Data Analysis in Imaging
The goal of the Data Analysis in Imaging Section is to support and develop the Image Analysis community in the UK and the application of this science to the field of microscopy in all its forms.
Other science section
The dependence of the biosciences on image analysis is growing . There is now a clear need for a trained and better-organised community of image analysts who will support this growth [2,3]. The NEUBIAS network  is a relatively new initiative, setup to help address these issues on a EU and, increasingly, international level. Presently, there is very little activity nationally in the UK that complements this work of supporting image analysis. At a recent meeting of the Royal Microscopy Society (RMS) council, the importance of image analysis for microscopy was discussed. The RMS are very keen to assist in the formation and activity of a Focused Interest Group (FIG) whose role will be to develop and support the image analysis community in the UK. To this end, following several successful meetings and discussions, this document has been drafted to describe the formation of the Image Analysis Focused Interest Group of the RMS (IAFIG-RMS). The goal of the IAFIG-RMS will be to support and develop the Image Analysis community in the UK and the application of this science to the field of microscopy in all its forms. In the first instance, Dr. Dominic Waithe will act as chair for the proposed group having being nominated by Mr. Alex Sossick and confirmed by Dr. Lucy Collinson, both section chairs of the RMS.
The NEUBIAS network has a key focus on developing the interests of bioimage analysts. A bioimage analyst is defined as follows: "Bioimage analysts are a new type of experts in bioImaging, they select appropriate image processing algorithms and their implementations, and assemble them for conducting practical Bioimage Analysis.” . The remit of the IAFIG-RMS will include the interests of the bioimage analysts in the UK as well as all the other types of scientist who in some way are involved in microscopy image analysis. This will include mathematicians, research engineers, bioinformaticians, biophysicists, bioscientists, microscopists, computer vision scientists and any other scientist who has some involvement in microscopy image analysis. We want to actively encourage scientists and engineers from a variety of disciplines to collaborate providing training and support to those in more applied roles. This will take the form of workshops, and conference sessions, designed to raise awareness for image analysis within microscopy and to attract skilled professionals to contribute to this field.
It is clear that at this stage no one model of career structure is appropriate for the image analysis community as a whole, especially for those embedded in non-numerical disciplines [2,3]. We believe it should be possible for image analysts of all levels to apply for funding and support based on the justifiable popularity of an algorithm or piece of software for example. Part of the responsibilities of the IAFIG-RMS will be to communicate with funding bodies to provide enhanced backing and resources for image analysts working actively in training, support, development and research. This will work in two ways: Firstly in terms of communicating what funding bodies are doing and planning for the community, as well as helping form a structured picture of the community for the benefit of the funding bodies. To help with representation, the IAFIG-RMS will encourage the appointment of image analysts and related members on funding bodies and other decision-making councils. The IAFIG-RMS will work to popularise these approaches and will work diligently with funding bodies, the scientific community and the government for more appropriate career options for those performing image analysis.
Many image analysts perform some kind of training in their day-to-day support and research work. We would like to incentivise the running of training courses in two ways. Firstly if individuals consistently organise or support image analysis events we would like to recognise their contribution with an affiliation (e.g. IAFIG-RMS Trainer). We would also like to reward those who have attained a certain level of training by attending multiple courses. We will also encourage and support users to make their materials public, taking advantage of the existing NEUBIAS infrastructure as well as content (website, mailouts) that publicise the resources already in existence. Furthermore, the IAFIG-RMS will encourage courses for its members of all levels boosting the skills and training of the community as a whole. In addition, we would act as a group to assist and reinforce the training being performed already for bioimage analysis in the UK. This would involve getting trainers accredited by other trainers before they run courses and through providing feedback as necessary, as well as through sharing teaching materials. The UK has many organisations and companies that actively apply image analysis in different ways and who also promote best practise for programming and software development. The IAFIG-RMS will work to actively encourage engagement with existing UK based training schemes, (e.g. Software Carpentry, NAG, ARCHER, ImageJ/Fiji, OME) as well as with companies (e.g. Google, Zeiss, Olympus, SVI, Leica).
UK Science is respected throughout the world and part of this reputation stems from the high-standards and integrity which it maintains. The IAFIG-RMS community believes that integrity, and its upkeep, is key to the future of research and that the IAFIG-RMS will be able to contribute to this positively. One of the goals of IAFIG-RMS will be to outline the key aspects of image acquisition, processing, and analysis and promote best practise for its practitioners. This will provide a guideline for reproducible image analysis which life scientists and physical scientists can refer to for the publication of their research. Journals will also be able to refer to this resource as it will represent a consistent guideline to which they can adhere. Journals will also will be able to request the assistance of IAFIG-RMS members for certain tasks which will have a positive effect on publication quality. Furthermore, grant-awarding bodies will be able to contact members of the IAFIG-RMS for reference and clarification.
The IAFIG-RMS will utilise the best online resources to support its members and create a community. An official website will be constructed, www.IAFIG-RMS.org, which will explain what IAFIG-RMS is and will also publicise its activities and members through web links. A JISC email list ([email protected]) and a forum will be created to support and promote day-to-day discussion on image analysis related topics. A committee will meet in person every 6 months to discuss progress and define goals. The meetings will be open to anyone to attend, and those who consistently attend meetings will be designated as IAFIG-RMS committee members.
 A Pilot Survey on Bioimage Analysis Needs 2015: Results Summary (Kota Miura)
Dr Martin Jones
Francis Crick Institute
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.
Dr Chas Nelson
University of Glasgow
Chas is currently an Honorary Research Fellow at the University of Glasgow whilst he is on secondment as Chief Technology Officer of gliff.ai. Chas' academic work has focussed on developing bioimage analysis and instrumentation tools for quantified imaging in the life sciences. His current focus is on gliff.ai, a Durham University spin-out he founded during his PhD whilst his research efforts continue to focus on quantitative bioimaging, light sheet fluorescence microscopy and zebrafish embryology. Chas is active in the microscopy community and involved in a variety of training courses, largely focussed on python for biologists and bioimage analysis. After a PhD in Computer Science at the Durham University, he did a post-doc at the University of Glasgow before being awarded both an EPSRC Doctoral Prize Research Fellowship and an LKAS Research Fellowship in Data Science, from which he is currently on secondment. Chas' interest in phototoxicity stems from years of quantifying biological images and seeing the unintended effects that imaging and experimentation have on the samples being studied.
University of Edinburgh
Peter completed his PhD at Queen’s University Belfast, focussing on the analysis of retinal images and calcium signals in retinal arterioles. He then moved to Germany, becoming a postdoc in the Nikon Imaging Center at Heidelberg University where he spent much of his time helping microscope users interpret their imaging data using open-source software. During this time he wrote a popular bioimage analysis handbook for biologists (https://petebankhead.gitbooks.io/imagej-intro/content/).
Upon returning to Belfast as a postdoc at the end of 2012, Peter encountered digital pathology for the first time. After applying existing open software tools to whole slide images with limited success, he wrote his own: QuPath (https://qupath.github.io). After a short time in industry, Peter is now a Senior Lecturer at the University of Edinburgh, where he is building a group dedicated to developing open AI and bioimage analysis methods for pathology and other imaging data.
Wolfson Bioimaging Facility, University of Bristol
Stephen is a bioimage analyst at the University of Bristol’s Wolfson Bioimaging Facility. Light microscopy has been the common theme throughout his academic career; prior to obtaining his current position, Stephen completed a PhD focused on the construction of a novel fluorescence-based magnetic tweezers microscope (York) and a postdoc position combining patch clamping techniques with fluorescence microscopy (Bristol). These led Stephen to his current position, where he develops custom analysis workflows across a multitude of imaging modalities and research fields for internal and external collaborators. It’s this exposure to a wide range of bioimaging problems that motivated his main research interest into development of open-source modularised image analysis tools for Fiji, which allow the rapid construction of pipelines without the need to ‘reinvent the wheel’ on a daily basis. Stephen also co-runs a series of image analysis workshops in topics such as ImageJ/Fiji and MATLAB.
Dr Stefania Marcotti
Early Career Representative for the DAIM Section
King's College London
Stefania is a postdoc in the Cellular Biophysics section at the Randall Centre for Cell and Molecular Biophysics at KCL. After a BSc and an MSc in biomechanical engineering under the guidance of Prof. Alberto Redaelli at Politecnico di Milano, 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 lie in developing and automating analysis pipelines for biological applications.
UCL Great Ormond Street Institute of Child Health
Dale is the Light Microscopy core facility manager at the UCL Great Ormond Street Institute of Child Health. He took up this position in 2014, having spent the previous 16 years as a postdoc in Liverpool and London. Dale completed his PhD in 1998 at the University of Liverpool, where he learnt the basics of confocal microscopy. In his current post he helps researchers with all aspects of light microscopy and image analysis. He runs an open access image analysis course designed to make image analysis as accessible as possible to the wider research community.
University of Cambridge
Leila Muresan is a Senior Research Associate in the Department of Physiology, Development and Neuroscience of University of Cambridge. She develops original methods and pipelines for the analysis of microscopy images and focuses on solutions for lightsheet microscopy data analysis as well as algorithms for single molecule localisation microscopy. Based at Cambridge Advanced Imaging Centre, she contributes with her expertise to exploit the cutting edge microscopy techniques available in the centre. Starting with 2018 she is an EPSRC Research Software Engineer Fellow.
University of Edinburgh
Laura Murphy completed her PhD in neurobiology at the institute of Genetics and Cancer (IGC), University of Edinburgh, in 2017. Her PhD involved the study of mitochondrial trafficking in neurons using live cell imaging and particle tracking analysis. Working since then as the bioimage analyst in the IGC Advanced Imaging Resource, she helps users extract quantitative information from their microscopy data. Her role involves training on commercial and open-source image analysis programs, holding workshops on image analysis and writing bespoke analysis scripts and workflows, to answer whatever the research question or imaging modality.
Dr Alice Pyne
University of Sheffield
Alice Pyne is a Lecturer in Polymers/Soft Matter & MRC/UKRI Innovation Fellow in the Department of Materials Science and Engineering at the University of Sheffield. Alice has over a decade of experience in scanning probe microscopy, spanning high-speed and high-resolution imaging, probe development and cantilever sensing. Alice’s current research aims to understand how variations in DNA structure can affect fundamental biological processes such as replication and transcription. She uses high-resolution AFM to observe variability in structure and conformation in individual DNA molecules and to understand how these variations influence interactions with oligonucleotides and proteins, with a long-term view to improved development of therapeutics.
Other Committee Members
- Dominic Waithe (Vice Chair)
- Rocco D'Antuono
- Dave Barry
- Sian Culley
- Eric Prestat
- Constantino Carlos Reyes-Aldasoro