ORCID 0000-0003-2808-4210
recent online talks
(full selection available on YouTube)
Evolution of neural computation
Integrative Chronobiology and Visual Neuroscience series. 02/06/2022
The retinal basis of vision in birds
Montreal University Seminar Series. 13/01/2023.
Principles of colour processing
FASEB Conference on Retinal Neurobiology, MA, USA. 22/06/2022.
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
2023
Seifert Mdirect link. (bioRxiv version). pdf.
, Roberts PA, Kafetzis G, Osorio D , Baden T . Birds multiplex spectral and temporal visual information via retinal On- and Off-channels. Nature Communications. 14, 5308 (2023).Baden T, Briseño J, Coffing G, [+48 authors, alphabetical], Simakov Odirect link
, Albertin C . Cephalopod-omics: Emerging Field and Technolgies in Caphalopod Biology. Integrative and Comparative Biology icad087. X , Roberts PA, Yoshimatsu T, Lagnado L* , Baden T* . Amacrine cells differentially balance zebrafish colour circuits in the central and peripheral retina. Cell Reports 42:112055. (2022
2021
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 MJYbioRxiv version).
, 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 (Baden Tdirect link. pdf.
, 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.Zhou M*, Bear J*, Roberts PA, Janiak FK, Semmelhack J, Yoshimatsu T, Baden TbioRxiv version). direct link. pdf.
Zebrafish Retinal Ganglion Cells Asymmetrically Encode Spectral and Temporal Information Across Visual Space. Current Biology 30, 2927-2942. (
Yoshimatsu Tdirect link. (bioRxiv version). pdf. Primer by Westo and Ala-Laurila.
Chagas AMdirect link. (preprints.org version). pdf.
, 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.Seifert Mdirect link. (preprints.org version). pdf.
, Baden T, Osorio D. The Retinal Basis of Vision in Chicken. Sem Cell Dev Biol.Ran Y*, Huang Z*, Baden T, Schubert T, Baayen H, Berens P#, Franke K#, Euler T#bioRxiv version). direct link. pdf.
. Type-specific dendritic integration in mouse retinal ganglion cells. Nature Communications 11:2001. (Baden Tdirect link. pdf.
, Euler T, Berens P. Understanding the retinal basis of vision across species. Nature Reviews Neuroscience, doi:10.1038/s41583-019-0242-1.2019
Euler Tpreprints.org version). direct link.
, 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. (Franke K*, Chagas AM*, Zhao Z, Zimmermann MJY, Bartel P, Qiu Y, Szatko K, Baden T, Euler T8:e48779. (bioRxiv version). direct link. pdf.
. An arbitrary-spectrum spatial visual stimulator for vision research. eLifeVlasits Adirect link. pdf.
and Baden T . Motion Vision: A new Mechanism in the Mammalian Retina. Current Biology 29(19):933-935.Nevala NE
and Baden TBaden Tpreprints.org version). direct link. pdf. F1000 recommendation by G Fain.
and Osorio D . The Retinal Basis of Vertebrate Color Vision. Annual Review of Vision Science (5). (Maina MBAfricArXiv version). pdf.
, 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. (2018
Baden TbioRxiv version). direct link. pdf.
, 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.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
.
2017
Chagas AMdirect link. (bioRxiv version). pdf.
, 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.Forman CJdirect link. (bioRxiv version). pdf.
Franke K and direct link.pdf.
. General features of inhibition in the inner retina. Journal of Physiology doi ;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*, pdf. direct link. (bioRxiv version). News and Views by Dick Masland.
, , , , . Inhibition decorrelates visual feature representations in the inner retina. Nature; doi: 10.1038/nature21394.2016
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
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
Tessa Herzog (2023). Information encoding at the first synapse of vision. pdf.
John Bear (2022). A Red Herring in the Zebrafish Retina: Regional Specialisations among Retinal Ganglion Cells in the Zebrafish Larva Linked to Chromatic Encoding of Prey Stimuli. pdf.
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