# Publications & Media

## Papers and preprints

### Neuroinformatics Unit publications
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: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
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:link: https://doi.org/10.1101/2025.03.04.641293
**Sirmpilatze, N., Felder, A.**, Abdulazhanova, D., Schwigon, L., Haase, K., Musielak, I., Margrie, T. W., Mouritsen, H., Heyers, D., **Tyson, A. L.**, Weiler, S. (2025) "Mapping the magnetoreceptive brain: A 3D digital atlas of the migratory bird Eurasian blackcap (Sylvia atricapilla)" *bioRxiv* 2025.03.04.641293, doi.org/10.1101/2025.03.04.641293
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: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
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### Publications relating to Neuroinformatics Unit software

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: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
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: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
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: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
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: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
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## Talks

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:::{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
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:::{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
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:::{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
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:::{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
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