public
Next generation imaging for biology across scales
IMAGINE will provide technologies to probe structure and function of biological specimens in their natural context
The IMAGINE project is continuously publishing its results from across our work packages as preprints and/or peer-reviewed publications. Committed to FAIR principles, all publications are available online.
Zang, R. X., Malaiwong, N., Wang, L., Maziarz, J. D., Jia, K., Drotleff, B., … & Musser, J. M. (2026). An ancient monoaminergic signaling system coordinates contractility in a nerveless sponge. bioRxiv, 2026-02. https://doi.org/10.64898/2026.02.14.704838
Ashesh, A., Carrara, F., Zubarev, I., Galinova, V., Croft, M., Pezzotti, M., … & Jug, F. (2026). Micro Split: semantic unmixing of fluorescent microscopy data. Nature Methods, 1-11. https://doi.org/10.1038/s41592-026-03082-1
Pyle, E., Steyer, A. M., Babenko, A., Rosa, H. V. D., & Mattei, S. (2025). The In Situ Structure and Distribution of V-ATPase in C. elegans Apical Membrane Stacks. bioRxiv, 2025-12. https://doi.org/10.64898/2025.12.19.695382
Magalhaes, V., Pinto, V., Sousa, P., Afonso, J. A., Gonçalves, L., Fernández, E., & Minas, G. (2025). A portable and low-cost optical device for pigment-based taxonomic classification of microalgae using machine learning. Sensors and Actuators B: Chemical, 423, 136819.
Ashesh, A., & Jug, F. (2025). scSplit: Bringing Severity Cognizance to Image Decomposition in Fluorescence Microscopy. arXiv preprint arXiv:2503.22983.
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
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
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
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
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
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
Krull, A., Di Sante, M., Silvio Pasqualini, F., & Jug, F. (2022). μSplit efficient image decomposition for microscopy data. arXiv e-prints, arXiv-2211. https://doi.org/10.48550/arXiv.2211.12872
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
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.
