Armin's profile

My research explores how nervous systems transform sensory information into decisions and actions. Using larval zebrafish as a model system, my lab investigates the neural algorithms and circuit mechanisms that allow animals to evaluate their environment, integrate evidence over time, and select adaptive behaviors. A central goal of our work is to understand how relatively small neural circuits can implement sophisticated computations underlying perception, decision-making, and intelligence.

To address these questions, we combine behavioral experiments, virtual reality technologies for freely behaving animals, and large-scale neural recording and manipulation. These approaches allow us to link sensory stimuli, neural activity, and behavior with high precision. In parallel, we use advanced microscopy and molecular techniques to uncover the cellular and circuit architectures that implement these computations in the brain.

More broadly, our research aims to bridge levels of analysis—from genes and synapses to neural circuits, algorithms, and collective behavior. By integrating experimental neuroscience with computational modeling and emerging molecular methods, we seek to uncover general principles of how brains process information and generate intelligent behavior, both in individuals and in interacting animal groups.

Positions

Education

Major Grants

2026

• Reynolds P., Marchi D., Ling Y. T., Slangewal K., Capelle M., Chalakova Z., Bahl A., Hindges R. (2026) Early visual experience elicits cellular and functional plasticity in the retina and alters behaviour. Neuron (accepted). https://doi.org/10.1101/2025.04.29.651180
• Slangewal K., Aimon S., Capelle M. Q., Kämpf F., Naumann H., Slanchev K., Baier H., Bahl A. (2026) Visuomotor decision-making through multifeature convergence in the larval zebrafish hindbrain. Nature Communications. https://doi.org/10.1038/s41467-026-69633-4
• Garza R., Hady A. E., Bahl A. (2026) Developmental and genetic modulation of evidence integration dynamics in zebrafish sensorimotor decision-making. bioRxiv. https://doi.org/10.64898/2026.03.01.708829
• Putti E., Faini G., Dang J. T., Savaliya J. H., Eggeler F., Duroure K., Vougny J., Ortiz-Álvarez G., Pujades C., Bahl A., Lichtman J. W., Engert F., Boulanger-Weill J., Bene F. D., Albadri S. (2026) Lrrn-mediated retinal ganglion cell targeting drives visual circuit assembly for brightness and contrast detection. Science Advances. https://doi.org/10.1126/sciadv.adz4585

2025

• Klusmann F. S., Kögler A. C., Slangewal K., Önder O., Naumann H., Marx A., Bahl A., Müller P. (2025) An RNA ligase shapes transcriptional profiles, neural function, and behaviour in the developing larval zebrafish. bioRxiv. https://doi.org/10.64898/2025.12.01.691575
• Krishnan K., Muthukumar A., Sterrett S., Pflitsch P., Fairhall A. L., Fishman M., Bahl A., Zwaka H., Engert F. (2025) Attentional switching in larval zebrafish. Science Advances. https://doi.org/10.1126/sciadv.ads4994
• Vohra S. K., Eberle M., Boulanger-Weill J., Petkova M. D., Schuhknecht G. F. P., Herrera K. J., Kämpf F., Ruetten V. M. S., Lichtman J. W., Engert F., Randlett O., Bahl A., Isoe Y., Hege H., Baum D. (2025) Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish. bioRxiv. https://doi.org/10.1101/2025.07.14.664689
• Capelle M. Q., Slangewal K., Eleftheriadis P. E., Bahl A. (2025) Behavioral algorithms of ontogenetic switching in larval and juvenile zebrafish phototaxis. bioRxiv. https://doi.org/10.1101/2025.06.13.659371
• Petkova M. D., Januszewski M., Blakely T., Herrera K. J., Schuhknecht G. F., Tiller R., Choi J., Schalek R. L., Boulanger-Weill J., Peleg A., Wu Y., Wang S., Troidl J., Vohra S. K., Wei D., Lin Z., Bahl A., Tapia J. C., Iyer N., Miller Z. T., Hebert K. B., Pavarino E. C., Taylor M., Deng Z., Stingl M., Hockling D., Hebling A., Wang R. C., Zhang L. L., Dvorak S., Faik Z., King K. I., Goel P., Wagner-Carena J., Aley D., Chalyshkan S., Contreas D., Li X., Muthukumar A. V., Vernaglia M. S., Carrasco T. T., Melnychuck S., Yan T., Dalal A., DiMartino J. M., Brown S., Safo-Mensa N., Greenberg E., Cook M., Finley-May S., Flynn M. A. (2025) A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain. bioRxiv. https://doi.org/10.1101/2025.06.10.658982
• Shanbhag R., Zoidl G. S., Nakhuda F., Sabour S., Naumann H., Zoidl C., Bahl A., Tabatabaei N., Zoidl G. R. (2025) Pannexin-2 deficiency disrupts visual pathways and leads to ocular defects in zebrafish. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. https://doi.org/10.1016/j.bbadis.2025.167807
• Boulanger-Weill J., Kämpf F., Schuhknecht G. F. P., Schalek R. L., Petkova M., Vohra S. K., Wu Y., Savaliya J. H., Tiller R., Herrera K. J., Naumann H., Eberle M., Rencken S., Stingl M., Hebling A., Hockling D., Slangewal K., Deng Z., Wang R. C., Zhang L. L., Kirchberger K. N., Bianco I. H., Baum D., Bene F. D., Engert F., Lichtman J. W., Bahl A. (2025) Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish. bioRxiv. https://doi.org/10.1101/2025.03.14.643363

2024

• Pflitsch P., Oury N., Krishnan K., Joo W., Lyons D. G., Capelle M., Herrera K. J., Bahl A., Rihel J., Engert F., Zwaka H. (2024) Sleep disruption improves performance in simple olfactory and visual decision-making tasks. bioRxiv. https://doi.org/10.1101/2024.11.02.621641
• Vohra S. K., Harth P., Isoe Y., Bahl A., Fotowat H., Engert F., Hege H., Baum D. (2024) A visual interface for exploring hypotheses about neural circuits. IEEE Transactions on Visualization and Computer Graphics. https://doi.org/10.1109/tvcg.2023.3243668
• Voigt F. F., Reuss A. M., Naert T., Hildebrand S., Schaettin M., Hotz A. L., Whitehead L., Bahl A., Neuhauss S. C. F., Roebroeck A., Stoeckli E. T., Lienkamp S. S., Aguzzi A., Helmchen F. (2024) Reflective multi-immersion microscope objectives inspired by the Schmidt telescope. Nature Biotechnology. https://doi.org/10.1038/s41587-023-01717-8

2023

• Voigt F. F., Naert T., Bahl A., Lienkamp S. S., Helmchen F. (2023) Reflective multi-immersion microscope objectives. Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXX. https://doi.org/10.1117/12.2648095

2021

• Harpaz R., Nguyen M. N., Bahl A., Engert F. (2021) Precise visuomotor transformations underlying collective behavior in larval zebrafish. Nature Communications. https://doi.org/10.1038/s41467-021-26748-0
• Harpaz R., Aspiras A. C., Chambule S., Tseng S., Bind M., Engert F., Fishman M. C., Bahl A. (2021) Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish. Science Advances. https://doi.org/10.1126/sciadv.abi7460
• Zhu M. L., Herrera K. J., Vogt K., Bahl A. (2021) Navigational strategies underlying temporal phototaxis in Drosophila larvae. Journal of Experimental Biology. https://doi.org/10.1242/jeb.242428
• Chen A. B., Deb D., Bahl A., Engert F. (2021) Algorithms underlying flexible phototaxis in larval zebrafish. Journal of Experimental Biology. https://doi.org/10.1242/jeb.238386

2020

• Bahl A., Engert F. (2020) Neural circuits for evidence accumulation and decision making in larval zebrafish. Nature Neuroscience. https://doi.org/10.1038/s41593-019-0534-9

2019

• Wee C. L., Song E. Y., Johnson R. E., Ailani D., Randlett O., Kim J., Nikitchenko M., Bahl A., Yang C., Ahrens M. B., Kawakami K., Engert F., Kunes S. (2019) A bidirectional network for appetite control in larval zebrafish. eLife. https://doi.org/10.7554/elife.43775

2018

• Ribeiro I. M., Drews M., Bahl A., Machacek C., Borst A., Dickson B. J. (2018) Visual projection neurons mediating directed courtship in Drosophila. Cell. https://doi.org/10.1016/j.cell.2018.06.020

2016

• Leonhardt A., Ammer G., Meier M., Serbe E., Bahl A., Borst A. (2016) Asymmetry of Drosophila ON and OFF motion detectors enhances real-world velocity estimation. Nature Neuroscience. https://doi.org/10.1038/nn.4262

2015

• Bahl A., Serbe E., Meier M., Ammer G., Borst A. (2015) Neural mechanisms for Drosophila contrast vision. Neuron. https://doi.org/10.1016/j.neuron.2015.11.004
• Ammer G., Leonhardt A., Bahl A., Dickson B. J., Borst A. (2015) Functional specialization of neural input elements to the Drosophila ON motion detector. Current Biology. https://doi.org/10.1016/j.cub.2015.07.014

2013

• Maisak M. S., Haag J., Ammer G., Serbe E., Meier M., Leonhardt A., Schilling T., Bahl A., Rubin G. M., Nern A., Dickson B. J., Reiff D. F., Hopp E., Borst A. (2013) A directional tuning map of Drosophila elementary motion detectors. Nature. https://doi.org/10.1038/nature12320
• Bahl A., Ammer G., Schilling T., Borst A. (2013) Object tracking in motion-blind flies. Nature Neuroscience. https://doi.org/10.1038/nn.3386

2012

• Bahl A., Stemmler M. B., Herz A. V., Roth A. (2012) Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. Journal of Neuroscience Methods. https://doi.org/10.1016/j.jneumeth.2012.04.006
• Plett J., Bahl A., Buss M., Kühnlenz K., Borst A. (2012) Bio-inspired visual ego-rotation sensor for MAVs. Biological Cybernetics. https://doi.org/10.1007/s00422-012-0478-6

2009

• Roth A., Bahl A. (2009) Divide et impera: optimizing compartmental models of neurons step by step. The Journal of Physiology. https://doi.org/10.1113/jphysiol.2009.170944