Trainer biographies
Anna Kreshuk – EMBL
Group leader of the Kreshuk group at the European Molecular Biology Laboratory, EMBL.
Awais Athar – EMBL-EBI
Awais Athar is a Software Development Project Leader at the European Bioinformatics Institute, working on BioStudies, BioImage Archive and ArrayExpress. Prior to joining EBI in 2015, he has worked in a diverse set of domains including artifical intelligence, data storage, industrial automation, e-Commerce, ERP, 3D graphics, and mobile apps. His research interests include Natural Language Processing, Information Retrieval and Speech Processing and he holds a PhD in Computer Science from the University of Cambridge.
Beth Cimini – Broad Institute
Dr. Beth Cimini is the Associate Director of Bioimage Analysis, CZI Imaging Scientist and head of the Cimini Lab in the Imaging Platform at the Broad Institute in Cambridge, MA. She obtained a PhD in Biochemistry and Molecular Biology with Dr. Elizabeth Blackburn at UCSF, studying splicing variants of the telomere master scaffolding protein TIN2. This work honed her interests in image analysis, leading her to postdoctoral and staff scientist roles with Dr. Anne Carpenter’s lab at the Broad, leading a team collaborating with ~30 outside scientists per year on custom image analysis projects. The Cimini lab focuses on bioimage analysis tool creation (Piximi) and maintenance (CellProfiler), as well as on applying open source tools to novel biological problems. She created and directs the Platform’s Postdoctoral Training Program in Bioimage Analysis, and also leads the Broad efforts towards community engagement and driving biological projects for the Center for Open Bioimage Analysis (COBA).
Callum Tromans-Coia – Broad Institute
My background is originally in wet-lab biology, where I studied the DNA damage response. Now I help other biologists gain deeper insight into their images using machine learning
Craig Russell – EMBL-EBI
Craig is a staff scientist at the European BioInformatics Institute – EMBL. His main interests are large biological imaging data analysis, cloud computing and infrastructure, and using machine learning for developing new image analysis tools. He obtained his PhD in microscope development from the University of Cambridge.
Damian Dalle Nogare – Human Technopole
Damian Dalle Nogare is the manager of NoBIAS, the National Bioimage Analysis Service, part of the National Facility for Data Handling and Analysis at the Fondazione Human Technopole in Milan, Italy where he leads a team of bioimage analysts and research software engineers. Prior to joining Human Technopole, he was a staff scientist in the section of neural developmental dynamics at the National Institutes of Health in Bethesda Maryland, where he worked on collective cell migration and organ patterning. He received his PhD in Biochemsitry and Cell Biology in 2008 from Rice University in Houston Texas, and his undergraduate degree in Biochemistry from the University of Otago in Dunedin, New Zealand.
Dominik Kutra – EMBL
Dominik is an electrical engineer by training who got absorbed by the software side of image analysis. After working as a researcher in medical image analysis at Philips Research, he joined the ilastik development team, led by Anna Kreshuk, in 2017. He is interested in delivering machine-learning based image analysis methods to domain experts in a user-friendly, reproducible way.
Esteban Miglietta – Broad Institute
I studied Biology at the University of Buenos Aires, Argentina, where I also got my PhD. Captured by the beauty of biological images and with the purpose of helping other fellow life-science researchers answer their biological questions, I worked as a Research Support Professional at the microscopy facility of the Leloir Institute (Buenos Aires, Argentina) for two years. There, I learned a lot about fluorescence, and especially confocal, microscopy and contributed to developing and improving acquisition and image analysis pipelines, as well as training new users and establishing a succesful training program. Currently, I am a Postdoctoral Associate at Beth Cimini’s lab in the Imaging Platform at the Broad Institute of Harvard and MIT (Cambridge, MA, USA). Here, I work on expanding my image analysis toolkit while working on a wide variety of projects with collaborators both from within and outside the institute. I am especially interested in using ML/DL approaches to image analysis as well as in collaborating with the development of the CellProfiler software, and with participating in trainings involving the use of this tool.
Estibalis Gomez de Mariscal – Instituto Gulbenkian de Ciência
I’m an EMBO postdoctoral fellowship in Henriques Lab at Instituto Gulbenkian de Ciência, Portugal, developing machine learning (ML) techniques to enable further biological discoveries from microscopy imaging. During my PhD at Universidad Carlos III de Madrid, Spain, I developed computational methods to characterise cancer cell motility and enable further research on sEVs-based inter-cellular communication. Together with colleagues, I work on the development of deepImageJ, the BioImage Model Zoo, and the ZeroCostDL4Mic platform.
Frances Wong – University of Dundee
Frances Wong leads the Image Data Resource (IDR) project and is the scientific curator for the IDR. She received her PhD in Developmental Biology from the University of Edinburgh. She then carried out post-doctoral research in molecular biology, genetics, genomics, neuroscience and biomedical imaging. She has also worked on atlas-based gene expression databases and created new online scientific resources.
Guillaume Jacquemet – Abo Akademi University
Guillaume Jacquemet is an Associate Professor at Abo Akademi University Turku, Finland. His research focuses on the molecular mechanisms of cell adhesion and migration in health and disease. He is particularly interested in the role of the extracellular matrix in cancer progression and metastasis. His lab uses a combination of cell biology, biochemistry, biophysics and advanced microscopy techniques to study the molecular mechanisms of cell adhesion and migration in health and disease.
Jason Swedlow – University of Dundee
Jason Swedlow OBE FRSE received a BA in Chemistry from Brandeis University (1982) and a Ph.D. in Biophysics from UC San Francisco (1994). He joined the Wellcome Trust Biocentre at the University of Dundee, Scotland in 1998 and is currently Professor of Quantitative Cell Biology in Dundee’s School of Life Sciences and serves as Program Director for Wellcome Leap’s Delta Tissue Program. His research interests are the mechanisms and regulation of chromosome segregation during mitotic cell division, and the development of software for handling and sharing large scientific image datasets. Prof Swedlow is a co-founder of the Open Microscopy Environment (OME), an international consortium that develops and releases open source software for biological imaging. He also founded Glencoe Software, Inc., which commercializes and customizes OME technology for use in biotech and pharma and data publishing, and BioImagingUK, a consortium of UK imaging scientists that define priorities for imaging in the life sciences. Prof Swedlow was named Social and Overall Innovator of the Year by the BBSRC in 2011, a Fellow of the Royal Society of Edinburgh in 2012 and was made an honorary Officer of the Order of the British Empire for services to bioimaging in 2021.
Jean-Marie Burel – University of Dundee
Jean-Marie Burel joined the staff of the Swedlow lab in 2003. Since then, he’s been contributing to the development of OME. He received his PhD in mathematics from the University of Brest in 2000. His research interests lie in the area of harmonic maps, harmonic morphisms and geometric structure. After his PhD, he worked in a private company as developer then moved (September 2001) to Lund University, Sweden, where he held a post-doctoral research position. Jean-Marie now enjoys the muddy rugby pitches of Scotland.
Le Liu – Broad Institute
I am currently a visiting Ph.D. student at the Broad Institute of MIT and Harvard, working in Beth Cimini’s lab. I am interested in applying high-throughput imaging techniques to address complex biological questions in context of development, plant-environment interaction. Alongside my scientific pursuits, I am deeply passionate about effectively communicating scientific concepts and methodologies to diverse audiences.
Matthew Hartley – EMBL-EBI
Matthew is Team Leader for the BioImage Archive at EMBL-EBI. The Archive is EMBL-EBI’s cross modality data resource that allows both deposition of biological images associated with peer reviewed publications, and reuse of existing imaging data. Prior to joining EBI, Matthew led the Informatics team at the John Innes Centre, a research institute focussing on plant and microbial sciences. Matthew’s background is in image analysis, numerical and statistical modelling and scientific data infrastructure.
Martin Weigert – EPFL
Martin Weigert studied Physics in Dresden, Germany and then did a PhD in computer science at the MPI-CBG in Dresden, where he worked on computational methods for the analysis, simulation, and restoration of fluorescence microscopy data. In 2019 he joined the SV faculty at EPFL as an ELISIR fellow, where his research focuses on machine-learning based methods for reconstruction and interpretation of large microscopy images.
Paula Llanos – Broad Institute
My name is Paula Llanos, and I am a postdoctoral researcher at the Cimini Lab at the Broad Institute. I earned my PhD in Biomedical Science, focusing on the self-organization of microtubules during cell division. Throughout my doctoral studies, I extensively utilized live imaging techniques and developed a passion for microscopy and image analysis. Currently, my work involves addressing various projects in image analysis, with a focus on 3D analysis from microscopy images. Additionally, I collaborate on building CellProfiler pipelines for image analysis
Petr Walczysko – University of Dundee
Petr Walczysko joined the OME project in October 2012 as a software specialist for testing and quality assurance. He studied at Charles University of Prague where he received Master of Science degree in Physics and the University of Freiburg in Germany where he received PhD in Biology. Throughout his PhD studies and his further career as a researcher he was intensively using conventional, confocal and multiphoton fluorescence microscopy applications on biological systems. He was adapting these optical microscopy techniques for particular biological problems, and also worked on the subsequent image analysis of microscopic images in a range of image analysis programs. He enjoys yoga, reading and chess.
Shatavisha Desgupta – Broad Institute
Shatavisha Dasgupta (MD, PhD) is a pathologist-scientist, currently pursuing a fellowship in bioimage analysis at the Cimini Lab of Broad Institute of MIT and Harvard. She trained in Surgical Pathology in India after completing her basic medical education. Thereafter, she completed her PhD degree from Erasmus University from the Netherlands, and a postdoctoral fellowship from Dana-Farber Cancer Institute. The focus of her research was precancerous lesions, meaning the growths that have a risk of becoming cancerous over time.
Suganya Sivagurunathan – Broad Institute
I am a cell biologist and currently getting trained on image analysis to understand the microscopic images better.
Ugis Sarkans – EMBL-EBI
Ugis Sarkans leads the BioStudies team at EMBL-EBI. He was involved in the development of ArrayExpress, a public gene expression data resource (and an ELIXIR core resource), and the associated community standards. Ugis’s team now develops and runs the BioStudies database, a resource for aggregation and publishing of heterogeneous life sciences data linked to publication. BioStudies now provides access to the ArrayExpress data collection and provides the underlying infrastructure for the BioImage Archive. We also collaborate on a number of European ‘multi-omics’ projects in a data management and publishing capacity. Prior to joining EBI Ugis was a postdoc at the University of Wales. His main scientific interests are related to knowledge and data management.
Virginie Uhlmann – University of Zurich and EMBL-EBI
Virginie Uhlmann is the Director of the BioVisionCenter at the University of Zurich and a Visiting Research Group Leader at the European Bioinformatics Institute (EMBL-EBI) in Cambridge. Her main research area is quantitative bioimage analysis, with strong interests in machine learning and computational geometry.
