Public archiving and data integration in the era of multi-modal imaging
Lead Research Organisation:
EMBL - European Bioinformatics Institute
Department Name: Protein Data Bank in Europe
Abstract
Consider a scenario in which one could image a whole organism, and then progressively zoom in to the level of organs, tissue, cells, molecules and finally atoms, at each step revealing more detail. Although the prospect of scaling from the level of organisms to atoms may seem far-fetched, there now do exist imaging techniques to cover almost all of these imaging scales. There is a growing body of biomedical research where information from different imaging techniques at different scales are combined, i.e., multi-modal imaging, to piece together a more comprehensive understanding of a problem than can be obtained from one technique alone. However the wider integration of imaging data is hampered by the lack of public accessibility to this data and commonly used formats for representing the information required to bring the different modalities into register. To address all scales of imaging at once would be extremely challenging given the enormous scope of the problem, the disparate user communities and the resources required.
In the field of molecular structural biology, which involves the study of the 3D structure of molecules, the concept of public archiving of structures is well established with archives such as the PDB (atomic model data) and EMDB (3D volumes derived from electron microscopy (EM) experiments including electron tomography) enjoying widespread community support. Our strategy has therefore been to first consider the integration between the cellular and molecular imaging scales in consultation with the relevant communities. We organized two 'expert' workshops inviting key specialists and community representatives which resulted in concrete recommendations including - exploring public archiving of large EM image datasets, the development of visualisation tools that provide an integrated, problem-centric view of structures piecing together information from the different imaging modalities, the imaging modalities which should be targeted first - 3D scanning electron microscopy (3DSEM), soft X-ray tomography (SXT) and correlative light and electron microscopy (CLEM) , and the development of a format to facilitate data integration. In an on-going MRC-funded project (grant MR/L007835; MOL2CELL) we have successfully developed EMPIAR - a public archive for raw EM image data, which is capable of handling data-sets in the terabyte range. We are developing a web-based visualisation tool (Volume browser) that provides an openly accessible integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB archives, and a format that supports one form of integration between these scales. In the proposed project we want to build upon the work started in the MOL2CELL project and a) extend archiving in EMPIAR to include full support for the proposed imaging modalities, b) extend format support to represent the information required to bring the different modalities into register and use this to improve and extend the Volume browser, and c) develop software and data pipelines from major microscopy centres to facilitate data deposition to EMDB and EMPIAR and to improve the quality and quantity of the information collected.
While the scope of the project is limited to the molecular and cellular imaging scales, the outcomes are potentially applicable to other imaging modalities. The inclusion of the new imaging modalities into EMPIAR can serve as one model for how public archiving can be organized and established, the format developed can be used for data integration between other imaging modalities and the Volume browser for integrated visualisation with other imaging scales. Furthermore developers of resources for multi-modal imaging data stand to gain from open access to the software developed in the project and the data in EMPIAR.
In the field of molecular structural biology, which involves the study of the 3D structure of molecules, the concept of public archiving of structures is well established with archives such as the PDB (atomic model data) and EMDB (3D volumes derived from electron microscopy (EM) experiments including electron tomography) enjoying widespread community support. Our strategy has therefore been to first consider the integration between the cellular and molecular imaging scales in consultation with the relevant communities. We organized two 'expert' workshops inviting key specialists and community representatives which resulted in concrete recommendations including - exploring public archiving of large EM image datasets, the development of visualisation tools that provide an integrated, problem-centric view of structures piecing together information from the different imaging modalities, the imaging modalities which should be targeted first - 3D scanning electron microscopy (3DSEM), soft X-ray tomography (SXT) and correlative light and electron microscopy (CLEM) , and the development of a format to facilitate data integration. In an on-going MRC-funded project (grant MR/L007835; MOL2CELL) we have successfully developed EMPIAR - a public archive for raw EM image data, which is capable of handling data-sets in the terabyte range. We are developing a web-based visualisation tool (Volume browser) that provides an openly accessible integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB archives, and a format that supports one form of integration between these scales. In the proposed project we want to build upon the work started in the MOL2CELL project and a) extend archiving in EMPIAR to include full support for the proposed imaging modalities, b) extend format support to represent the information required to bring the different modalities into register and use this to improve and extend the Volume browser, and c) develop software and data pipelines from major microscopy centres to facilitate data deposition to EMDB and EMPIAR and to improve the quality and quantity of the information collected.
While the scope of the project is limited to the molecular and cellular imaging scales, the outcomes are potentially applicable to other imaging modalities. The inclusion of the new imaging modalities into EMPIAR can serve as one model for how public archiving can be organized and established, the format developed can be used for data integration between other imaging modalities and the Volume browser for integrated visualisation with other imaging scales. Furthermore developers of resources for multi-modal imaging data stand to gain from open access to the software developed in the project and the data in EMPIAR.
Technical Summary
The use of imaging modalities spanning the transition from the molecular to the cellular imaging scales such as electron tomography (ET), 3D scanning electron microscopy (3DSEM), soft X-ray tomography (SXT), and correlative light and electron microscopy (CLEM) in biomedical research is growing rapidly. At present there is no established public archiving for this data except for ET data, which is archived in EMDB. In consultations with the EM and cellular imaging communities it is clear that extending public archiving to include these imaging modalities and improving data integration between different scales of imaging would confer enormous benefits with regards to the potential reuse of the data, enabling for instance the problem-centric visualisation of structural data where information from the cellular and molecular scales are combined. In the context on an on-going MRC funded project (grant MR/L007835; MOL2CELL) we have developed EMPIAR - a pilot archive for raw 2D image data related to EMDB entries, and are in the process of developing a web-based Volume browser that will provide integrated visualisation of EMDB and PDB entries where the link between the molecular and cellular scales is provided by segmentation information. In the proposed project we want build on the momentum and experience from the MOL2CELL project to a) extend EMPIAR to support 3D Scanning Electron Microscopy (3DSEM), Soft X-ray Tomography (SXT) and Correlative Light and Electron Microscopy (CLEM) data, b) develop standards for correlative imaging data and for relating sub-tomogram averages to tomograms, and extend the Volume browser to accommodate CLEM visualisation as well as overlays of sub-tomogram averages on tomograms, and c) develop data-harvesting and submission pipelines to EMDB and EMPIAR to facilitate deposition and to improve the quality and quantity of experimental information collected.
Planned Impact
Public archiving of 3D Scanning Electron Microscopy (3DSEM), Soft X-ray Tomography (SXT) and Correlative Light and Electron Microscopy (CLEM) data
Public archiving of these modalities will benefit end users in the structural biology and cellular imaging communities who want to reuse it, e.g., for data mining or validation. EMPIAR already serves as a useful source of test data for methods developers and this will also apply to developers working with these imaging modalities. It will lessen the archiving burden on individual labs. It will help journals improve the quality and transparency of publications related to these imaging modalities. It can also serve as a model for other bio-imaging communities for how image archiving can be set-up, managed and organized.
Visualisation of and standards for correlative imaging and for relating sub-tomogram averages to tomograms
The transformation format and related libraries will benefit software developers in the tomography and correlative imaging fields by reducing the burden on them to handle conversions between different packages.
The extensions to the Volume browser will enable the integrated visualisation of CLEM, 3DSEM and SXT data in EMPIAR with data from EMDB and PDB. It will thus be a unique publicly accessible tool providing exceptional added value to the data stored in these archives. The problem-centric views to structural data that it will provide will create opportunities for data-mining and knowledge discovery by the wider biomedical community. For teachers and students of biology and biochemistry the resource will provide an evidence-based visual exposition of many key biological systems and processes. For the pharmaceutical industry the resource will open new avenues to visually understanding how potential drug targets behave in the context of the cell environment. The extensive linkage of information will also mean that the resource will rank highly in common search engines like Google when searching for more general biological and medical terms used by the general public. It will thus provide a valuable entry point for general users to develop a better visual appreciation for the basis of biology and medicine on the micro scale.
Data-harvesting and submission pipelines to EMDB and EMPIAR
These developments will substantially simplify the deposition process and reduce the time it takes thereby enabling the microscopy centres and depositors to cope with the expected rise in data volumes in the future. We will also work with the Cambridge Pharmaceutical Cryo-EM Research Consortium to better understand the requirements of industry and tailor the data-harvesting and pipelining software so that it could more broadly be used by other industry related microscopy centres. These developments will also lead to an improvement in the quality and quantity of the information being collected about the experiment which will benefit the end users of the data, primarily the structural biology and cellular imaging communities.
Public archiving of these modalities will benefit end users in the structural biology and cellular imaging communities who want to reuse it, e.g., for data mining or validation. EMPIAR already serves as a useful source of test data for methods developers and this will also apply to developers working with these imaging modalities. It will lessen the archiving burden on individual labs. It will help journals improve the quality and transparency of publications related to these imaging modalities. It can also serve as a model for other bio-imaging communities for how image archiving can be set-up, managed and organized.
Visualisation of and standards for correlative imaging and for relating sub-tomogram averages to tomograms
The transformation format and related libraries will benefit software developers in the tomography and correlative imaging fields by reducing the burden on them to handle conversions between different packages.
The extensions to the Volume browser will enable the integrated visualisation of CLEM, 3DSEM and SXT data in EMPIAR with data from EMDB and PDB. It will thus be a unique publicly accessible tool providing exceptional added value to the data stored in these archives. The problem-centric views to structural data that it will provide will create opportunities for data-mining and knowledge discovery by the wider biomedical community. For teachers and students of biology and biochemistry the resource will provide an evidence-based visual exposition of many key biological systems and processes. For the pharmaceutical industry the resource will open new avenues to visually understanding how potential drug targets behave in the context of the cell environment. The extensive linkage of information will also mean that the resource will rank highly in common search engines like Google when searching for more general biological and medical terms used by the general public. It will thus provide a valuable entry point for general users to develop a better visual appreciation for the basis of biology and medicine on the micro scale.
Data-harvesting and submission pipelines to EMDB and EMPIAR
These developments will substantially simplify the deposition process and reduce the time it takes thereby enabling the microscopy centres and depositors to cope with the expected rise in data volumes in the future. We will also work with the Cambridge Pharmaceutical Cryo-EM Research Consortium to better understand the requirements of industry and tailor the data-harvesting and pipelining software so that it could more broadly be used by other industry related microscopy centres. These developments will also lead to an improvement in the quality and quantity of the information being collected about the experiment which will benefit the end users of the data, primarily the structural biology and cellular imaging communities.
Publications

Bárcena M
(2021)
Structural biology in the fight against COVID-19.
in Nature structural & molecular biology

Hartley M
(2022)
The BioImage Archive - Building a Home for Life-Sciences Microscopy Data.
in Journal of molecular biology

Iudin A
(2023)
EMPIAR: the Electron Microscopy Public Image Archive.
in Nucleic acids research


Kleywegt G
(2021)
Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive
in Microscopy and Microanalysis

Kleywegt GJ
(2018)
Structural biology data archiving - where we are and what lies ahead.
in FEBS letters

Sarkans U
(2021)
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
in Nature methods

Thakur M
(2023)
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.
in Nucleic acids research

Walter A
(2021)
Correlative multimodal imaging: Building a community.
in Methods in cell biology
Description | WT EMPIAR A2O Biomedical Resources Grant (2021-2026) - 1.4 MGBP |
Amount | £1,418,003 (GBP) |
Funding ID | 221371/Z/20/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2021 |
End | 02/2026 |
Title | EMPIAR |
Description | Raw image data related to EMDB structures |
Type Of Material | Database/Collection of data |
Year Produced | 2014 |
Provided To Others? | Yes |
Impact | EMPIAR is being used regularly for validation, methods development, teaching and training. There are already over 10 publications linking to EMPIAR. |
URL | http://pdbe.org/empiar |
Description | Building EMDB/EMPIAR mirrors in China |
Organisation | Chinese Academy of Sciences |
Department | Institute of Biophysics |
Country | China |
Sector | Academic/University |
PI Contribution | Provided assistance to China to build EMDB mirrors |
Collaborator Contribution | Dissemination of the importance of archiving in China |
Impact | EMDB mirror being setup in China |
Start Year | 2017 |
Title | EMDB-SFF Toolkit |
Description | Translators to/from EMDB segmentation file format (EMDB-SFF) |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | Others can use EMDB-SFF more easily |
URL | https://ccpforge.cse.rl.ac.uk/svn/ccpem/src/ccpem_progs/emdb_sfftk |
Title | EMPIAR deposition system |
Description | Web based deposition system to deposit data and meta data to EMPIAR |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | This tool makes it easier to deposit data to EMPIAR |
URL | https://www.ebi.ac.uk/pdbe/emdb/empiar/deposition/login/?next=/pdbe/emdb/empiar/deposition/ |
Title | EMPIAR website |
Description | Website providing access for downloading and viewing EMPIAR data |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | The amount of data downloaded from EMPIAR has grown to 13TB on average per month |
URL | http://pdbe.org/empiar |
Title | Volume slicer |
Description | A web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | The general public has direct access to slice views of EMDB reconstructions. |
URL | http://www.ebi.ac.uk/pdbe/emdb/3dslice/EMD-2363 |
Description | "EMDB and EMPIAR"; S2C2 CryoEM CCP-EM Modeling Workshop presentation, November 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Workshop presentation on EMDB and EMPIAR which generated interest and questions from the audience as well as potential collaborations. |
Year(s) Of Engagement Activity | 2020 |
Description | "Bioimage data archiving at EMBL-EBI", invited talk, "Exascale challenges for ML in multiscale life sciences" workshop, virtual, January 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Bioimage data archiving at EMBL-EBI", invited talk, "Exascale challenges for ML in multiscale life sciences" workshop, virtual, January 2021 |
Year(s) Of Engagement Activity | 2021 |
Description | "EM Validation by wwPDB & EMDB", presentation at the EMBO Course "Cryo-Electron Microscopy and 3D Image Processing", EMBL Heidelberg, virtual, September 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | "EM Validation by wwPDB & EMDB", presentation at the EMBO Course "Cryo-Electron Microscopy and 3D Image Processing", EMBL Heidelberg, virtual, September 2020 |
Year(s) Of Engagement Activity | 2020 |
Description | "EM data archiving", lecture Gerard Kleywegt and lectures and practical Osman Salih in the EM EMBO Course, Birkbeck, London, UK, September 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Contributed to this course for young EM practitioners. |
Year(s) Of Engagement Activity | 2019 |
Description | "EMDB and EMPIAR" by Ardan Patwardhan at EMBO Practical Course: Cryo-Electron Microscopy and 3D Image Processing (virtual), April 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Course presentation on EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2020 |
Description | "EMPIAR: recent developments and outlook", presentation Andrii Iudin at the 2nd CryoNet Annual Symposium, Stockholm, Sweden, October 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presented recent developments and plans for EMPIAR, Volume Browser, Segmentation Annotation Tool, BioImage Archive Glue project |
Year(s) Of Engagement Activity | 2019 |
Description | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk, Global Bioimaging workshop ""Image Data: data management, cloud-based sharing, and image data repositories", virtual, January 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk, Global Bioimaging workshop ""Image Data: data management, cloud-based sharing, and image data repositories", virtual, January 2021 |
Year(s) Of Engagement Activity | 2021 |
Description | "Introduction to structural biology data", lecture Gerard Kleywegt, "Computational Structural Biology" course, EMBL-EBI, Cambridge, UK, September 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Taught in this course for young scientists with an interest in using structural biology data. |
Year(s) Of Engagement Activity | 2019 |
Description | "Introduction to structural biology data", lecture, "Structural Bioinformatics" course, EMBL-EBI, virtual, November 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | "Introduction to structural biology data", lecture, "Structural Bioinformatics" course, EMBL-EBI, virtual, November 2020 |
Year(s) Of Engagement Activity | 2020 |
Description | "Open EM Data (BIG and small)", invited talk Gerard Kleywegt at the EM-UK Meeting, Plymouth (UK), January 2020. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | "Open EM Data (BIG and small)", invited talk Gerard Kleywegt at the EM-UK Meeting, Plymouth (UK), January 2020. |
Year(s) Of Engagement Activity | 2020 |
Description | "Validation by EMDB and wwPDB", symposium on "Cryo-EM Validation in the Age of SARS-CoV-2: Methods, Tools and Applications", virtual, November 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Validation by EMDB and wwPDB", symposium on "Cryo-EM Validation in the Age of SARS-CoV-2: Methods, Tools and Applications", virtual, November 2020 |
Year(s) Of Engagement Activity | 2020 |
Description | "What's new at EMDB and EMPIAR?", lecture Gerard Kleywegt at the CCP-EM Spring Symposium, Nottingham, UK, April 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave an overview of new developments and plans concerning cryo-EM data archiving in PDB, EMDB and EMPIAR. |
Year(s) Of Engagement Activity | 2019 |
Description | "What's new in EMDB and EMPIAR" by Ardan Patwardhan at the CCP-EM Spring Symposium (virtual), April 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation of new developments in EMDB and EMPIAR including uses cases of validation resources applied to SARS-CoV-2 |
Year(s) Of Engagement Activity | 2020 |
Description | 2018 International Conference of the Korean Society for Structural Biology |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation on EMDB and EMPIAR and discussions on collaborations with the South Korean community |
Year(s) Of Engagement Activity | 2018 |
Description | 3DEM Gordon Research Conference, Rhode Island USA |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Poster presentation on EMDB and EMPIAR activities |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.grc.org/three-dimensional-electron-microscopy-conference/2018/ |
Description | CCP-EM Icknield Model Building Workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk focusing on validation for cryo EM but also highlighting other resources for EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2018 |
Description | CCP-EM Spring Symposium, Keele University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Talk and poster presentations on various aspects of the activities and plans relating to EMDB and EMPIAR |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.ccpem.ac.uk/training/spring_symposium_2018/spring_symposium.php |
Description | Community workshop on Volume EM, Wellcome Trust, October 2019 - organised jointly with Ardan Patwardhan, Lucy Collinson and Paul Verkade |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We organised a workshop for the Volume EM community to discuss needs and opportunities with members of the community and funder representatives. Main outcome was agreement to work on a roadmap for Volume EM in the UK. |
Year(s) Of Engagement Activity | 2019 |
Description | Cryo EM and 3D Image Processing (CEM3DIP) course New Delhi 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presentation on EMDB and EMPIAR to make audience aware of activities and resources available, plans for the future and how they could enhance their research by interacting with us. |
Year(s) Of Engagement Activity | 2018 |
URL | http://meetings.embo.org/event/18-cem3dip |
Description | G.J. Kleywegt - "EMPIAR - update & plans", talk at the Third Annual Volume EM Community Town Hall Meeting, virtual, October 2019. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "EMPIAR - update & plans", talk at the Third Annual Volume EM Community Town Hall Meeting, virtual, October 2019. |
Year(s) Of Engagement Activity | 2021 |
URL | https://drive.google.com/file/d/1_lUuuSgP2rRqLooa3ArIqm7f7xt6tgB7/view?usp=sharing |
Description | G.J. Kleywegt - "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Global BioImaging, virtual, January 2022. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Global BioImaging, virtual, January 2022. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.youtube.com/watch?v=z8yPcO-MR5I |
Description | G.J. Kleywegt - "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Microscopy Australia, virtual, June 2021. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Electron Microscopy Public Image Archive (EMPIAR)", invited webinar for Microscopy Australia, virtual, June 2021. |
Year(s) Of Engagement Activity | 2021 |
Description | G.J. Kleywegt - "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk in PETRA IV workshop, DESY Hamburg, Germany, virtual (presented by Ardan Patwardhan), March 2021. |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk in PETRA IV workshop, DESY Hamburg, Germany, virtual (presented by Ardan Patwardhan), March 2021. |
Year(s) Of Engagement Activity | 2021 |
Description | G.J. Kleywegt - "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk, Global Bioimaging workshop "Image Data: data management, cloud-based sharing, and image data repositories", virtual, January 2021 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | "Image Archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk, Global Bioimaging workshop "Image Data: data management, cloud-based sharing, and image data repositories", virtual, January 2021 |
Year(s) Of Engagement Activity | 2021 |
Description | G.J. Kleywegt - "Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk at Microscopy & Microanalysis 2021 (session "From Images to Insights: Working with Large Multi-modal Data in Cell Biological Imaging"), Pittsburgh, USA, virtual, August 2021. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive", invited talk at Microscopy & Microanalysis 2021 (session "From Images to Insights: Working with Large Multi-modal Data in Cell Biological Imaging"), Pittsburgh, USA, virtual, August 2021. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.youtube.com/watch?v=NR1Kxauukjo |
Description | Invited speaker talk on Structural Biology Data Archiving at FEBS Congress 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Structural biology data archiving - where are we and what lies ahead?", invited lecture, FEBS Congress, Prague, Czech Republic, July 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | Lecture on Structural Biology Data Archiving |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | "Structural biology data archiving - where are we and what lies ahead?", seminar, EMBL, Heidelberg, Germany, September 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | O. Salih - Talk & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Bioinformatics Resources for Protein Biology 2022 (EMBL-EBI), Virtual, 22 February 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | O. Salih - Talk & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Bioinformatics Resources for Protein Biology 2022 (EMBL-EBI), Virtual, 22 February 2022 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ebi.ac.uk/training/events/bioinformatics-resources-protein-biology-2022/#vf-tabs__sectio... |
Description | O. Salih, J. Turner, G.J. Kleywegt - Talks & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Structural Bioinformatics 2021 (EMBL-EBI), Virtual, 13 October 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | O. Salih, J. Turner, G.J. Kleywegt - Talks & Practical: "EMDB & EMPIAR: Public Archiving of Cryo-EM Data"; Event - Structural Bioinformatics 2021 (EMBL-EBI), Virtual, 13 October 2021 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ebi.ac.uk/training/materials/structural-bioinformatics-materials/day-3/emdb-and-empiar/ |
Description | O. Salih, S. Weyand, A. Iudin, G.J. Kleywegt - Talks & Practical: "EMPIAR: Depositing & Accessing Data"; Event - Microscopy Data Analysis: Machine learning and the BioImage Archive (EMBL-EBI), Virtual, 14 July 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | O. Salih, S. Weyand, A. Iudin, G.J. Kleywegt - Talks & Practical: "EMPIAR: Depositing & Accessing Data"; Event - Microscopy Data Analysis: Machine learning and the BioImage Archive (EMBL-EBI), Virtual, 14 July 2021 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.ebi.ac.uk/training/materials/microscopy-image-analysis-materials/bioimage-databases-reso... |
Description | Organised "expert workshop on Frontiers in Cryo-EM Validation" with the Wellcome Trust-funded UK EM Validation Network partners, EMBL-EBI, Cambridge, UK, January 2019 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We organised this expert workshop to explore frontiers and community needs w.r.t. cryo-EM validation. |
Year(s) Of Engagement Activity | 2019 |
Description | Organised expert virtual workshop on "Public archiving of volume-EM data: needs, opportunities and challenges", 6-8 December 2021, with 46 community experts participating |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Organised expert virtual workshop on "Public archiving of volume-EM data: needs, opportunities and challenges", 6-8 December 2021, with 46 community experts participating. Topics discussed: - Data-model and deposition - Dissemination (formats, APIs, data-streaming) - Segmentation This will inform our future work on fully supporting vEM data in the resource. |
Year(s) Of Engagement Activity | 2021 |
Description | S. Somasundharam, "Specimen Preparation Workflow Widget - Demo", virtual, October 2021 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | S. Somasundharam, "Specimen Preparation Workflow Widget - Demo", virtual, October 2021 Relevant Sandbox URL: https://wwwdev.ebi.ac.uk/emdb/spw/empiar/widget |
Year(s) Of Engagement Activity | 2021 |
URL | https://wwwdev.ebi.ac.uk/emdb/spw/empiar/widget |
Description | School visit and presentation at Bar Hill School |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Public engagement presentation on microscopy to primary school students |
Year(s) Of Engagement Activity | 2018 |
Description | Scipion Facilities Meeting 2018 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discussions on how to interface Scipion which is now being used by a number of cryo-EM centers with EMPIAR to enable data pipelining |
Year(s) Of Engagement Activity | 2018 |
URL | http://i2pc.es/2nd-i2pc-cryoem-facilities-meeting-madrid-june-26-27-2018/ |
Description | Structural bioinformatics training course |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Co-organiser of and lecturer in this practical course, interacting with students and fellow instructors. |
Year(s) Of Engagement Activity | 2016,2017,2018 |
URL | http://www.ebi.ac.uk/training/events/2016/structural-bioinformatics-2016 |
Description | Talk & Practical Session on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for Bioinformatics Resources for Protein Biology Course (Cambridge University) - April 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Undergraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. Practical: Investigative Question & Answer session on using EMDB and EMPIAR resources, downloading data, visualising data & assessing the data quality. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk & Practical Session on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for Bioinformatics Resources for Protein Biology Course (EMBL-EBI) - February 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. Practical: Investigative Question & Answer session on using EMDB and EMPIAR resources, downloading data, visualising data & assessing the data quality. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for CCP-EM Icknield Model Building Workshop (RAL/DLS, Oxford) - April 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for EMBO Practical Course CEM3DIP 2020 (IISER-Kolkata, India) - January 2020 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave an overview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2020 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for EMBO Practical Course for Cryo-EM Image Processing (Birkbeck) - September 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave overviews of the resources we provide (PDBe, EMDB, EMPIAR), and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk on "PDBe, EMDB & EMPIAR: Public Archiving of Cryo-EM Data" for Structural Bioinformatics Course (EMBL-EBI) - September 2019 (by Osman Salih) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk: Gave an overiview of the Cryo-EM field and the "resolution revolution", then showed statistics concerning EM Data coming into the PDB, EMDB & EMPIAR archives. Gave overviews of the resources we provide, and how to access, visualise and evaluate the quality of EM data. Also spoke about Validation reports and how to deposit EM data. |
Year(s) Of Engagement Activity | 2019 |
Description | Wellcome Trust Cryo EM User Meeting |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Discussion on needs of the UK cryo EM community where the role of EMDB and EMPIAR were also highlighted and discussed. |
Year(s) Of Engagement Activity | 2018 |
Description | Workshop on Computational Methods in Bio-imaging Sciences, National University of Singapore, Institute of Mathematical Sciences |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Introduction to EM and EM databases to a wider scientific post-grad audience |
Year(s) Of Engagement Activity | 2018 |
URL | https://ims.nus.edu.sg/events/2017/data/wk3.php |