Recent advancements in microscopy technology have revolutionized our ability to routinely acquire large, multi-dimensional image datasets. However, gaps remain in the effective analysis of this data, primarily due to a lack of computational skills among researchers. This often results in a reliance on qualitative, manual image assessments, which lack the precision, reproducibility, and scalability that automated, quantitative analysis can provide.
To bridge this gap, this two-day workshop is designed to empower microscopists and researchers with the necessary skills and tools to confidently analyse their data. Under the instruction of experienced core facility staff from the Francis Crick Institute and King’s College London, participants will be introduced to open-source tools such as FIJI and napari, and will be introduced to methodologies for automating their image analyses, thus enhancing research precision, efficiency, and reproducibility.
This workshop is suitable for any researcher, from early career researchers to experienced group leaders, engaged in the acquisition of significant amounts of microscopy image data. No prior experience in image analysis or coding is required, although a basic understanding of microscopy and image acquisition will be beneficial. Attendees will leave the workshop equipped with a knowledge of the tools needed to design and execute automated, unbiased, reproducible image analysis workflows.
The workshop will be taking place at the University of Galway, Ireland.
Scientific Organiser
David Barry
Dave is a bioimage analyst with over 15 years’ experience of developing algorithms and open-source software in life science research. After completing his undergraduate studies in Electronic Engineering at University College Dublin (2004), Dave did his PhD at the Dublin Institute of Technology (now TU Dublin) with Dr Gwilym Williams, using image analysis to relate the morphology of filamentous microbes to their metabolite yield in fermentations (2010). He then spent six years as a post-doc in the lab of Dr Michael Way at the Cancer Research UK London Research Institute (which became part of the Francis Crick Institute in 2015), where he used live cell imaging and developed software to analyse cellular and sub-cellular processes. Since 2017, Dave has worked as a dedicated image analyst at the Francis Crick Institute and is now Deputy Head of the Crick Advanced Light Microscopy Science Technology Platform.
Martin Jones
Martin is currently Deputy Head of Microscopy Prototyping in the Electron Microscopy Science Technology Platform at the Francis Crick Institute. His work focuses on developing new software and hardware tools for dealing with the deluge of data coming from modern microscopes. His background is in experimental quantum optics from the University of Sussex. After postdoctoral research and teaching fellowships in physics, he moved to the Vascular Biology Lab led by Holger Gerhardt at Cancer Research UK’s London Research Institute to work on microscope development and image analysis. From there he moved to the LRI’s Electron Microscopy core facility, led by Lucy Collinson, which subsequently moved to its current home at the Francis Crick Institute. Martin now works closely with the Crick’s Scientific Computing Science Technology Platform to work on methods for analysing large complex imaging datasets and has a strong interest in training.
Stefania Marcotti
Stefania is a postdoc and bioimage analyst at King's College London. After a BSc and an MSc in biomechanical engineering in Milan, she obtained a PhD at the University of Sheffield focused on the mechanical characterisation of bone cells with atomic force microscopy and finite element modelling. Thanks to the possibility of combining both experimental and computational approaches in all of her projects, she developed an interest in data and image quantitative analysis. In 2018 she joined Brian Stramer's group and her current research interest lies in developing and automating analysis pipelines for biological applications. Since 2023, she also offers image analysis support to the Nikon Imaging Centre and Microscopy Innovation Centre users at KCL.
Emma McDermott
Emma is a Senior Technical Officer in electron microscopy in the Centre for Microscopy and Imaging at the University of Galway. She received her BSc in Anatomy and MSc in Regenerative Medicine, both at the University of Galway, and completed her PhD at the University of Aberdeen in 2018. During her PhD, she used electron tomography to visualise the complex 3D ultrastructure of bone-resorbing cells called osteoclasts. As the representative for the Microscopical Society of Ireland on the Early Career Committee, Emma aims to increase engagement and encourage networking between the RMS and Irish Early Career Researchers.
Kerry Thompson
Kerry is a Lecturer in Anatomy at the University of Galway since 2017. She is the Programme Director for the newly established MSc in Microscopy & Imaging at Galway. In 2010 she was awarded her PhD for a microscopy heavy research project which focused on structure function relations in the human endometrium. In 2011 she began work as a Postdoctoral Microscopy Facility Scientist in the Centre for Microscopy and Imaging (CMI) in Galway and was a key member in its establishment.
In the 2014/2015 academic year Kerry acted as a project lead in the “Under the Microscope” Programme, which brought the Microscope Activity Kits from the RMS into Irish Primary Schools for the first time. Following this Kerry was elected on the Outreach & Education Committee of the RMS. With the support of both the RMS and the Microscopy Society of Ireland, the team continue to visit schools all over Ireland and partake in outreach events. In 2018 she succeed Prof Susan Anderson as the Honorary Secretary of Outreach and Education of the RMS. Her current research is focused on the development of correlative light and advanced electron microscopy techniques and technologies. She is keenly involved in the acquisition of microscopy related research infrastructure, and the development of adequate training and career progression pathways for Imaging Scientists and Core Facility Staff.
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