Published in arXiv, 2025
You can read the paper at arXiv
Recommended citation: 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
Published in Cell Systems, 2025
You can read the paper here.
Recommended citation: De Vries, M., Dent, L. G., Curry, N., Rowe-Browen, L., Bousgouni, V., Fourkioti, O., Naidoo, R., Sparks, H., Tyson, A., Dunsby, C., Bakal, C. (2025). "Geometric deep learning and multiple-instance learning for 3D cell-shape profiling" Cell Systems v16(3) 101229
Published in bioRxiv, 2025
You can read the paper at bioRxiv or read more about the atlas here.
Recommended citation: 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
Published in bioRxiv, 2024
You can read the paper at bioRxiv or try the software here.
Recommended citation: 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
Published in Neuron, 2022
You can read the paper here.
Recommended citation: Keshavarzi, S., Bracey, E. F., Faville, R. A., Campagner, D., Tyson, A. L., Lenzi, S. C., Branco, T., Margrie, T. W. (2022). "Multisensory coding of angular head velocity in the retrosplenial cortex" Neuron v110(3), p532
Published in Scientific Reports, 2022
You can read the paper at Scientific Reports or try the software here.
Recommended citation: 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
Published in Progress in Biophysics and Molecular Biology, 2022
You can read the paper here.
Recommended citation: Tyson, A. L., Margrie, T. W. (2022). "Mesoscale microscopy and image analysis tools for understanding the brain" Progress in Biophysics and Molecular Biology v168 p81
Published in PLoS Computational Biology, 2021
You can read the paper at PLoS Computational Biology or try the software here.
Recommended citation: 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 Comp Bio 17(5): e1009074.
Published in eLife, 2021
You can read the paper at eLife or try brainrender here.
Recommended citation: 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
Published in Scientific Reports, 2021
You can read the paper here.
Recommended citation: Brown, A. P. Y.*, Cossell, L.*, Strom, M., Tyson, A. L., Vélez-Fort, M., Margrie, T.W. (2021). "Analysis of segmentation ontology reveals the similarities and differences in connectivity onto L2/3 neurons in mouse V1" Sci. Rep. v11 #4983.
Published in Journal of Open Source Software, 2020
You can read the paper here and find the software here.
Recommended citation: 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
Published in Cell, 2020
You can read the paper here and find the software for:
Recommended citation: Koundouros, N., Karali, E., Tripp, A., Valle, A., Inglese, P., Perry, N. J. S, Magee, D. J., Virmouni, S. A., Elder, G. A., Tyson, A. L., Luisa Doria, M., van Weverwijk, A., Soares, R. F., Isacke, C. M., Nicholson, J. K., Glen, R. C., Takats, Z., Poulogiannis, G. (2020) "Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids" Cell v181 p1
Published in Journal of Cell Biology, 2020
You can read the paper here and find the image analysis software here.
Recommended citation: Jackman, M.*, Marcozzi, C.*, Barbiero, M., Pardo, M., Yu, L., Tyson, A. L., Choudray, J., Pines, J. (2020). "Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint" J. Cell Biol. v219(6)
Published in Scientific Reports, 2019
You can read the paper here.
Recommended citation: Tyson, A. L., Akhtar, A., Andreae, L. C. (2019). "Optimisation and validation of hydrogel-based brain tissue clearing shows uniform expansion across anatomical regions and spatial scales" Sci. Rep. v9 #12084.
Published in Molecular Autism, 2019
You can read the paper here.
Recommended citation: Pervolaraki, E.*, Tyson, A. L.*, Pibiri, F., Poulter, S. L., Reichelt, A. C., Rodgers, R. J., Clapcote, S. J., Lever, C., Andreae, L. C.*, Dachtler, J.* (2019). "The within-subject application of diffusion tensor MRI and CLARITY reveals brain structural changes in Nrxn2 deletion mice" Mol. Autism v10 p8.
Published in Epilepsia Open, 2017
You can read the paper here.
Recommended citation: McGinnity, C. J., Smith, A. B., Yaakub, S. N., Gerbase, S. W., Gammerman, A., Tyson, A. L., Bell, T. K., Elmasri, M., Barker G. J., Richardson, M. P., Pal, D. K. (2017). "Decreased functional connectivity within a language subnetwork in benign epilepsy with centrotemporal spikes" Epilepsia Open v494 p651.
Published in International Journal of Pharmaceutics, 2015
You can read the paper heres.
Recommended citation: Tyson, A. L., Hilton, S. T., Andreae, L. C. (2015). "Rapid, simple and inexpensive production of custom 3D printed equipment for large-volume fluorescence microscopy" Int. J. Pharma. v494 p651.
Published in The Einstein Journal of Biology and Medicine, 2013
You can read the paper here.
Recommended citation: Tyson, A. L. (2013). "What do we know about spatial navigation, and what else could model-based fMRI tell us?" Einstein J. Biol. Med. v29 p32.