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Jonatan Alvelid

I am an engineering physicist by training, and did my PhD in the lab of Ilaria Testa working on automating STED microscopy for functional and structural live-cell imaging. The thesis included development of a STED microscope, and work on microscope control software and automation, image analysis, fluorophores, and various applications. I am currently interested in and focusing on microscopy automation and image analysis, and developing tools to support more advanced use of super-resolution microscopes for biological applications. I work on applying smart microscopy automation and data analysis to MINFLUX microscopy, both for imaging and tracking. In that I aim to let the sample tell us when, where, and how to acquire, thereby allowing more efficient data collection and experiments that are not feasible with manual control. 
Publication list
  • Lukinavičius, G., Alvelid, J., Gerasimaitė, R., Rodilla-Ramirez, C., Nguyễn, V.T., Vicidomini, G., Bottanelli, F., Han, K.Y., Testa, I., Stimulated emission depletion microscopy, Nature Reviews Methods Primers, doi.org/10.1038/s43586-024-00335-1 (2024).
  • Damenti, M., Coceano, G., Mendes Silva, M., Alvelid, J., Sgattoni, C., Volpato, A., Rems, L., Masullo, L.A., Unterauer, E.M., Kowalewski, R., Delemotte, L., Sezgin, E., Jungmann, R., Testa, I., Structural diversity of Arc oligomers within the excitatory synapse, bioRxiv, doi.org/10.1101/2024.06.05.597462 (2024).
  • Hirabayashi, Y., Lewis, T.L.J., Du, Y., Virga, D.M., Decker, A.M., Coceano, G., Alvelid, J., Paul, M.A., Hamilton, S., Kneis, P., Takahashi, Y., Gaublomme, J.T., Testa, I., Polleux, F., Most axonal mitochondria in cortical pyramidal neurons lack mitochondrial DNA and consume ATP, biorXiv, doi.org/10.1101/2024.02.12.579972 (2024).
  • Pennacchietti, F., Alvelid, J., Morales, R.A., Damenti, M., Ollech, D., Oliinyk, O.S., Shcherbakova, D.M., Villablanca, E.J., Verkhusha, V.V., Testa, I., Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms, Nature Communications, doi.org/10.1038/s41467-023-44054-9 (2023).
  • Volpato, A., Ollech, D., Alvelid, J., Damenti, M., Müller, B., York, A.G., Ingaramo, M., Testa, I., Extending fluorescence anisotropy to large complexes using reversibly switchable proteins, Nature Biotechnology, doi.org/10.1038/s41587-022-01489-7 (2023).
  • Alvelid, J., Bucci, A., Testa, I., Far Red-Shifted CdTe Quantum Dots for Multicolour Stimulated Emission Depletion Nanoscopy, ChemPhysChem, doi.org/10.1002/cphc.202200698 (2023).
  • Alvelid, J., Damenti, M., Sgattoni, C., Testa, I., Event-triggered STED imaging, Nature Methods, doi.org/10.1038/s41592-022-01588-y (2022).
  • Jalalvand, E., Alvelid, J., Coceano, G., Edwards, S., Robertson, B., Grillner, S., Testa, I., ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal, Elife, doi.org/10.7554/eLife.73114 (2022).
  • Casas Moreno, X., Al-Kadhimi, S., Alvelid, J., Bodén, A., Testa, I., ImSwitch: Generalizing microscope control in Python, Journal of Open Source Software, doi.org/10.21105/joss.03394 (2021).
  • Fang, T., Alvelid, J., Spratt, J., Ambrosetti, E., Testa, I., Teixeira, A.I., Spatial Regulation of T-Cell Signaling by Programmed Death-Ligand 1 on Wireframe DNA Origami Flat Sheets, ACS Nano, doi.org/10.1021/acsnano.0c10632 (2021).
  • Alvelid, J. and Testa, I., Stable stimulated emission depletion imaging of extended sample regions, Journal of Physics D: Applied Physics, doi.org/10.1088/1361-6463/ab4c13 (2020).
  • Matlashov, M.E.*, Shcherbakova, D.M.*, Alvelid, J.*, Baloban, M., Pennacchietti, F., Shemetov, A.A., Testa, I., Verkhusha, V.V., A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales, Nature Communications, doi.org/10.1038/s41467-019-13897-6(2020).
  • Alvelid, J. and Testa, I., Fluorescence microscopy at the molecular scale, Current Opinion in Biomedical Engineering,  doi.org/10.1016/j.cobme.2019.09.009(2019)-
  • Schramm, F.D., Schroeder, K., Alvelid, J., Testa, I., Jonas, K., Growth-driven displacement of protein aggregates along cell length ensures partitioning to both daughter cells in Caulobacter crescentus, Molecular Microbiology, doi.org/10.1111/mmi.14228 (2019).

CV
  • 2023-              Postdoc, Laboratory of Christian Eggeling, Department of Biophysical Imaging, Leibniz Institute of Photonic Technology, Jena, Germany
  • 2021-2023       Postdoc, Laboratory of Ilaria Testa, Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
  • 2016–2021      PhD, Laboratory of Ilaria Testa, Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
  • 2014–2016      Master of Science in Nanotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
  • 2011-2014       Bachelor of Science in Engineering Physics, KTH Royal Institute of Technology, Stockholm, Sweden