Euro-BioImaging is currently processing proposals related to COVID-19 research under Fast Track conditions. Submit your proposal or contact us if you need more information. All proposals will have high priority and will be forwarded directly to the Nodes.
Resources for COVID-19 and related imaging research
Biomedical sciences are key for rapidly addressing the societal challenges posed by the emergence of e.g. novel infectious diseases. Life science research infrastructures offering open and coordinated access to cutting-edge technologies and research services are crucial for facilitating scientific excellence in the biomedical field.
Biological and biomedical imaging technologies are essential for addressing many research questions, such as those related to Covid-19, from fundamental research at the molecular and cellular level to medical applications and diagnostics. Currently, computed tomography (CT) is the imaging method of choice to diagnose and monitor patients with COVID-19 because of its resolution, availability in intensive care units, and cost-effectiveness. However, most of the available imaging modalities – including light and electron microscopy techniques - will be centrally involved in research projects aimed at the development of therapeutics and diagnostics to combat coronavirus infection. The need for an in-depth understanding of the molecular processes of the infection will require the design and testing of innovative imaging probes and the access to proper cellular and animal models that are in the domain of Euro-BioImaging Nodes. Moreover the skills in image analysis together with the access to the powerful AI tools will represent an area where our research infrastructure aims to support the biological and biomedical communities.
Euro-BioImaging provides open access to imaging technologies, training and data services in biological and biomedical imaging at our 21 Nodes. In the current COVID-19 pandemic situation, it is not surprising that Euro-BioImaging’s physical user access services are limited. Nevertheless, imaging research is essential in the fight against the pandemic, and Euro-BioImaging continues to support life science research. The COVID-19 repository below lists a range of imaging-associated services and resources, as well as lots of useful information on imaging research, pulled together from our Hub and Nodes.
Available Euro-BioImaging services (status 27.05.2020)
- User access proposals are received and processed in a normal fashion by the Euro-BioImaging Hub.
- The Population Imaging Node in Rotterdam provides service as usual and accepts access proposals.
- The microscopy facility at the ALM and Molecular Imaging Node in Brno is open for user access.
- The Finnish Advanced Light Microscopy Node in Turku is currently inviting proposals for remote access projects from Finnish and international Euro-BioImaging users and is pleased to provide virtual access to its microscopes until lockdown restrictions are completely lifted
- The Phase Contrast Imaging Flagship Node (Elettra) is now open. A new procedure allows remote access (without physical presence of users) to its services.
- A number of Euro-BioImaging Nodes are providing remote support to users, such as consultation, planning of future activities, and data analysis.
- Euro-BioImaging supports image data sharing, including those for COVID-19 related research projects. Image data sets can be hosted in the BioImage Archive, the Image Data Resource, and EMPIAR, data services supported by national funding awards in the UK and elsewhere, and by Euro-BioImaging and hosted by EMBL-EBI. Experts from these resources and Euro-BioImaging can also help with any computational task related to images and provide support with image data processing or analysis steps.
- Many of the Euro-BioImaging Nodes have or will set up the means to provide remote/virtual access as an alternative to physical user access for the future.
Euro-BioImaging Research collaborations and initiatives
The Dutch Society of Radiology has started an initiative to collect radiological images and clinical information of patients with corona in the Netherlands. The EuroBioimaging Node European population Imaging Infrastructure has been asked to provide expertise for building a central-image storage infrastructure based on the open source XNAT platform and the connections with the different hospitals. The main aim of the initiative is to foster large scale data analysis with AI to improve diagnosis and prediction of outcome.
Euro-BioImaging can support image data sharing for COVID-19 related research projects, such as e.g. large drug screening projects. In this area, we are working together with our partner research infrastructure EU-OPENSCREEN. EU-OPENSCREEN screened 5632 compounds for their inhibition of viral induced cytotoxicity using human cells and a SARS-CoV-2 isolate to identify possible candidates for progression towards clinical studies against SARS-CoV-2. Article in preprint: https://www.researchsquare.com/article/rs-23951/v1
Other image data sets on COVID-19 (subcellular and cellular structure architecture, molecular localization and dynamics, etc.) can be hosted in the BioImage Archive, the Image Data Resource (IDR), and EMPIAR, data services supported by national funding awards in the UK and elsewhere, and by Euro-BioImaging and hosted by EMBL-EBI. One such example is an extensive IDR data set on SARS-CoV-2 in human gut enterocytes available via IDR and EMPIAR. Read the article in Science. Experts from these resources and Euro-BioImaging can also help with any computational task related to images and provide support with image data processing or analysis steps. As just one example, an existing EOSC-Life demonstrator project on the re-analysis of publicly available image datasets provides a template for the development of further workflows using Galaxy and CellProfiler that will be made accessible and reusable by all researchers.
The Euro-BioImaging EMBL Node is using its electron-microscopy technology and expertise to collaborate with virologists from Heidelberg University Hospital to better understand the impact of COVID-19 on human cells. Article on EMBL website: https://www.embl.org/news/science/taking-a-closer-look-at-infected-cells-to-better-understand-covid-19/ Video: https://youtu.be/dtKT0FUKKxA
Euro-BioImaging’s French Node in Bordeaux is contributing to an important study led by the University of Bordeaux to understand COVID-19 infection and inflammatory response using fully differentiated human bronchial epithelium as model. Fluorescent imaging techniques such as immune fluorescence and RNAscope technology will be used in this highly relevant physiological system to determine if a particular cell type is (preferentially) infected by the virus.
Imaging-based COVID-19 diagnostic tools are being developed at the Weizmann Institute in Israel in collaboration with Idea Bio-Medical an Israeli Company that specializes on advanced robotic imaging solutions. The detection principles use automated microscopy and multiplexing fluorescently-labeled reagents that minimize the risk of false negatives and false positives in SARS-CoV2 Virus testing.
The San Raffaele Hospital, one of the sites of the Molecular Imaging Italian Node, in collaboration with Microsoft and NVIDIA, is starting the AI-SCoRE project. The project is aimed at creating an Artificial Intelligence platform to recognise in advance, on the basis of diagnostic and clinical data, COVID19 patients who will develop the worst form of the disease. Patients stratification will allow to perform earlier and targeted therapies, reducing the impact on the healthcare system.
At the Institute for Biostructures and Bioimages of Italian CNR (IBB), which is part of the Euro-BioImaging Molecular Imaging Italian Node, an important achievement in the Covid-19 research, has been obtained. By starting from the available structural data on the interaction between SARS-CoV-2 Spike protein and the host ACE2 receptor, a mini-protein has been engineered with the aim of creating a soluble and stable Spike interactor. The work will continue towards the design of diagnostic and therapeutic tools. (https://doi.org/10.1101/2020.04.29.067728.)
On the clinical side, at the Dept. of Advanced Biomedical Sciences of the University Federico II in Naples, which also collaborates with the Node, a study is ongoing addressing the impact of the Covid-19 pandemic on FDG-PET/CT workflow and the occurrence of abnormal imaging findings suspicious or potentially diagnostic for interstitial pneumonia by Covid-19 infection in a south Italy hospital.
Useful links, information resources and initiatives
To support the global effort to tackle the coronavirus pandemic, many of our partner research infrastructures in the Life Sciences are prioritising COVID-19 research. The benefits of using established research infrastructures are clear: they are ready and able to provide expert advice and resources to meet a variety of research needs. Although in-person visits to facilities may be restricted, many infrastructure services are still available via remote access and, where possible, the cost of access will be minimised or waived. Find more information via the following link: https://lifescience-ri.eu/ls-ri-response-to-covid-19.html
EMBL-EBI and partners have set up a COVID-19 Data Portal, the aim of which is to facilitate data sharing and analysis, and to accelerate coronavirus research. An unprecedented number of scientific efforts are taking place worldwide in order to help combat the new coronavirus epidemic, and one of the biggest challenges in this fast-moving situation is to share data and findings in a coordinated way, in order to understand the disease and to develop treatments and vaccines. To address this challenge, the COVID-19 Data Portal will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data, enabling researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into a wider project, the European COVID-19 Data Platform, an initiative of EMBL-EBI in partnership with the European Commission, the European Open Science Cloud and ELIXIR. https://www.covid19dataportal.org
A list of data resources linked to the outbreak of coronavirus, including cryo-EM structures, can be found here: https://www.ebi.ac.uk/ena/pathogens/covid-19
The World Molecular Imaging Society yields a webinars series which presents a summary of what we know of COVID-19 and the need for imaging of infectious diseases: https://www.wmis.org/education/webinars-2/imaging-of-infection-webinar-series/ A working group dedicated to the imaging of infectious diseases (Imaging Of Infections, IOI) is also active within the Society: https://www.wmis.org/wmis-interest-groups-main/imaging-of-infections-interest-group-main/
Research Data Alliance (RDA) has set up a fast track Working Group titled the “RDA COVID-19 Working Group” and has launched an urgent call for contributions. As an international, consensus-driven, community based organisation, the Research Data Alliance (RDA) has been asked to leverage on the global RDA data community to support the urgent Coronavirus COVID-19 pandemic. https://www.eosc-portal.eu/news/rda-covid-19-working-group-urgent-call-expert-contributions
A dataset of 100 axial CT images from ~60 patients with Covid-19, converted from the openly accessible JPG images from the Italian Society for Medical and Interventional Radiology (https://www.sirm.org/en/), can be found here: http://medicalsegmentation.com/covid19/
A COVID-19 Open Research dataset of scholar articles can be found here: https://pages.semanticscholar.org/coronavirus-research
GitHub is building an open database of COVID-19 cases with chest X-ray or CT images: https://github.com/ieee8023/covid-chestxray-dataset
The Radiological Society of North America (RSNA) has set up a page gathering resources and information about COVID-19, to help radiologists managing the disease: https://www.rsna.org/covid-19
ECRIN has launched the Clinical Research Metadata Repository (Beta-version 0.3), including COVID-19 data, allowing the discovery of clinical studies and related data objects, as there are for example protocol, information sheet and consent form, data management plan, statistical analysis plan, case report form, results, publications, descriptive metadata, etc. https://ecrin.org/clinical-research-metadata-repository
Best practices for operations
- German BioImaging has prepared recommendations on facility management during current virus conditions: https://www.gerbi-gmb.de/Corona
- At the confocal microscopy list, a relevant example relating to facility cleaning can be found: http://confocal-microscopy-list.588098.n2.nabble.com/COVID19-Instrument-cleaning-protocols-td7590586.html
- Zeiss Quick Guide to disinfecting microscopes: https://p.widencdn.net/xovbuw/EN_quick-guide_cleaning-disinfecting-microscope
- Leica tips for sanitizing microscopy systems: https://www.leica-microsystems.com/science-lab/how-to-sanitize-a-microscope/
- A collection of research articles on imaging of COVID-19 can be found below in the literature section.
- EC - 2nd call to ask for new CoVid19 focused research projects:https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/opportunities/topic-search;freeTextSearchKeyword=;typeCodes=1;statusCodes=31094501,31094502,31094503;programCode=H2020;programDivisionCode=null;focusAreaCode=null;crossCuttingPriorityCode=null;callCode=H2020-SC1-PHE-CORONAVIRUS-2020-2;sortQuery=submissionStatus;orderBy=asc;onlyTenders=false;topicListKey=callTopicSearchTableState
- Science Business Corona Virus Funding opportunitieshttps://sciencebusiness.net/coronavirus-funding-opportunities
EU RI Resources
- ESFRI (https://www.esfri.eu/covid-19)
- ERIC Forum website (https://www.eric-forum.eu/2020/03/31/european-research-infrastructure-consortia-and-covid-19-research/)
- LifeScience RI website (https://lifescience-ri.eu/ls-ri-response-to-covid-19.html)
- EOSC-Life (https://www.eosc-life.eu/resources/ls-ri-response-to-covid-19/)
- ERF-AISBL ((https://erf-aisbl.eu/research-infrastructures-offer-for-research-on-covid-19/)
In a time when most research staff are working from home, imaging related online resources can be of particular interest. Here are few examples:
- Engage in a spot of imaging related Citizen Science and Crowd Sourcing, e.g.: https://www.zooniverse.org/projects/h-spiers/etch-a-cell-powerhouse-hunt
- Support to image analysis: https://forum.image.sc/
- NEUBIAS Academy, webinars on bioimage analysis: https://neubiasacademy.org
- Online talks and opportunities by the Royal Microscopy Society: https://www.rms.org.uk/study-read/news-listing-page/online-microscopy-talks-list.html
- Online training opportunities for microscopy techniques: https://myscope.training/
- For homeschooling: http://myscope-explore.org.au/
Literature on COVID-19 and Imaging
Generalities on COVID-19
- Candace Makeda Moore, Daniel J Bell et al., “COVID-19”, https://radiopaedia.org/articles/covid-19-3?lang=us
- Ran Liu, Aisi Fu et al., “Promising methods for detection of novel coronavirus SARS-CoV-2”, https://doi.org/10.1002/viw2.4
- Ewen Callaway, “Monkeys and mice enlisted to fight Coronavirus”, https://media.nature.com/original/magazine-assets/d41586-020-00660-x/d41586-020-00660-x.pdf
- Jean Kaoru Millet and Gary R. Whittaker, Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells”,https://doi.org/10.1016/j.virol.2017.12.015
- Renhong Yan, Yuanyuan Zhang et al., “Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2”, https://doi.org/10.1126/science.abb2762
- Fang Li, “Structure, Function, and Evolution of Coronavirus Spike Proteins”, https://doi.org/10.1146/annurev-virology-110615-042301
- Alexandra C. Walls, Young-Jun Park et al., “Structure, Function, and Antigenicity of the SARSCoV- 2 Spike Glycoprotein”, https://doi.org/10.1016/j.cell.2020.02.058
- Tao Liu, Jieying Zhang et al, “The potential role of IL-6 in monitoring Coronavirus disease 19”, https://doi.org/10.1101/2020.03.01.20029769
CT of patients positive to COVID-19
- Michael D Hope, Constantine A Raptis et al., “A role for CT in COVID-19? What data really tell us so far”, https://doi.org/10.1016/S0140-6736(20)30728-5
- Lin Li, Lixin Qin et al., “Artificial Intelligence Distinguishes COVID-19 from Community Acquired Pneumonia on Chest CT”, https://doi.org/10.1148/radiol.2020200905
- Jiong Wu, Xiaojia Wu et al., “Chest CT Findings in Patients with Corona Virus Disease 2019 and its Relationship with Clinical Features”, https://doi.org/10.1097/RLI.0000000000000670
- Zhiming Zhou & Dajing Guo, “Coronavirus disease 2019: initial chest CT findings”, https://doi.org/10.1007/s00330-020-06816-7
- Kunwei Li & Yijie Fang, “CT image visual quantitative evaluation and clinical classification of coronavirus disease (COVID-19)”, https://doi.org/10.1007/s00330-020-06817-6
- Wanhua Guan, Jinxin Liu, Chengcheng Yu, “CT Findings of Coronavirus Disease (COVID-19) Severe Pneumonia”, https://doi.org/10.2214/AJR.20.23035
- Chunqin Long, Huaxiang Xu et al., “Diagnosis of the Coronavirus disease (COVID-19): rRT-PCR or CT?”, https://doi.org/10.1016/j.ejrad.2020.108961
- Yuhui Wang, Chengjun Dong et al., “Temporal Changes of CT Findings in 90 Patients with COVID-19 Pneumonia: A Longitudinal Study”, https://pubs.rsna.org/doi/pdf/10.1148/radiol.2020200843
- Michael Chung, Adam Bernheim, Xueyan Mei, et al. “CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV)”, https://doi.org/10.1148/radiol.2020200230
- Domenico Albano, Francesco Bertagna et al., " Incidental findings suggestive of COVID-19 in asymptomatic patients undergoing nuclear medicine procedures in a high prevalence region" https://doi.org/10.2967/jnumed.120.246256
- Eric J. Snijder, Ronald W.A.L. Limpens et al., “A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis”, https://doi.org/10.1101/2020.03.24.005298
- Daniel Wrapp, Nianshuang Wang et al., “Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation”, https://doi.org/10.1126/science.abb2507
- Adam D. Cawte, Peter J. Unrau et al., “Live cell imaging of single RNA molecules with fluorogenic Mango II arrays”, https://doi.org/10.1038/s41467...
Imaging of infectious diseases - abstracts from past European Molecular Imaging Meetings
Here are some examples about what you can find
- Ex vivo Laser-based Endomicroscopy of Infections in Explant Human Lungs (#216): https://www.eventclass.org/contxt_emim2019/online-program/session?s=PW22#e806
- In vivo imaging of infection and immunity in nonhuman primate models of infectious diseases (#295): https://www.eventclass.org/contxt_emim2019/online-program/session?s=PW22#e812
- 68Ga-siderophores for Pseudomonas aeruginosa infection imaging (#103): https://www.eventclass.org/contxt_emim2019/online-program/session?s=PW22#e805
- Spectral photon-counting CT of lungs of mice infected with Mycobacterium Tuberculosis: potential for locating Tuberculosis involvement (#82): http://eventclass.org/contxt_emim2018/online-program/session?s=PW-08#82