Resources for COVID-19 and related imaging research
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.
Euro-BioImaging provides open access to imaging technologies, training and data services in biological and biomedical imaging at our 25 Nodes. Our Nodes have adapted to the current COVID-19 pandemic situation, and the infrastructure fast-tracks projects related to COVID-19. Most of our Nodes are again open to external users, following local safety guidelines. Many Euro-BioImaging Nodes also offer remote access services to accommodate travel restrictions. If you are interested in a remote access project, please contact us to learn more about the options.
Imaging research is essential in the fight against the pandemic, and Euro-BioImaging continues to support life science research in these extraordinary times. The COVID-19 repository below lists a range of imaging-associated services and resources, as well as lots of useful information on imaging research related to COVID-19. Many of our Nodes are themselves engaged in research related to COVID-19 and you can find out more about these efforts below.
Available Euro-BioImaging services (status 03.03.2021)
- User access proposals are being processed in a normal fashion by the Euro-BioImaging Hub.
- Euro-BioImaging offers Fast Track processing of all applications for COVID-19 related projects, and pre-reviewed research projects. Contact us directly for more information: firstname.lastname@example.org.
- The majority of the Euro-BioImaging Nodes are again open to external users, following local safety guidelines.
- Many Euro-BioImaging Nodes also offer remote access services for certain user projects to accommodate travel restrictions
- If you are interested in the services offered by a given Node, please contact the Hub or the respective Node to learn more about the access options.
Adapting to a new normal
With travel restrictions and new hygiene measures in place, Euro-BioImaging Nodes are adapting to the COVID-19 context in order to provide services to external users.
Learn about some new services and working procedures below:
- From Finland: Virtual STED microscopy
- From Italy: Remote access in preclinical imaging services
- From Finland: Remote access to Finnish ALM Node
- From Italy: Running remote experiments in Italy's Elettra Synchrotron laboratory
- From EMBL: Remote experiments with STED microscopy
Contributing to COVID-19 Research
- French Node: Imaging technologies used to understand COVID-19 infection
- EMBL Node: How high-throughput microscopy can contribute to COVID-19 diagnosis
- EMBL Node: Understanding SARS-CoV-2 replication cycle in human cells
- Molecular Imaging Italian Node: Imaging techniques and COVID19 diagnosis
- Molecular Imaging Italian Node: CT Imaging and Artificial Intelligence: United for COVID-19 prognostics
Best practices for facility 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/
In a time many are working from home and home schooling; 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/
Euro-BioImaging Research collaborations and initiativesThe 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...
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 our website: https://www.eurobioimaging.eu/news/how-high-throughput-microscopy-can-contribute-to-covid-19-diagnosis 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. Read the article: https://www.eurobioimaging.eu/news/imaging-technologies-used-to-understand-covid-19-infection-/
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. Read the article: https://www.eurobioimaging.eu/news/ct-imaging-and-artificial-intelligence-united-for-covid-19-prognostics/
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. Read the article: https://www.eurobioimaging.eu/news/imaging-techniques-and-covid19-diagnosis/
Imaging technologies are central to investigating the cause-and-effect mechanisms involved in the COVID-19 disease and the damage it causes. Read more about Finland's contribution from the Finnish Advanced Light Microscopy Node.
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
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/)
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