# Publications & Media ## Papers and preprints ### Neuroinformatics Unit publications ::::{grid} 1 1 1 1 :gutter: 3 :::{grid-item-card} :link: https://doi.org/10.1016/j.cub.2026.03.034 **Sirmpilatze, N., Felder, A.**, Abdulazhanova, D., Schwigon, L., **Tatarnikov, I.**, Haase, K., Musielak, I., Kobylkov, D., Margrie, T. W., Mouritsen, H., Heyers, D., **Tyson, A. L.**, Weiler, S. (2026) "An open-source three-dimensional digital brain atlas of a migratory bird, the Eurasian blackcap" *Current Biology* 2025.03.04.641293, doi.org/10.1016/j.cub.2026.03.034 ::: :::{grid-item-card} :link: https://doi.org/10.5281/zenodo.19945701 **Felder, A.**, Chapuis, G., **Tatarnikov, I., Sirmpilatze, N., Tyson, A.** (2026). Mapping the state of neuroscientific software - a vision for collaboration beyond single institutes or labs (1.0). *Zenodo*, doi.org/10.5281/zenodo.19945701 ::: :::{grid-item-card} :link: https://doi.org/10.48550/arXiv.2505.16882 Duporge, I., **Minano, S., Sirmpilatze, N., Tatarnikov, I.**, Wolf, S., **Tyson, A. L.**, Rubenstein, D. (2025) "Tracking the Flight: Exploring a Computational Framework for Analyzing Escape Responses in Plains Zebra (Equus quagga)" *arXiv* 2505.16882, doi.org/10.48550/arXiv.2505.16882 ::: :::{grid-item-card} :link: https://doi.org/10.1101/2024.03.06.583699 Domine, C. C. J., Carrasco-Davis, R., Hollingsworth L., **Sirmpilatze, N., Tyson, A. L.**, Jarvis, D., Barry, C., Saxe, A. M. (2024) “NeuralPlayground: A Standardised Environment for Evaluating Models of Hippocampus and Entorhinal Cortex” *bioRxiv*, doi.org/10.1101/2024.03.06.583699 ::: :::: ### Publications relating to Neuroinformatics Unit software ::::{grid} 1 1 1 1 :gutter: 3 :::{grid-item-card} :link: https://doi.org/10.1038/s41598-021-04676-9 **Tyson, A. L.**, Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022) "Accurate determination of marker location within whole-brain microscopy images" *Scientific Reports*, doi.org/10.1038/s41598-021-04676-9 ::: :::{grid-item-card} :link: https://doi.org/10.1371/journal.pcbi.1009074 **Tyson, A. L.**, Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., Margrie, T. W. (2021) "A deep learning algorithm for 3D cell detection in whole mouse brain image datasets" *PLOS Computational Biology* 17(5): e1009074, doi.org/10.1371/journal.pcbi.1009074 ::: :::{grid-item-card} :link: https://doi.org/10.7554/eLife.65751 Claudi, F., **Tyson, A. L.**, Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) "Visualizing anatomically registered data with Brainrender" *eLife* 2021;10:e65751 doi.org/10.7554/eLife.65751 ::: :::{grid-item-card} :link: https://doi.org/10.21105/joss.02668 Claudi, F., Petrucco, L., **Tyson, A. L.**, Branco, T., Margrie, T. W., Portugues, R. (2020) "BrainGlobe Atlas API: a common interface for neuroanatomical atlases" *Journal of Open Source Software* 5(54), 2668 doi.org/10.21105/joss.02668 ::: :::: ## Talks ::::{grid} 1 1 1 1 :gutter: 3 :::{grid-item-card} movement: a Python toolbox for analysing motion tracking data :link: https://www.youtube.com/watch?v=RUDhXB1ZZIg Niko Sirmpilatze, The Behaviour Forum virtual workshop, April 2026 ::: :::{grid-item-card} Trusted by design: set up your research software for community adoption :link: https://fosdem.org/2026/schedule/event/VPJH8F-trusted-by-design/ Niko Sirmpilatze, FOSDEM, February 2026 ::: :::{grid-item-card} movement: a Python toolbox for analysing motion tracking data :link: https://fosdem.org/2026/schedule/event/9VLSXV-movement-tracks-python/ Niko Sirmpilatze, FOSDEM, January 2026 ::: :::{grid-item-card} Aligning spikes to histology with BrainGlobe :link: https://youtu.be/yER8ynNdJcE?si=9_9eTJv--0GZMntn Alessandro Felder, UCL Neuropixels course, October 2025 ::: :::{grid-item-card} movement: A Python toolbox for analysing animal body movements :link: https://youtu.be/GXBQsqqZZTg?si=0bt5Q_lGY8GXw6dx Niko Sirmpilatze, ABIDE seminar, February 2025 ::: :::{grid-item-card} Aligning spikes to histology with BrainGlobe :link: https://youtu.be/ck-2vNR7qwo?si=awOA9sEw7xRl9-Nf Alessandro Felder, UCL Neuropixels course, October 2024 ::: :::{grid-item-card} Aligning spikes to histology with BrainGlobe :link: https://www.youtube.com/watch?v=JQ-vYx42L6s Adam Tyson, UCL Neuropixels course, October 2023 ::: :::{grid-item-card} BrainGlobe: a Python ecosystem for computational (neuro)anatomy :link: https://www.youtube.com/watch?v=Ndsssf_gHns Adam Tyson, World Wide Series | Open Neuroscience, May 2021 ::: :::: ## Mentions in the media ::::{grid} 1 1 1 1 :gutter: 3 :::{grid-item-card} Scientists map migratory bird brain :link: https://ucl.ac.uk/news/2026/apr/scientists-map-migratory-bird-brain UCL News, April 2026 ::: :::{grid-item-card} Scientists map the blackcap bird brain, opening a new era of 3D digital atlases :link: https://www.sainsburywellcome.org/research-news/scientists-map-blackcap-bird-brain-opening-new-era-3d-digital-atlases Sainsbury Wellcome Centre, April 2026 ::: :::{grid-item-card} The Neuro – Irv and Helga Cooper Foundation Open Science Prizes: Meet the winners of an exceptional edition :link: https://www.mcgill.ca/neuro/article/neuro-irv-and-helga-cooper-foundation-open-science-prizes-meet-winners-exceptional-edition The Neuro (Montreal Neurological Institute-Hospital), October 2025 ::: :::{grid-item-card} The BrainGlobe Initiative wins 2025 International Prize :link: https://www.sainsburywellcome.org/web/research-news/brainglobe-initiative-wins-2025-international-prize Sainsbury Wellcome Centre, October 2025 ::: :::{grid-item-card} Mapping the migratory bird brain :link: https://www.sainsburywellcome.org/web/blog/mapping-migratory-bird-brain Sainsbury Wellcome Centre, March 2025 ::: :::{grid-item-card} BrainGlobe Initiative celebrates open-source software award :link: https://www.sainsburywellcome.org/web/blog/brainglobe-initiative-celebrates-open-source-software-award Sainsbury Wellcome Centre, October 2024 ::: ::::