studies, supported by systemsx.ch, Diego focused on network theory to study the migration and interaction of immune cells in vivo, contributing to bridging the gap between computer vision and immunology. Moreover, he recently translated these techniques from cells to patients and is currently co-PI in a project aiming at monitoring longitudinally a cohort of patients with chronic liver disease. Diego serves as a teaching assistant and lecturer at USI in subjects related to machine learning in medicine, computing theory, and signal processing.

Project partners

Immunemap is a collaborative project supported by a network of international laboratories willing at making 2-photon imaging data of the immune system FAIR (Findable, Accessible, Interoperable, Reusable).

 

Britta Engelhardt (Theodor Kocher Institute, University of Bern, Bern, Switzerland). The group of Prof. Engelhardt developed an extensive in vivo imaging biobank that includes 2P-IVM imaging of T cell interactions in the cervical spinal cord microvessels of mice suffering from experimental autoimmune encephalomyelitis. Prof. Engelhard has a solid career as a relevant world expert on imaging autoimmune diseases. Mykhailo Vladymyrov (University of Bern), Neda Haghayegh Jahromi (System Biology Division, Philip Morris International, Neuchâtel, Switzerland).

Hans Uwe Simon (University of Bern, Bern, Switzerland). MD Uwe’s laboratory explores apoptosis and autophagy in inflammatory diseases and cancer, focusing on atopic dermatitis, hypereosinophilic syndromes, eosinophilic esophagitis, bullous pemphigoid, and malignant melanoma. They aim to identify novel drug targets for therapeutic interventions. Additionally, they have developed in vitro and in vivo systems to assess drug effects on the immune system. Engaged in clinical drug studies, their research bridges pathogenesis understanding with translational medicine for improved disease management. Nina Germic (Respiratory Infections Division, Roche, Rotkreuz, Switzerland).

Jens Volker Stein (University of Fribourg, Switzerland). Dr. Stein wants to clarify the molecular and cellular processes that govern adaptive immune responses mediated by cytotoxic CD8+ T cells. His research line examines lymphoid tissue using two-photon microscopy (2PIVM) to define the key regulators of T cell activation by using genetically modified CD8+ T cells. Petra Pfenninger, Jun Abe.

Cornelia Halin (ETH, Zurich, Switzerland). The group of Prof. Halin specializes in the study of intravital microscopy observations of migratory T cells and dendritic cells in and around dermal lymphatic capillaries in murine skin. Since the establishment of her lab in ETH, Prof. Halin has published her innovative research in the most important journal in the field of immunology. Morgan Hunter.

Wolfgang Kastenmuller (University of Bonn, Bonn, Germany). Prof. Kastenmuller directs a dynamic group that focuses on the characterization of the interactions between DC and CD8 and CD4 T cell subsets in the LN in response to different conditions. The Kastenmuller lab has significantly contributed to the field of immuno-imaging and has published innovative imaging articles in top journals like Immunity or Nature Immunology. Sarah Eickhoff (University Hospital Bonn, Bonn, Germany).

Andres Hidalgo (Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain). The group of Dr. Hidalgo is specialized in the study of the migration mechanisms that lead to the recruitment of inflammatory cells from the blood vessels following different insults. He has published his recent papers on neutrophil dynamics in journals like Cell or Science. Miguel Palomino-Segura, Georgiana Crainiciuc, José M. Androver.

Matteo Iannacone (San Raffaele Research Institute, Milan, Italy). MD PhD Iannacone directs a group specialized in studying the activation of adaptive immune cells and immunopathology during viral infection and cancer. He has developed specific models to study the dynamics of T cells in the liver in response to viral infection. Iannaccone’s group has recently published novel research that regards liver imaging in the journal Cell. Xenia Fitch, Federica Moalli, Alexandre Bénéchet (CHUV, Lausanne University Hospital)

Philippe Bousso (Pasteur Institute, Paris, France). Dr. Bousso leads the group Dynamics of Immune Response at the Pasteur Institute. By further developing functional in vivo imaging, they aim at identifying critical aspects of T cell and NK cell activation and function during tumor growth, during infection by an intracellular parasite, and transplantation. Hélène Moreau.

Ana-Maria Lennon-Duménil (Curie Institute, Paris, France). Dr. Ana-Maria Lennon-Duménil's scientific career has been built on the use of multidisciplinary approaches to understand, at different scales, the functioning of cells in the immune system. In 2008, she set up a consortium including cell biologist M. Piel (I. Curie) and theoretical physicist R. Voituriez (UPMC, Paris). Their goal was to apply quantitative imaging and microfluidics to study molecular mechanisms and physical principles governing the ability of cells of the immune system to move. Their work has opened up a still unexplored line of research into the mechanisms that allow dendritic cells, to coordinate their functions with their migration in time and space. They have given rise to more than 25 publications, including some in very prestigious journals such as Science, Cell, Nature Cell Biology, Nature Physics, and Developmental Cell. Dorian Obino.

Milka Sarris (University of Cambridge, Cambridge, UK). Dr. Sarris' laboratory investigates how immune cell movement is orchestrated during inflammation using zebrafish larvae as a model. Leveraging advanced microscopy and genetic manipulation, they decipher the molecular and physical cues guiding leukocyte recruitment to damaged tissues. Their goal is to obtain a better understanding of how leukocytes interpret complex environmental cues to generate effective immune responses. Antonios Georgantzoglou (University of Copenhagen, Copenhagen, Denmark).

Johannes Textor (Radboud University, Nijmegen, Netherlands). Dr. Johannes Textor leads the Computational Immunology group at Radboud University, employing simulation models, machine learning, and causal inference to study the adaptive immune system. Their research aims to understand immune responses to pathogens and tumors, informing immunological treatments. They develop Artificial Immune Systems to compare immune and nervous system information processing, investigating their distinct architectures and complementary roles. Collaborating with colleagues at Radboudumc's Tumor Immunology department, they provide computational support, advancing immunological research through diverse methodologies. Inge M. N. Wortel.

 

Thomas Murooka (University of Manitoba, Manitoba, Canada). The laboratory of Dr. Murooka specialized in the study of T cells and DC as well as their migration during HIV infection in lymphoid tissues. Additionally, they studied the effector and regulatory T cell behaviors during Leishmania major infection in mouse skin. During his career, Dr. Murooka has published high-impact factor papers in journals like Nature.

Michael Carroll (Harvard Medical School, Boston, USA). The group of Prof. Carroll has made important contributions to the field of antigen trafficking and B cell biology. He has extensive experience characterizing the behavior of DC and B cells in different models including infectious diseases and autoimmune diseases. The group publishes their research in a regular base in the highest impact factor journals in the field including Nature, Science or Cell.

Francesco Marangoni (University of California - Irvine, USA) . Dr. Marangoni studies immune-evasion mechanisms, especially the ones favouring the development of tumours. His primary technological approach combines multiphoton intravital microscopy with functional reporters of biological processes (functional intravital microscopy or F-IVM). His long-term goal is to devise new forms of immunotherapy through the manipulation of immune-evasion mechanisms. His Functional Immuno-Imaging Lab investigates whether checkpoint blockade immunotherapy enhances the function of tumour-associated Treg, which in turn may limit therapeutic efficacy. Moreover, their studies hinge on new mouse models allowing to map the function of TAM (Tumor-associated macrophages) to identify the factors leading to TAM reprogramming towards pro-inflammatory functions in vivo.

Michael D. Cahalan (University of California - Irvine, USA). Dr. Chalan's research incorporates single-cell approaches to investigate the immune response, using the patch-clamp method to characterize ion channels and a variety of imaging techniques to monitor motility, cellular interactions, Ca2+ signalling, and gene expression.  His pioneering work identified the pivotal role of ion channels in the immune response. He elucidated physiological functions and the molecular basis for calcium signalling that activates T lymphocytes. By imaging lymphoid organs, his work revealed an elegant cellular choreography that underlies immune responses in vivo. Shivashankar Othy.

Thorsten Mempel (Massachusetts General Hospital, USA). Dr. Mempel's Laboratory is seeking to understand how the function of T cells is regulated through their interaction with other cells, structural tissue components, and soluble mediators that they encounter in tissues. Their main approach to this end is direct dynamic in vivo visualization of immune processes at cellular and subcellular resolution in living mice, using multiphoton intravital microscopy.

Mauro Di Pilato (MD Anderson Cancer Center, Houston, Texas, USA). The laboratory of Dr. Di Pilato investigates and characterizes which immune signals are involved in the intratumoral infiltration of unstable Treg. Specifically, they want to focus on pathways that are involved in Treg intratumoral destabilization, proliferation and survival and define new strategies of Treg accumulation. Their goal is to develop new approaches that will increase the effectiveness of cancer immunotherapy and the number of cancer patients who will respond to immune checkpoint blockade inhibitors, and finally to prevent the progression of primary melanomas.

Chris Xu (Cornell University, Ithaca, NY, USA). Dr. Xu is currently a Professor of Applied and Engineering Physics, at Cornell University, the Mong Family Foundation Director of Cornell Neurotech– Engineering, and the Director of the Cornell NeuroNex Hub, an NSF-funded center for developing neurotechnology. Before Cornell, he was a member of the technical staff at Bell Laboratories, where he developed new long-haul fiber optic communication systems. His current research areas are biomedical imaging and fiber optics. He is a fellow of the Optical Society of America and a fellow of the National Academy of Inventors. Kibaek Choe.

 Michael Hickey (Monash University, Melbourne, Australia). Professor Michael Hickey is the Director of the Monash Centre for Inflammatory Diseases at Monash Medical Centre. The main focus of his current research is white blood cell-mediated inflammatory injury of the kidney, a major cause of kidney failure. He investigates the mechanisms whereby white blood cells are attracted to the glomerulus and understands their behaviour once they get there. His laboratory examines inflammatory disease of the skin and how regulatory T cells dampen down skin inflammation. The ultimate aim of this work is to develop a detailed molecular understanding of the mechanisms whereby leukocytes cause or control injury in inflamed tissues. Ursula Norman.

 

 

 Data curation and communication responsible

• Pau Carrillo Barberà is a Bioimage Analyst at IRB. Pau is responsible for handling the curation and integration of IVM data from an international network of laboratories contributing to the IMMUNEMAP database and the establishment of a data annotation workflow. In his doctoral studies at BIOTECMED (University of Valencia) he worked on the deployment of microscopy-based screening protocols and bioimage analysis workflows for the study of neural stem cells.
• Elisa Palladino is an Imaging Specialist at IRB. Elisa is responsible for gathering data and populating the IMMUNEMAP platform. She also takes care to establish collaborations with new partners, around the world. 

Imaging specialists and developers

• Benedikt Thelen is a Biomedical Engineer at USI. Benedikt is responsible for the development of the IT infrastructure and software backend of the database. After completing his master at the university of Bern, he has participated in multiple scientific projects as researcher and programmer.
• Kevin Ceni is a Biomedical Engineer at IRB. Kevin is responsible for the development of the client-side software of the project (frontend) and the implementation of web-based tools for the analysis of IVM data. In his master thesis at the University of Bern he worked on the development of a convolutional neural network able to classify and locate different diseases affecting the retina.
• Alain Pulfer is a PhD student in Bioimage Analysis at IRB. Alain works on the design of diverse bioimage data analysis tools for IVM data, e.g., for quality assessment or action recognition.
• Joy Bordini is a Bioinformatician and Bioimage Analyst at IRB. Joy works on the design of diverse bioimage data analysis tools for IVM data, e.g., segmentation or colocalization methods.
• Enrico Moscatello is a Engineering of Computing Systems student at POLIMI. Enrico is responsible for the development of the software and debugging.