| Korir PK, Iudin A, Somasundharam S, Weyand S, Salih O, Hartley M, Sarkans U, Patwardhan A, Kleywegt GJ (2023). “Ten Recommendations for Organising Bioimaging Data for Archival.“, F1000Research, 12 (ELIXIR), 1391. (Opinion article.) Publication Details: Ten Recommendations for Organising Bioimaging Data for Archival. |
A number of recommendations are described whose implementation would contribute towards better organised data in preparation for archival, based on our experience with archiving bioimaging data at EMBL-EBI. We hope that this this contribution provides food for thought and discussion for the relevant communities. |
| Hartley M, Iudin A, Padwardhan A, Sarkans U, Küpcü Yoldaş A, Kleywegt GJ (2023). “Providing open imaging data at scale: an EMBL-EBI perspective.“, Hist Cell Biol, 160, 211-221 DOI: 10.1007/s00418-023-02216-2. PMID: 37537341; PMCID: PMC10492673. |
This paper provides an overview of at-scale archival and dissemination of open imaging data through EMPIAR and the BioImage Archive. It also discusses the challenges and efforts to provide such data following the FAIR data guidelines. Finally, a number of lessons that can be used in making vast amounts of FAIR and open imaging data available in the future are discussed. |
| Iudin A, Hartley M, Kleywegt GJ, Patwardhan A (2023). “Public archiving of volume EM data.“, Methods in Cell Biology, volume 181, Volume Electron Microscopy, Verkade P, Collinson L, Narayan K (Eds.), chapter 15, 389-399. (Book chapter.) DOI: 10.1016/bs.mcb.2023.02.002. PMID: 37451775. |
This book chapter describes public archiving/dissemination efforts for volume EM (and correlative) data in EMPIAR and the BioImage Archive, both located at EMBL-EBI. The benefits of public data archiving are also summarised. |
| Collinson LM, Bosch C, Bullen A, Burden JJ, Carzaniga R, Cheng C, Darrow M, Fletcher G, Johnson E, Narayan K, Peddie CJ, Winn M, Wood C, Patwardhan A, Kleywegt GJ, Verkade P (2023). “Volume EM: A quiet revolution takes shape.“, Nature Methods, 20, 777-782. (Comment.) DOI: 10.1038/s41592-023-01861-8. PMID: 37076630; PMCID: PMC7614633 |
This comment describes the principles and application of a group of techniques to study the 3D ultrastructure of cells and tissues: volume EM (vEM). It also describes efforts by the international vEM community to bring together experts and users and to build capacity for these techniques. |
| Iudin A, Korir PK, Somasundharam S, Weyand S, Cattavitello C, Fonseca N, Salih O, Kleywegt GJ, Patwardhan A (2023). “EMPIAR: The Electron Microscopy Public Image Archive”, Nucleic Acids Research, 51, pp. D1503–D1511 DOI: 10.1093/nar/gkac1062. PMID: 36440762 |
This publication on EMPIAR, describing the status of the archive in 2022, serves as the paper to cite if you have used or deposited into EMPIAR. |
| Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A (2021). “The BioImage Archive – building a home for life-sciences microscopy data.“, Journal of Molecular Biology, 434, 167505. DOI: 10.1016/j.jmb.2022.167505. PMID: 35189131; PMCID: ???. (Pre-print DOI: 10.1101/2021.12.17.473169. PMID: PPR435232.) |
EMPIAR uses the IT infrastructure of EMBL-EBI's BioImage Archive, which is described in this paper. |
| Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A (2021). “REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology”, Nature Methods, 18, 1418-1422. DOI: 10.1038/s41592-021-01166-8. PMID: 34021280; PMCID: PMC8606015. |
This white paper, emanating from a workshop held at EMBL-EBI, proposes draft metadata guidelines for archiving bioimaging data in public archives, including EMPIAR. |
| Walter A, Kleywegt GJ & Verkade P (2021). “Correlative multimodal imaging: building a community”, in Methods in Cell Biology, volume 162, chapter 17, pp. 417-430. DOI: 10.1016/bs.mcb.2020.12.010. PMID: 33707022. |
This book chapter includes a discussion of archiving of correlative (CLEM and CLXM) data in public resources, including EMPIAR. |
| Iudin, A, Sarkans, U, Koronfel, MA, Fish, T, Dobbie, I, Harkiolaki, M, Patwardhan, A & Kleywegt, GJ (2021). “Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications”, STAR Protocols, 2, 100253. DOI: 10.1016/j.xpro.2020.100253. PMID: 33490973; PMCID: PMC7811169. |
This protocol describes how correlative (multimodal) imaging data can be deposited to EMPIAR and the BioImage Archive at EMBL-EBI. |
| Kleywegt GJ, Velankar S, & Patwardhan A, “Structural biology data archiving: where we are and what lies ahead”, FEBS Letters, 592, 2153-2167 (2018). DOI: 10.1002/1873-3468.13086. PMID: 29749603; PMCID: PMC019198. |
This review provides an overview of the state-of-the-art (in 2018) of archiving in structural biology, as well as future directions. It focuses on PDB, EMDB and EMPIAR. |
| Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M & Kleywegt GJ, “Building bridges between cellular and molecular structural biology”, Elife, 6, e25835 (2017). DOI: 10.7554/eLife.25835. PMID: 28682240; PMCID: PMC5524535. |
White paper of the third EM-expert workshop at EMBL-EBI. The input fed into the second EMPIAR grant application and underpinned the work on segmentations including EMDB-SFF, the Volume Browser and the Segmentation Annotation Tool. |
| Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ & Patwardhan A, “Web-based volume slicer for 3D electron-microscopy data from EMDB”, Journal of Structural Biology, 194, 164-170 (2016). DOI: 10.1016/j.jsb.2016.02.012. PMID: 26876163; PMCID: PMC4819904. |
This paper describes a predecessor of the Volume Browser that is now used to inspect 2D slices through 3D datasets archived in EMPIAR. |
| Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ & Patwardhan A, “EMPIAR: a public archive for raw electron microscopy image data”, Nature Methods, 13, 387-388 (2016). DOI: 10.1038/nmeth.3806. PMID: 27067018. |
Three years after the first EMPIAR entries had been released, this publication officially announced the existence of the archive to the scientific world. |
| Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR & Kleywegt GJ, “A 3D cellular context for the macromolecular world”, Nature Structural & Molecular Biology, 21, 841-845 (2014). DOI: 10.1038/nsmb.2897. PMID: 25289590; PMCID: PMC4346196. |
White paper of the second EM-expert workshop at EMBL-EBI. It did a lot of the groundwork for a subsequent (successful) funding application to establish EMPIAR. |
| Patwardhan A., Carazo J-M., Carragher B., Henderson R., Heymann J.B., Hill E., Jensen G.J., Lagerstedt I., Lawson C.L., Ludtke S., Mastronarde S., Moore W.J., Roseman A., Rosenthal P., Sorzano C-O., Sanz-Garcia E., Scheres S.H.W., Subramaniam S., Westbrook J., Winn M., Swedlow J.R. & Kleywegt G.J., “Data management challenges in three-dimensional EM”, Nature Structural & Molecular Biology, 19, 1203-1207 (2012). DOI: 10.1038/nsmb.2426. PMID: 23211764; PMCID: PMC4048199. |
White paper from the first of the famous EM-expert workshops at EMBL-EBI. This paper expresses the need for an archive with raw cryo-EM data (which would eventually become EMPIAR). |
