Next generation imaging technologies to probe structure and function of biological specimen across scales in their natural context

Información del proyecto

IMAGINE

Identificador del acuerdo de subvención: 101094250

DOI

10.3030/101094250

Fecha de la firma de la CE 2 Diciembre 2022

Fecha de inicio 1 Mayo 2023

Fecha de finalización 30 Abril 2028

Financiado con arreglo a

• Research infrastructures

Coste total

€ 9 569 677,52

Aportación de la UE

€ 9 569 677,50

Coordinado por

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Documents, reports (3)

Publication of project website

Deliverable 44 (also D13.3) is associated with WP13 and pat of Task 13.2: Establish and implement internal and external communication channels (Lead: EMBL-HD; Participants: Euro-BioImaging ERIC, Instruct ERIC)

Plan for Dissemination and Exploitation including Communication Activities

This deliverable is an obligatory to be submitted and updated on each periodic report of the project. The first draft within the first period has been submitted through EC Portal communication channel with the EC PO

Report on establishment of Project Management structure and procedures

Deliverable 42 (also D13.1) is associated with WP13 and is part of Task 13.1: Establish and implement the Project Management structure (Lead: EMBL-HD; Participants: Euro-BioImaging, Instruct ERIC, EMBRC ERIC, ESRF, MPG, SU)

Data Management Plan (1)

IMAGINE Data Management Plan

Deliverable 43 (also D13.2) is associated with WP13 and concludes Task 13.1: Establish and implement the Project Management structure (Lead: EMBL-HD; Participants: Euro-BioImaging, Instruct ERIC, EMBRC ERIC, ESRF, MPG, SU)

Publicaciones

Peer reviewed articles (22)

Exploring shaped focused ion beams for lamella preparation

Autores: Juergen Plitzko, Sven Klumpe
Publicado en: BioRxiv, 2025, ISSN 2692-8205
Editor: BioRxiv
DOI: 10.1101/2025.04.01.646235

Cryo-electron tomography: <i>en route</i> to the molecular anatomy of organisms and tissues

Autores: Oda Helene Schiøtz, Sven Klumpe, Juergen M. Plitzko, Christoph J. O. Kaiser
Publicado en: Biochemical Society Transactions, Edición 52, 2024, ISSN 0300-5127
Editor: Portland Press Ltd.
DOI: 10.1042/BST20240173

Tiling artifacts and trade-offs of feature normalization in the segmentation of large biological images

Autores: Elena Buglakova, Anwai Archit, Edoardo D'Imprima, Julia Mahamid, Constantin Pape, Anna Kreshuk
Publicado en: Cornell University Arxiv Computer Vision and Pattern Recognition, 2025, ISSN 2414-1895
Editor: Cornell University Arxiv Computer Vision and Pattern Recognition
DOI: 10.48550/ARXIV.2503.19545

Accelerated dynamic light sheet microscopy: unifying time-varying patterned illumination and low-rank and sparsity constrained reconstruction

Autores: Marco Tobia Vitali, Alessia Candeo, Andrea Farina, Paolo Pozzi, Alessia Brix, Andrea Bassi, Teresa M Correia
Publicado en: Journal of Physics: Photonics, Edición 7, 2025, ISSN 2515-7647
Editor: IOP Publishing
DOI: 10.1088/2515-7647/ADAD23

Cryo-plasma FIB/SEM volume imaging of biological specimens

Autores: Dumoux, M., Glen, T., Smith, J.L., Ho, E.M., Perdigão, L.M., Pennington, A., Klumpe, S., Yee, N.B., Farmer, D.A., Lai, P.Y. and Bowles, W.
Publicado en: eLife Sciences, Edición eLife 12:e83623., 2023, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/eLife.83623

Plasma FIB milling for the determination of structures in situ

Autores: Casper Berger, Maud Dumoux, Thomas Glen, Neville B.-y. Yee, John M. Mitchels, Zuzana Patáková, Michele C. Darrow, James H. Naismith & Michael Grange
Publicado en: Nature Communications, Edición Article number 629 (2023), 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-36372-9

Cryo-FIB milling for cryo-ET - shaping the future for biological specimens

Autores: Juergen Plitzko, Sven Klumpe
Publicado en: Current Opinion in Structural Biology, Edición Volume 94, October 2025, 103138, 2025, ISSN 0922-3444
Editor: Elsevier
DOI: 10.1016/J.SBI.2025.103138

Reduction of SEM charging artefacts in native cryogenic biological samples

Autores: Abner Velazco, Thomas Glen, Sven Klumpe, Avery Pennington, Jianguo Zhang, Jake L. R. Smith, Calina Glynn, William Bowles, Maryna Kobylynska, Roland A. Fleck, James H. Naismith, Judy S. Kim, Michele C.
Publicado en: Nature Communications, Edición 16, 2025, ISSN 2041-1723
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-60545-3

A whole-body cell type atlas mapped into an electron microscopy volume of an annelid worm

Autores: Oel Adam Phillip, Cros Cyril Christophe Daniel Robert, Pan Leslie, Buglakova Elena, Haury Parra Samuel, Santangeli Luca, Gerber Tobias, Papalopoulos Nikolaos, Vergara Hernando Martinez, Puga David, Di
Publicado en: BioRxiv, 2025, ISSN 2692-8205
Editor: BioRxiv
DOI: 10.1101/2025.10.30.685666

ToMoDL: A model-based deep learning framework for optical projection tomography

Autores: Marcos Obando, Andrea Bassi, Nicolas Ducros, Germán Mato, Teresa Correia
Publicado en: Research Square, Edición Article no. 21735 (2023), 2023, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-47650-3

Streamlining segmentation of cryo-electron tomography datasets with Ais

Autores: T. Sharp
Publicado en: Structural Biology and Molecular Biophysics, 2024, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/ELIFE.98552.3

Mesoscopic axially swept oblique plane microscope for the imaging of freely moving organisms with near-isotropic resolution

Autores: Samuel Davis, Sebastian Hambura, Robert Prevedel
Publicado en: Biomedical Optics Express, Edición Vol. 15, Edición 12, pp. 6715-6724, 2024, ISSN 2156-7085
Editor: Biomedical Optics Express
DOI: 10.1364/BOE.537262

denoiSplit: a method for joint microscopy image splitting and unsupervised denoising

Autores: A. Ashesh, F. Jug
Publicado en: Cornell University Arxiv Computer Vision and Pattern Recognition (cs.CV), 2024, ISSN 2331-8422
Editor: Cornell University Arxiv Computer Vision and Pattern Recognition (cs.CV)
DOI: 10.48550/ARXIV.2403.11854

Serial Lift-Out: sampling the molecular anatomy of whole organisms

Autores: Oda Helene Schiøtz, Christoph J. O. Kaiser, Sven Klumpe, Dustin R. Morado, Matthias Poege, Jonathan Schneider, Florian Beck, David P. Klebl, Christopher Thompson & Jürgen M. Plitzko
Publicado en: Nature Methods, 2023, ISSN 1548-7105
Editor: Nature Methods
DOI: 10.1038/s41592-023-02113-5

High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III

Autores: Albers, Jonas, Marina Nikolova, Angelika Svetlove, Nedal Darif, Matthew J. Lawson, Thomas R. Schneider, Yannick Schwab, Gleb Bourenkov, and Elizabeth Duke
Publicado en: Journal of Synchrotron Radiation, Edición Volume 3, Part 1, 2024, ISSN 1600-5775
Editor: Journal of Synchrotron Radiation
DOI: 10.1107/S160057752300944X

Xenon plasma focused ion beam lamella fabrication on high-pressure frozen specimens for structural cell biology

Autores: Casper Berger, Helena Watson, James H. Naismith, Maud Dumoux, Michael Grange
Publicado en: Nature Communications, Edición 16, 2025, ISSN 2041-1723
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-57493-3

Xenon plasma focused ion beam lamella fabrication on high-pressure frozen specimens for structural cell biology

Autores: Casper Berger, Helena Watson, James H. Naismith, Maud Dumoux, Michael Grange
Publicado en: Nature Communications, Edición 16, 2025, ISSN 2041-1723
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-57493-3

Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii

Autores: Juergen Plitzko
Publicado en: BioRxiv, 2024, ISSN 2692-8205
Editor: BioRxiv
DOI: 10.1101/2024.12.28.630444V1

Colour science with lasers, gummy bears, and rainbows (educational paper)

Autores: Rute C. Félix, David Paleček, Teresa M. Correia
Publicado en: Science in School: The European Journal for Science Teachers Edición 66, Edición Edición 66, 2024, ISSN 0140-5284
Editor: Science in School: The European Journal for Science Teachers
DOI: 10.5281/zenodo.10608950

Model-based deep learning framework for accelerated optical projection tomography

Autores: Marcos Obando, Andrea Bassi, Nicolas Ducros, Germán Mato & Teresa M. Correia
Publicado en: Nature - Scientific Reports, Edición Article no. 21753 (2023), 2023, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-47650-3

Making plant tissue accessible for cryo-electron tomography

Autores: Juergen Plitzko, Christoph Kaiser, Sven Klumpe
Publicado en: Plant Biology, 2025, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/ELIFE.106455.1

Microplit: Semantic Unmixing of Fluorescent Microscopy Data

Autores: A. Ashesh, F. Jug
Publicado en: BioRxiv, 2025, ISSN 2692-8205
Editor: BioRxiv
DOI: 10.1101/2025.02.10.637323

Conference proceedings (1)

μSplit: image decomposition for fluorescence microscopy

Autores: Ashesh Ashesh, Alexander Krull, Moises Di Sante, Francesco Pasqualini, Florian Jug;
Publicado en: Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV), 2023, ISSN 2380-7504
Editor: ICCV Paris
DOI: 10.1109/ICCV51070.2023.01940

Other (1)

EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control

Autores: Olivier Gemin, Victor Armijo, Michael Hons, Caroline Bissardon, Romain Linares, Matthew W. Bowler, Georg Wolff,, Kirill Kovalev, Anastasiia Babenko, Veijo T. Salo, Sarah Schneider, Christopher Rossi, Léa Lecomte, Thibault Deckers, Kévin Lauzier, Robert Ja
Publicado en: BioRxiv, 2024, ISSN 2692-8205
Editor: Biorxiv
DOI: 10.1101/2024.01.18.576170