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Next generation imaging for biology across scales
IMAGINE will provide technologies to probe structure and function of biological specimens in their natural context
IMAGINE project is continuously publishing its results as papers and/or journals. These publications have been published by different WPs across the project. Committed to FAIR principles, all publications are available online.
Brenner, J., Plitzko, J. M., & Klumpe, S. (2026). Exploring shaped focused ion beams for lamella preparation. Ultramicroscopy, 282, 114302. https://doi.org/10.1016/j.ultramic.2025.114302
Buglakova, E., Archit, A., D’Imprima, E., Mahamid, J., Pape, C., & Kreshuk, A. (2025). Tiling artifacts and trade‑offs of feature normalization in the segmentation of large biological images (arXiv:2503.19545). arXiv. https://doi.org/10.48550/arXiv.2503.19545
Berger, C., Watson, H., Naismith, J. H., et al. (2025). Xenon plasma focused ion beam lamella fabrication on high-pressure frozen specimens for structural cell biology. Nature Communications, 16, 2286. https://doi.org/10.1038/s41467-025-57493-3
Klumpe, S., & Plitzko, J. M. (2025). Cryo-focused ion beam milling for cryo-electron tomography: Shaping the future of in situ structural biology. Current Opinion in Structural Biology, 94, 103138. https://doi.org/10.1016/j.sbi.2025.10313
Last, M. G. F., van Klaveren, M., Janssen, L., Jensen, N., Jansen, I., Jakobs, S., Voortman, L. M., & Sharp, T. H. (2025). Dual-colour super-resolution cryoCLEM in mammalian cells using the fluorescent proteins rsTagRFP and rsEGFP2. Journal of structural biology, 217(4), 108267. https://doi.org/10.1016/j.jsb.2025.108267
Last, M. G. F., Voortman, L. M., & Sharp, T. H. (2025). Scaling data analyses in cellular cryoET using comprehensive segmentation [Preprint]. bioRxiv. https://doi.org/10.1101/2025.01.16.633326
Oel, A. P., Cros, C. C. D. R., Pan, L., Buglakova, E., Haury Parra, S., Santangeli, L., Gerber, T., Papalopoulos, N., Martinez Vergara, H., Puga, D., Disela, V., Niederhaus, L., Bertucci, P. Y., Witte, V., Kilic, A. B., Quintana Urzainqui, I., Acevedo, J. M., Musser, J., Kreshuk, A., & Arendt, D. (2025). A whole-body cell type atlas mapped into an electron microscopy volume of an annelid worm [Preprint]. bioRxiv. https://doi.org/10.1101/2025.10.30.685666
Pacureanu, A., Thies, T., Bosch, C., Holler, M., Guizar-Sicairos, M., Müller, E., Reuteler, J., Karpov, D., Schaefer, A. T., Cloetens, P., Menzel, A., & Diaz, A. (2025). Experimental comparison of X-ray ptychographic and holographic nanotomography of metal-stained neuronal tissue. Optics Express, 33(13), 26915–26929. https://doi.org/10.1364/OE.563186
Pöge, M., Dickmanns, M., Xu, P., Li, M., Schiøtz, O. H., Kaiser, C. J. O., Ma, J., Bieber, A., Capitanio, C., Brenner, J., Riggi, M., Klumpe, S., Miras, M., Kazemein Jasemi, N. S., Schulze, W. X., Simon, R., Frommer, W. B., Plitzko, J. M., & Baumeister, W. (2025). Making plant tissue accessible for cryo-electron tomography [Reviewed preprint, version 1]. eLife.
Velazco, A., Glen, T., Klumpe, S., et al. (2025). Reduction of SEM charging artefacts in native cryogenic biological samples. Nature Communications, 16, 5204. https://doi.org/10.1038/s41467-025-60545-3 https://doi.org/10.7554/eLife.106455.1
Vitali, M. T., Candeo, A., Farina, A., Pozzi, P., Brix, A., Bassi, A., & Correia, T. M. (2025). Accelerated dynamic light sheet microscopy: Unifying time-varying patterned illumination and low-rank and sparsity constrained reconstruction. Journal of Physics: Photonics, 7(2), 025005. https://doi.org/10.1088/2515-7647/adad23
Albers, J., Nikolova, M., Svetlove, A., Darif, N., Lawson, M. J., Schneider, T. R., Schwab, Y., Bourenkov, G., & Duke, E. (2024). High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III. Journal of synchrotron radiation, 31(Pt 1), 186–194. https://doi.org/10.1107/S160057752300944X
Ashesh, A., & Jug, F. (2024). denoiSplit: A method for joint microscopy image splitting and unsupervised denoising(arXiv:2403.11854). arXiv. https://arxiv.org/abs/2403.11854
Davis, S., Sommernes, J.-R., Hambura, S., Riedel, L., Gil, A., Ikmi, A., Ströhl, F., & Prevedel, R. (2024). Mesoscopic axially swept oblique plane microscope for the imaging of freely moving organisms with near-isotropic resolution. Biomedical Optics Express, 15(12), 6715–6724. https://doi.org/10.1364/BOE.539123
Félix, R; Paleček, D; Correia, T. Colour science with lasers, gummy bears, and rainbows. Issue 66. Science in School: The European Journal for Science Teachers. https://www.scienceinschool.org/wp-content/uploads/2024/01/Issue-66-Gummy-Bears.pdf
Gemin, O., Armijo, V., Hons, M., Bissardon, C., Linares, R., Bowler, M. W., … & Papp, G. (2024). EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control. bioRxiv, 2024-01. https://doi.org/10.1101/2024.01.18.576170
Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., Chakraborty, S., Tagiltsev, G., Michael, A. K., van Dorst, S., Waltz, F., McCafferty, C. L., Lamm, L., Zufferey, S., Van der Stappen, P., van den Hoek, H., Wietrzynski, W., Harar, P., Wan, W., Briggs, J. A. G., Plitzko, J. M., Engel, B. D., & Kotecha, A. (2024). Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. bioRxiv. https://doi.org/10.1101/2024.12.28.630444
Mart, G. F., Last, L., Leoni, A., Abendstein, L. M., Voortman, T. H., & Sharp, T. H. (2024). Streamlining segmentation of cryo-electron tomography datasets with AI. eLife, 13, RP98552. https://doi.org/10.7554/eLife.98552.3
Ruperti, F., Becher, I., Stokkermans, A., Wang, L., Marschlich, N., Potel, C., Maus, E., Stein, F., Drotleff, B., Schippers, K. J., Nickel, M., Prevedel, R., Musser, J. M., Savitski, M. M., & Arendt, D. (2024). Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. Current biology : CB, 34(2), 361–375.e9. https://doi.org/10.1016/j.cub.2023.12.021
Schiøtz, O. H., Klumpe, S., Plitzko, J. M., & Kaiser, C. J. O. (2024). Cryo-electron tomography: En route to the molecular anatomy of organisms and tissues. Biochemical Society Transactions, 52(6), 2415–2425. https://doi.org/10.1042/BST20240173
Schiøtz, O. H., Kaiser, C. J. O., Klumpe, S., et al. (2024). Serial lift-out: Sampling the molecular anatomy of whole organisms. Nature Methods, 21(12), 1684–1692. https://doi.org/10.1038/s41592-023-02113-5
Albers, J., Nikolova, M., Svetlove, A., Darif, N., Lawson, M. J., Schneider, T. R., … & Duke, E. (2024). High throughput tomography (HiTT) on EMBL beamline P14 on PETRA III. Journal of Synchrotron Radiation, 31(1). https://doi.org/10.1107/S160057752300944X
Berger, C., Dumoux, M., Glen, T. et al. Plasma FIB milling for the determination of structures in situ. Nat Commun 14, 629 (2023). https://doi.org/10.1038/s41467-023-36372-9
Dumoux, M; Glen, T; Smith, J; Ho, E; Perdigão, L; Pennington, A; Klumpe, S; Yee, N; Farmer, D; Lai, P; Bowles, W; Kelley, R; Plitzko, J; Wu, L; Basham, M; Clare, D; Siebert, C; Darrow, M; Naismith, J; Grange, M (2023). Cryo-plasma FIB/SEM volume imaging of biological specimens. eLife 12:e83623. https://doi.org/10.7554/eLife.83623
Obando, M., Bassi, A., Ducros, N. et al. Model-based deep learning framework for accelerated optical projection tomography. Sci Rep 13, 21735 (2023). https://doi.org/10.1038/s41598-023-47650-3
Obando, M; Bassi, A; Ducros, N; et al. ToMoDL: A model-based deep learning framework for optical projection tomography, 07 September 2023, PREPRINT (Version 1) available at Research Square. https://doi.org/10.21203/rs.3.rs-3318045/v1
Schiøtz, O.H., Kaiser, C.J.O., Klumpe, S. et al. Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat Methods (2023). https://doi.org/10.1038/s41592-023-02113-5
This project is funded by the European Union (GA#101094250). Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them.
