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

Informations projet

IMAGINE

N° de convention de subvention: 101094250

DOI

10.3030/101094250

Date de signature de la CE 2 Decembre 2022

Date de début 1 Mai 2023

Date de fin 30 Avril 2028

Financé au titre de

• Research infrastructures

Coût total

€ 9 569 677,52

Contribution de l’UE

€ 9 569 677,50

Coordonné par

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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)

Publications

Peer reviewed articles (22)

Exploring shaped focused ion beams for lamella preparation

Auteurs: Juergen Plitzko, Sven Klumpe
Publié dans: BioRxiv, 2025, ISSN 2692-8205
Éditeur: BioRxiv
DOI: 10.1101/2025.04.01.646235

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

Auteurs: Oda Helene Schiøtz, Sven Klumpe, Juergen M. Plitzko, Christoph J. O. Kaiser
Publié dans: Biochemical Society Transactions, Numéro 52, 2024, ISSN 0300-5127
Éditeur: Portland Press Ltd.
DOI: 10.1042/BST20240173

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

Auteurs: Elena Buglakova, Anwai Archit, Edoardo D'Imprima, Julia Mahamid, Constantin Pape, Anna Kreshuk
Publié dans: Cornell University Arxiv Computer Vision and Pattern Recognition, 2025, ISSN 2414-1895
Éditeur: 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

Auteurs: Marco Tobia Vitali, Alessia Candeo, Andrea Farina, Paolo Pozzi, Alessia Brix, Andrea Bassi, Teresa M Correia
Publié dans: Journal of Physics: Photonics, Numéro 7, 2025, ISSN 2515-7647
Éditeur: IOP Publishing
DOI: 10.1088/2515-7647/ADAD23

Cryo-plasma FIB/SEM volume imaging of biological specimens

Auteurs: 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.
Publié dans: eLife Sciences, Numéro eLife 12:e83623., 2023, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/eLife.83623

Plasma FIB milling for the determination of structures in situ

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

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

Auteurs: Juergen Plitzko, Sven Klumpe
Publié dans: Current Opinion in Structural Biology, Numéro Volume 94, October 2025, 103138, 2025, ISSN 0922-3444
Éditeur: Elsevier
DOI: 10.1016/J.SBI.2025.103138

Reduction of SEM charging artefacts in native cryogenic biological samples

Auteurs: 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.
Publié dans: Nature Communications, Numéro 16, 2025, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: BioRxiv, 2025, ISSN 2692-8205
Éditeur: BioRxiv
DOI: 10.1101/2025.10.30.685666

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

Auteurs: Marcos Obando, Andrea Bassi, Nicolas Ducros, Germán Mato, Teresa Correia
Publié dans: Research Square, Numéro Article no. 21735 (2023), 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-47650-3

Streamlining segmentation of cryo-electron tomography datasets with Ais

Auteurs: T. Sharp
Publié dans: Structural Biology and Molecular Biophysics, 2024, ISSN 2050-084X
Éditeur: 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

Auteurs: Samuel Davis, Sebastian Hambura, Robert Prevedel
Publié dans: Biomedical Optics Express, Numéro Vol. 15, Numéro 12, pp. 6715-6724, 2024, ISSN 2156-7085
Éditeur: Biomedical Optics Express
DOI: 10.1364/BOE.537262

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

Auteurs: A. Ashesh, F. Jug
Publié dans: Cornell University Arxiv Computer Vision and Pattern Recognition (cs.CV), 2024, ISSN 2331-8422
Éditeur: 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

Auteurs: 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
Publié dans: Nature Methods, 2023, ISSN 1548-7105
Éditeur: Nature Methods
DOI: 10.1038/s41592-023-02113-5

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

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

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

Auteurs: Casper Berger, Helena Watson, James H. Naismith, Maud Dumoux, Michael Grange
Publié dans: Nature Communications, Numéro 16, 2025, ISSN 2041-1723
Éditeur: 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

Auteurs: Casper Berger, Helena Watson, James H. Naismith, Maud Dumoux, Michael Grange
Publié dans: Nature Communications, Numéro 16, 2025, ISSN 2041-1723
Éditeur: 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

Auteurs: Juergen Plitzko
Publié dans: BioRxiv, 2024, ISSN 2692-8205
Éditeur: BioRxiv
DOI: 10.1101/2024.12.28.630444V1

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

Auteurs: Rute C. Félix, David Paleček, Teresa M. Correia
Publié dans: Science in School: The European Journal for Science Teachers Numéro 66, Numéro Numéro 66, 2024, ISSN 0140-5284
Éditeur: Science in School: The European Journal for Science Teachers
DOI: 10.5281/zenodo.10608950

Model-based deep learning framework for accelerated optical projection tomography

Auteurs: Marcos Obando, Andrea Bassi, Nicolas Ducros, Germán Mato & Teresa M. Correia
Publié dans: Nature - Scientific Reports, Numéro Article no. 21753 (2023), 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-47650-3

Making plant tissue accessible for cryo-electron tomography

Auteurs: Juergen Plitzko, Christoph Kaiser, Sven Klumpe
Publié dans: Plant Biology, 2025, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/ELIFE.106455.1

Microplit: Semantic Unmixing of Fluorescent Microscopy Data

Auteurs: A. Ashesh, F. Jug
Publié dans: BioRxiv, 2025, ISSN 2692-8205
Éditeur: BioRxiv
DOI: 10.1101/2025.02.10.637323

Conference proceedings (1)

μSplit: image decomposition for fluorescence microscopy

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

Other (1)

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

Auteurs: 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
Publié dans: BioRxiv, 2024, ISSN 2692-8205
Éditeur: Biorxiv
DOI: 10.1101/2024.01.18.576170