Google scholar profile

ORCID 0000-0003-2808-4210

Recent talk videos and slides

The evolution of computation in the brain: Principles in colour processing. FASEB Conference on Retinal Neurobiology, MA, USA. Held 22/06/2022. Slides (pdf,pptx) (video will be added once available).
The evolution of computation in the brain: Insights from studying the retina. Integrative Chronobiology and Visual Neuroscience series. Recorded 02/06/2022. video.
Retinal circuits for colour vision: From fish to humans. Young IBRO NextInNeuro online webinar series, inaugural lecture. Recorded 19/03/2021. video.

posters

All recent conference posters are available online:

Many posters are shared on F1000Research collection (citable)
Full self-archived collection here (not citable yet)

preprints

Wang X^§, Roberts PA, Yoshimatsu T, Lagnado L*^§, Baden T*^§. Amacrine cells differentially balance zebrafish colour circuits in the central and peripheral retina. bioRxiv doi: https://doi.org/10.1101/2022.01.22.477338. direct link. pdf.

Strauss S*, Korympidou MM*, Ran Y, Franke K, Schubert T, Baden T, Berens P, Euler T^§ and Vlasits AL^§. Center-surround interactions underlie bipolar cell motion sensing in the mouse retina. bioRxiv doi: https://doi.org/10.1101/2021.05.31.446404. direct link. pdf.

2022

Baden T and Nilsson DE. Is our retina really upside down? Current Biology 32(7) R300-303. direct link. pdf.

Janiak FK^§, Bartel P, Bale M, Yoshimatsu T, Komulainen EH, Zhou M, Staras K, Prieto Godino LL, Euler T, Maravall M, Baden T^§. Non-Telecentric Two-photon Microscopy for 3D Random Access Mesoscale Imaging. Nature Communications (2022)13:544. direct link. (bioRxiv version). pdf. See also Filip Janiak’s WWN online talk here.

2021

Bartel P, Yoshimatsu T, Janiak FK, Baden T^§. Spectral inference reveals principal cone-integration rules of the zebrafish inner retina. Current Biology 31 1-13. (bioRxiv version). direct link. pdf. Recommendation by Gordon Fain. Dispatch by Marco Garbelli and Stephan Neuhauss.

Yoshimatsu T, Bartel P, Schroeder C, Janiak FK, St-Pierre F, Berens P, Baden T^$. Ancestral circuits for vertebrate colour vision emerge at the first retinal synapse. Science Advances 7(24):eabj6815 (bioRxiv version). direct link. pdf.

Schroeder C^$, Oesterle J, Berens P*, Yoshimatsu T*, Baden T*^$. Distinct Synaptic Transfer Functions in Same-Type Photoreceptors. eLife 10:e67851. (bioRxiv version). direct link. pdf.

Baden T^$. Circuit-Mechanisms for Colour Vision in Zebrafish. Current Biology 31:12 PR807-R820. direct link. pdf.

Dehmelt FA, Meier R, Hinz J, Yoshimatsu T, Simacek CA, Huang R, Wang K, Baden T, Arrenberg A^§. Spherical arena reveals optokinetic response tuning to stimulus location, size and frequency across entire visual field of larval zebrafish. eLife 10:e63355. (bioRxiv version). direct link. pdf.

Maina MB^$, Ahmad U, Ibrahim HA, Hamidu SK, Nasr FE, Salihu AT, Abushouk AI, Abdurrazak M, Awadelkareem MA, Amin A, Imam A, Akinrinade ID, Yakubu AH, Azeez IA, Yunusa GM, Adamu AA, Ibrahim HB, Bukar AM, Yaro AU, Prieto-Godino LL^$ and Baden T^$. Two decades of neuroscience publication trends in Africa. Nature Communications 12:3429 . (bioRxiv version). direct link. pdf.

Bartel P^$, Janiak FK, Osorio D, Baden T^$. Colourfulness as a possible measure of object proximity in the larval zebrafish brain. Current Biology 31(5): R235-6. (bioRxiv version). direct link. pdf.

Independent publications by lab members:

Roberts PA. Mathematical Models of Retinitis Pigmentosa. The Trophic Factor Hypothesis. bioRxiv (direct link).

Roberts PA. Inverse Problem Revealse Conditions for Characteristic Retinal Degeneration Patterns in Retinitis Pigmentosa under the Trophic Factor Hypothesis. bioRxiv (direct link).

2020

Zimmermann MJY^§, Chagas AM, Bartel P, Pop S, Prieto Godino LL, Baden T^§. LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging. HardwareX e00127 (bioRxiv version). direct link. pdf.

Baden T^§, Maina MB, Maia Chagas A, Mohammed YG, Auer TO, Silbering A, von Tobel L, Pertin M, Hartig R, Aleksic J, Akinrinade I, Awadelkareem MA, Koumoundourou A, Jones A, Arieti F, Beale A, Munch D, Cury Salek S, Yusuf S, Prieto Godino LL^§. TReND in Africa: Towards a Truly Global (Neuro)science Community. Neuron107(3): 412-416. direct link. pdf.

Zhou M*, Bear J*, Roberts PA, Janiak FK, Semmelhack J, Yoshimatsu T, Baden T^§. Zebrafish Retinal Ganglion Cells Asymmetrically Encode Spectral and Temporal Information Across Visual Space. Current Biology 30, 2927-2942. (bioRxiv version). direct link. pdf.

Baden T^§. (2020). Editorial for special issue on “Vertebrate Vision: Lessons from Non-Model Species”. Sem Cell Dev Biol. https://doi..org/10.1016/j.semcdb.2020.05.028. direct link. pdf. (The full special issue, including all 13 reviews, can be accessed –> here <–)

Yoshimatsu T^§, Schroeder C, Nevala NE, Berens P, Baden T^§. Fovea-like Photoreceptor Specializations Underlies Single UV Cone Driven Prey-Capture Behaviour in Zebrafish. Neuron (107):1-18. direct link. (bioRxiv version). pdf. Primer by Westo and Ala-Laurila.

Chagas AM^§, Molloy JC, Prieto Godino LL, Baden T. Leveraging Open Hardware to Alleviate the Burden of COVID-19 on Global Health Systems. PLoS Biology pbio.3000730. direct link. (preprints.org version). pdf.

Seifert M^§, Baden T, Osorio D. The Retinal Basis of Vision in Chicken. Sem Cell Dev Biol. direct link. (preprints.org version). pdf.

Ran Y*, Huang Z*, Baden T, Schubert T, Baayen H, Berens P^#, Franke K^#, Euler T^#^§. Type-specific dendritic integration in mouse retinal ganglion cells. Nature Communications 11:2001. (bioRxiv version). direct link. pdf.

Baden T^§, Euler T, Berens P. Understanding the retinal basis of vision across species. Nature Reviews Neuroscience, doi:10.1038/s41583-019-0242-1. direct link. pdf.

2019

Euler T^§, Franke K, Baden T. Studying a light sensor with light: multiphoton imaging in the retina. In Multiphoton Microscopy, Ed. Espen Hartveit, Neuromethods book series, NM (148), Springer Nature. pp 225-250. (preprints.org version). direct link. pdf .

Franke K*, Chagas AM*, Zhao Z, Zimmermann MJY, Bartel P, Qiu Y, Szatko K, Baden T, Euler T^§. An arbitrary-spectrum spatial visual stimulator for vision research. eLife 8:e48779. (bioRxiv version). direct link. pdf.

Vlasits A^§ and Baden T^§. Motion Vision: A new Mechanism in the Mammalian Retina. Current Biology 29(19):933-935. direct link. pdf.

Nevala NE^§ and Baden T^§. A low-cost hyperspectral scanner for natural imaging above and under water. Scientific Reports (9) 10799. (biorXiv version). direct link. pdf.

Baden T^§ and Osorio D^§. The Retinal Basis of Vertebrate Color Vision. Annual Review of Vision Science (5). (preprints.org version). direct link. pdf. F1000 recommendation by G Fain.

Maina MB^§, Yunusa MG, Bukar AM, Ahmad U, Salihu AT, Ibrahim HA, Muhammad A, Hamidu SK, Yaro AU, Awadelkareem MA, and Baden T. African Neuroscience on the Global Stage: Nigeria as a Model. Europ. J Neurosci, doi 10.1111/ejn.14372. (AfricArXiv version). pdf.

2018

Baden T^§, James B, Zimmermann M, Bartel P, Griseels D, Lagnado L* and Maravall M*. Spikeling: a low-cost hardware implementation of a spiking neuron for neuroscience teaching and outreach. PLoS Biology doi.org/10.1371/journal.pbio.2006760. (bioRxiv version). direct link. pdf.

Chagas AM (2018). Haves and have nots must find a better way: the case for open scientific hardware. PloS Biology doi.org/10.1371/journal.pbio.3000014. direct link.

Zimmermann MJY*, Nevala NE*, Yoshimatsu T*, Osorio D, Nilsson DE, Berens P, Baden T^§. Zebrafish differentially process colour across visual space to match natural scenes. Current Biology 28(1-15). direct link. (bioRxiv version). pdf. Dispatch by Stephan Neuhauss.

Baden T^§, Schubert T, Berens P, Euler T. The Functional Organization of Vertebrate Retinal Circuits for Vision. In Oxford Research Encyclopedia of Neuroscience. Ed. S. Murray Sherman. New York: Oxford University Press. DOI 10.1093/acrefore/9780190264086. direct link. pdf.

2017

Chapot CA, Behrens C, Rogerson LE, Baden T, Pop S, Berens P, Euler T^§, Schubert T^§. Local signals in mouse horizontal cell dendrites. Current Biology 27(1-13). direct link. (bioRxiv version). pdf.

Chagas AM^§, Prieto Godino LL, Arrenberg AB and Baden T^§. The 100 Euro Lab: A 3-D Printable Open Source Platform For Fluorescence Microscopy, Optogenetics And Accurate Temperature Control During Behaviour Of Zebrafish, Drosophila And C. elegans. PLoS Biology. direct link. (bioRxiv version). pdf.

Forman CJ^§, Tomes H, Mbobo B, Burman, RJ, Jacobs M, Baden T^§, Raimondo JV^§. Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes. Scientific Reports. 7:2188. direct link. (bioRxiv version). pdf.

Franke K and Baden T. General features of inhibition in the inner retina. Journal of Physiology doi 10.1113/JP273648; direct link.pdf.

Baden T, Schaeffel F and Berens P. Visual Neuroscience: A Retinal Ganglion Cell to Report Image Focus? Current Biology; http://dx.doi.org/10.1016/j.cub.2016.12.022. direct link. pdf.

Franke K*, Berens P*, Schubert T, Bethge M, Euler T^§, Baden T^§. Inhibition decorrelates visual feature representations in the inner retina. Nature; doi: 10.1038/nature21394. pdf. direct link. (bioRxiv version). News and Views by Dick Masland.

2016

Baden T and Euler T. Retinal Physiology: Non-Bipolar-Cell Excitatory Drive in the Inner Retina. Current Biology26(15):706:8. pdf. direct link.

Euler T and Baden T. Computational Neuroscience: Species Specific Motion Detectors. Nature doi:10.1038/nature18454. pdf.direct link.

Theis L, Berens P^§ , Froudarakis E, Reimer J, Roman Roson M, Baden T, Euler T, Tolias AS, Bethge M. Benchmarking spike rate inference in population calcium imaging. Neuron 90(3):471-82. pdf, direct link. (bioRxiv version here).

Baden T*, Berens *P, Franke K*, Roman Roson M, Bethge M, Euler T^§. The functional diversity of mouse retinal ganglion cells. Nature. doi:10.1038/nature16468.pdf; direct link. F1000 recommendation by Dick Masland.

2015

Kulkarni MM, Schubert T, Baden T, Wissinger B, Euler T, Paquet-Durand F^§. Imaging Ca2+ dynamics in cone photoreceptor axon terminals of the mouse retina”. Journal of Visualized Experiments (99) doi 10.3791/52588; direct Link.

Baden T^§, Chagas AM, Gage G, Marzullo T, Prieto Godino LL, Euler T. Open Labware – 3D printing your own lab equipment. PLoS Biology. 13(3):e1002086.doi:10.1371/journal.pbio.1002086. pdf; direct link.

2014

Baden T*, Nikolaev A*, Esposti F, Dreosti E, Odermatt B and Lagnado L^§. (2014). A synaptic mechanism for temporal filtering of visual signals. PLoS Biology. 12(10): e1001972. doi:10.1371/journal.pbio.1001972. pdf Supplementary [1] [2] [3] [4] [Primer by Suh & Baccus].

Euler T^§, Haverkamp S, Schubert T and Baden T. (2014). Retinal Bipolar cells: Elementary building blocks of vision. Nature Reviews Neuroscience. 15:507-519. pdf Suppementary [1] [2].

2013

Baden T*, Schubert T*, Chang L, Wei T, Zaichuk M, Wissinger B and Euler T^§. (2013). A Tale of Two Retinal Domains: Near Optimal Sampling of Achromatic Contrasts in Natural Scenes Through Asymmetric Photoreceptor Distribution. Neuron80: 1206-1217. pdf Supplementary [1].

Yusuf S, Baden T and Prieto Godino LL. (2013). Bridging the Gap: Establishing the Necessary Infrastructure and Knowledge for Teaching and Research in Neuroscience in Africa. Metabolic Brain Disease. DOI 10.1007/s11011-013-9443-x. pdf.

Baden T and Euler T. (2013). Early Vision: Where (Some of) the Magic Happens. Current Biology23(24):1096-1098. pdf.

Baden T^§, Euler T, Weckström M and Lagnado L. (2013). Spikes and Ribbon Synapses in Early Vision. Trends in Neurosciences 36(8):480-8. pdf.

Baden T^§, Berens P, Bethge M and Euler T. (2013). Spikes in Mammalian Bipolar Cells Support Temporal Layering of the Inner Retina. Current Biology 23(1), 48-52 pdf Supplementary [1].

2012

Auferkorte ON, Baden T, Kaushalya SK, Zabouri N, Rudolph U, Haverkamp S and Euler T^§. (2012). GABA(A) receptors containing the a2 subunit are critical for direction-selective inhibition in the retina, PLoS One, 7(4):e35109. pdf.

2011

Baden T, Esposti F, Nikolaev A and Lagnado L^§. (2011). Spikes in retinal bipolar cells code visual stimuli with millisecond precision. Current Biology(21): 1-11. pdf Supplementary [1].

Dreosti E*, Esposti F*, Baden T and Lagnado L^§. (2011). In vivo evidence that retinal bipolar cells generate spikes modulated by light. Nature Neuroscience14(8): 951-2. pdf Supplementary [1].

Cederlund ML, Morrissey ME, Baden T, Scholz D, Vendrell V, Lagnado L, Connaughton VP and Kennedy BN^§. (2011). Zebrafish Tg(7.2mab21l2:EGFP) Transgenics reveal a Unique Population of Retinal Amacrine Cells. Invest Ophthalmol Vis Sci. 52(3):1613-21. pdf.

2010 and earlier

Baden T and Hedwig B^§. (2010). Primary Afferent Depolarisation and Frequency Processing in Auditory Afferents. Journal of Neuroscience 30(44): 14862-9. pdf.

Baden T and Hedwig B^§. (2009). Dynamics of free intracellular Ca2+ during synaptic and spike activity of cricket tibial motoneurons. European Journal of Neuroscience. 29(7):1357-68. pdf.

Baden T and Hedwig B^§. (2008). Front leg movements and tibial motoneurons underlying auditory steering in the cricket (Gryllus bimaculatus deGeer). Journal of Experimental Biology. 211(13):2123-33. pdf.

Baden T and Hedwig B^§. (2007). Neurite-specific Ca2+ dynamics underlying sound processing in an auditory interneurone. Developmental Neurobiology 67(1):68-80. pdf.

Becker AJ, Klein H, Baden T, Aigner L, Normann S, Elger CE, Schramm J, Wiestler OD and Blumcke I^§. (2002). Mutational and expression analysis of the reelin pathway components CDK5 and doublecortin in gangliogliomas. Acta Neuropathologica. 104(4):403-8. pdf.

Becker AJ, Urbach H, Scheffler B, Baden T, Normann S, Lahl R, Pannek HW, Tuxhorn I, Elger CE, Schramm J, Wiestler OD and Blumcke I^§. (2002). Focal cortical dysplasia of Taylor’s balloon cell type: mutational analysis of the TSC1 gene indicates a pathogenic relationship to tuberous sclerosis. Annuals of Neurology. 52(1):29-37. pdf.

PhD theses

John Bear (2021). A Red Herring in the Zebrafish Retina: Regional Specialisations among Retinal Ganglion Cells in the Zebrafish Larva Linked to Chromatic Encoding of Prey Stimuli. (viva pending)

Mingyi Zhou (2021). What the fish’s eye tells the fish’s brain: functional complement of zebrafish retinal ganglion cells. pdf.

Philipp Bartel (2021). Zebrafish Colour Vision: A survey of spectral processing in the zebrafish visual system. pdf.

Maxime Y Zimmermann (2021). Chromatic processing in the zebrafish inner retina: Bipolar cell physiology and open hardware designs for spectrally accurate stimulation under two-photon. pdf.

Noora E Nevala (2020). Mapping the natural visual world of the zebrafish (Danio rerio): from sensory input to behavioural output. pdf.

Andre Maia Chagas (2020). Open Neuroscience: Challening scientific barriers with open sourece hardware. pdf. (from Tuebingen, /w Thomas Euler)

Katrin Franke (2016). Functional characterisation of the excitatory pathways in the mouse inner retina. pdf. (from Tuebingen, /w Thomas Euler)

Other

Nature / Eppendorf Prize Interview and media. Link. Nature Podcast. Interview published in Nature 2017.

Maia Chagas A and Baden T (2015). Open Source Toolkit. PLoS Blogs. link

Baden T. Habilitation thesis. Nonlinearities in early vision. pdf

Baden T, et al. (2013). Neurowissenschaften in Afrika – Kooperationen und Perspektiven. Neuroforum. 2:73-74. pdf

Baden T, Zorovic M and Hedwig B. (2008). Motorische Kontrolle der akustischen Orientierung von Grillen. Neuroforum 4:267-273

Baden T. (2008). PhD thesis. Activity Patterns and Calcium Dynamics of Sensory Interneurons and Motoneurons of the Cricket Auditory Pathway. (Supervisor: B Hedwig, Department of Zoology, University of Cambridge). pdf

Baden T. Analysing the neuronal computer (2007). ßluesci 8:1. doc