Our lab investigates how cortical circuits interact to form transformation-invariant object representations that can guide behavior. Natural environment contains large number of objects with overlapping sensory input, and our brain is capable of using information from different sensory modalities to extract their identities with ease. Yet, despite extensive research in the last few decades, we are still far from having a complete understanding of how the brain creates untangled object representations. If we understood how cortex achieves this extraordinary ability at the algorithmic level, this would represent a significant advance in our understanding of brain computation in general. To address this question, we combine advanced imaging techniques for recording neural activity with high-throughput behavioral training and computational modeling to understand the algorithm used by the mouse visual cortex to extract relevant features from complex environments and guide natural behaviors.

Google Scholar: https://scholar.google.com/citations?user=peGMCr8AAAAJ&hl

A. Peer-reviewed articles
• Consortium, Mic., Bae, J. A.; Baptiste, M.; Bodor, A. L.; Brittain, D.; Buchanan, J.; Bumbarger, D. J.; Castro, M. A.; Celii, B.; Cobos, E.; Collman, F.; Costa, N. M. da; Dorkenwald, S.; Elabbady, L.; Fahey, P. G.; Fliss, T.; Froudarakis, E.; Gager, J.; Gamlin, C.; Halageri, A.; Hebditch, J.; Jia, Z.; Jordan, C.; Kapner, D.; Kemnitz, N.; Kinn, S.; Koolman, S.; Kuehner, K.; Lee, K.; Li, K.; Lu, R.; Macrina, T.; Mahalingam, G.; McReynolds, S.; Miranda, E.; Mitchell, E.; Mondal, S. S.; Moore, M.; Mu, S.; Muhammad, T.; Nehoran, B.; Ogedengbe, O.; Papadopoulos, C.; Papadopoulos, S.; Patel, S.; Pitkow, X.; Popovych, S.; Ramos, A.; Reid, R. C.; Reimer, J.; Schneider-Mizell, C. M.; Seung, H. S.; Silverman, B.; Silversmith, W.; Sterling, A.; Sinz, F. H.; Smith, C. L.; Suckow, S.; Takeno, M.; Tan, Z. H.; Tolias, A. S.; Torres, R.; Turner, N. L.; Walker, E. Y.; Wang, T.; Williams, G.; Williams, S.; Willie, K.; Willie, R.; Wong, W.; Wu, J.; Xu, C.; Yang, R.; Yatsenko, D.; Ye, F.; Yin, W.; Yu, S (2025). Functional connectomics spanning multiple areas of mouse visual cortex. Nature 640, 435–447.
• Celii, B., Papadopoulos, S., Ding, Z., Fahey, P.G., Wang, E., Papadopoulos, C., Kunin, A.B., Patel, S., Bae, J.A., Bodor, A.L., Brittain, D., Buchanan, J., Bumbarger, D.J., Castro, M.A., Cobos, E., Dorkenwald, S., Elabbady, L., Halageri, A., Jia, Z., Jordan, C., Kapner, D., Kemnitz, N., Kinn, S., Lee, K., Li, K., Lu, R., Macrina, T., Mahalingam, G., Mitchell, E., Mondal, S.S., Mu, S., Nehoran, B., Popovych, S., Schneider-Mizell, C.M., Silversmith, W., Takeno, M., Torres, R., Turner, N.L., Wong, W., Wu, J., Yu, S.-C., Yin, W., Xenes, D., Kitchell, L.M., Rivlin, P.K., Rose, V.A., Bishop, C.A., Wester, B., Froudarakis, E., Walker, E.Y., Sinz, F., Seung, H.S., Collman, F., da Costa, N.M., Reid, R.C., Pitkow, X., Tolias, A.S., Reimer, J. (2025). NEURD offers automated proofreading and feature extraction for connectomics. Nature 640, 487–496.
• Ding, Z., Fahey, P.G., Papadopoulos, S., Wang, E.Y., Celii, B., Papadopoulos, C., Chang, A., Kunin, A.B., Tran, D., Fu, J., Ding, Zhiwei, Patel, S., Ntanavara, L., Froebe, R., Ponder, K., Muhammad, T., Bae, J.A., Bodor, A.L., Brittain, D., Buchanan, J., Bumbarger, D.J., Castro, M.A., Cobos, E., Dorkenwald, S., Elabbady, L., Halageri, A., Jia, Z., Jordan, C., Kapner, D., Kemnitz, N., Kinn, S., Lee, K., Li, K., Lu, R., Macrina, T., Mahalingam, G., Mitchell, E., Mondal, S.S., Mu, S., Nehoran, B., Popovych, S., Schneider-Mizell, C.M., Silversmith, W., Takeno, M., Torres, R., Turner, N.L., Wong, W., Wu, J., Yin, W., Yu, S.-C., Yatsenko, D., Froudarakis, E., Sinz, F., Josić, K., Rosenbaum, R., Seung, H.S., Collman, F., da Costa, N.M., Reid, R.C., Walker, E.Y., Pitkow, X., Reimer, J., Tolias, A.S. (2025). Functional connectomics reveals general wiring rule in mouse visual cortex. Nature 640, 459–469.
• Allam, A., Allam, V., Reddy, S., Rohren, E.M., Sheth, S.A., Froudarakis, E., Papageorgiou, T.D. (2024). Individualized functional magnetic resonance imaging neuromodulation enhances visuospatial perception: a proof-of-concept study. Philos Trans R Soc Lond B Biol Sci 379, 20230083.
• Fu, J., Pierzchlewicz, P.A., Willeke, K.F., Bashiri, M., Muhammad, T., Diamantaki, M., Froudarakis, E., Restivo, K., Ponder, K., Denfield, G.H., Sinz, F., Tolias, A.S., Franke, K. (2024). Heterogeneous orientation tuning in the primary visual cortex of mice diverges from Gabor-like receptive fields in primates. Cell Rep 43, 114639.
• Genzel, L., Froudarakis, E., Rapti, G. (2024). Openness and transparency in animal research: Why and how. Eur J Neurosci 60, 6866–6873.
• Liu, Z., Lu, X., Villette, V., Gou, Y., Colbert, K.L., Lai, S., Guan, S., Land, M.A., Lee, J., Assefa, T., Zollinger, D.R., Korympidou, M.M., Vlasits, A.L., Pang, M.M., Su, S., Cai, C., Froudarakis, E., Zhou, N., Patel, S.S., Smith, C.L., Ayon, A., Bizouard, P., Bradley, J., Franke, K., Clandinin, T.R., Giovannucci, A., Tolias, A.S., Reimer, J., Dieudonné, S., St-Pierre, F. (2022). Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell S0092-8674(22)00916–3.
• Ash, R.T., Palagina, G., Fernandez-Leon, J.A., Park, J., Seilheimer, R., Lee, S., Sabharwal, J., Reyes, F., Wang, J., Lu, D., Sarfraz, M., Froudarakis, E., Tolias, A.S., Wu, S.M., Smirnakis, S.M. (2022). Increased Reliability of Visually-Evoked Activity in Area V1 of the MECP2-Duplication Mouse Model of Autism. J Neurosci 42, 6469–6482.
• Franke, K., Willeke, K.F., Ponder, K., Galdamez, M., Zhou, N., Muhammad, T., Patel, S., Froudarakis, E., Reimer, J., Sinz, F.H., Tolias, A.S. (2022). State-dependent pupil dilation rapidly shifts visual feature selectivity. Nature 610, 128–134.
• Turner, N.L., Macrina, T., Bae, J.A., Yang, R., Wilson, A.M., Schneider-Mizell, C., Lee, K., Lu, R., Wu, J., Bodor, A.L., Bleckert, A.A., Brittain, D., Froudarakis, E., Dorkenwald, S., Collman, F., Kemnitz, N., Ih, D., Silversmith, W.M., Zung, J., Zlateski, A., Tartavull, I., Yu, S.-C., Popovych, S., Mu, S., Wong, W., Jordan, C.S., Castro, M., Buchanan, J., Bumbarger, D.J., Takeno, M., Torres, R., Mahalingam, G., Elabbady, L., Li, Y., Cobos, E., Zhou, P., Suckow, S., Becker, L., Paninski, L., Polleux, F., Reimer, J., Tolias, A.S., Reid, R.C., da Costa, N.M., Seung, H.S. (2022). Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity. Cell 185, 1082-1100.e24.
• Dorkenwald, S., Turner, N.L., Macrina, T., Lee, K., Lu, R., Wu, J., Bodor, A.L., Bleckert, A.A., Brittain, D., Kemnitz, N., Silversmith, W.M., Ih, D., Zung, J., Zlateski, A., Tartavull, I., Yu, S.-C., Popovych, S., Wong, W., Castro, M., Jordan, C.S., Wilson, A.M., Froudarakis, E., Buchanan, J., Takeno, M.M., Torres, R., Mahalingam, G., Collman, F., Schneider-Mizell, C.M., Bumbarger, D.J., Li, Y., Becker, L., Suckow, S., Reimer, J., Tolias, A.S., Macarico da Costa, N., Reid, R.C., Seung, H.S. (2022). Binary and analog variation of synapses between cortical pyramidal neurons. Elife 11, e76120.
• Schneider-Mizell, C.M., Bodor, A.L., Collman, F., Brittain, D., Bleckert, A., Dorkenwald, S., Turner, N.L., Macrina, T., Lee, K., Lu, R., Wu, J., Zhuang, J., Nandi, A., Hu, B., Buchanan, J., Takeno, M.M., Torres, R., Mahalingam, G., Bumbarger, D.J., Li, Y., Chartrand, T., Kemnitz, N., Silversmith, W.M., Ih, D., Zung, J., Zlateski, A., Tartavull, I., Popovych, S., Wong, W., Castro, M., Jordan, C.S., Froudarakis, E., Becker, L., Suckow, S., Reimer, J., Tolias, A.S., Anastassiou, C.A., Seung, H.S., Reid, R.C., Costa, N.M. da (2021). Structure and function of axo-axonic inhibition. Elife 10, e73783.
• Tehovnik, E.J., Froudarakis, E., Scala, F., Smirnakis, S.M., Patel, S.S., and Tolias, A.T. (2021). Visuomotor Control in Mice and Primates. Neurosci Biobehav Rev S0149-7634(21)00352-3.
• Baker, C., Froudarakis, E., Yatsenko, D., Tolias, A.S., and Rosenbaum, R. (2020). Inference of synaptic connectivity and external variability in neural microcircuits. J Comput Neurosci 48, 123–147.
• Cheng, J.X., Scala, F., Blanco, F.A., Niu, S., Firozi, K., Keehan, L., Mulherkar, S., Froudarakis, E., Li, L., Duman, J.G., Jiang, X., Tolias, K.F., (2020). The Rac-GEF Tiam1 Promotes Dendrite and Synapse Stabilization of Dentate Granule Cells and Restricts Hippocampal-Dependent Memory Functions. J. Neurosci. 41, 1191–1206.
• Froudarakis, E., Fahey, P.G., Reimer, J., Smirnakis, S.M., Tehovnik, E.J., and Tolias, A.S. (2019). The Visual Cortex in Context. Annual Review of Vision Science 5, 317–339 (2019)
• Liu, G.*, Froudarakis, E.*, Patel, J.M., Kochukov, M.Y., Pekarek, B., Hunt, P.J., Patel, M., Ung, K., Fu, C.-H., Jo, J., et al. (2019). Target specific functions of EPL interneurons in olfactory circuits. Nature Communications 10, 1–14.
• Scala, F., Kobak, D., Shan, S., Bernaerts, Y., Laturnus, S., Cadwell, C.R., Hartmanis, L., Froudarakis, E., Castro, J.R., Tan, Z.H., et al. (2019). Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas. Nat Commun 10, 1–12.
• Walker, E.Y., Sinz, F.H., Cobos, E., Muhammad, T., Froudarakis, E., Fahey, P.G., Ecker, A.S., Reimer, J., Pitkow, X., and Tolias, A.S. (2019). Inception loops discover what excites neurons most using deep predictive models. Nat. Neurosci. 22, 2060–2065.
• Berens, P., Freeman, J., Deneux, T., Chenkov, N., McColgan, T., Speiser, A., Macke, J.H., Turaga, S.C., Mineault, P., Rupprecht, P., Gerhard, S., Friedrich, R.W., Friedrich, J., Paninski, L., Pachitariu, M., Harris, K.D., Bolte, B., Machado, T.A., Ringach, D., Stone, J., Rogerson, L.E., Sofroniew, N.J., Reimer, J., Froudarakis, E., Euler, T., Rosón, M.R., Theis, L., Tolias, A.S., Bethge, M., (2018). Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. PLOS Computational Biology 14, e1006157
• Quast, K.B., Ung, K., Froudarakis, E., Huang, L., Herman, I., Addison, A.P., Ortiz-Guzman, J., Cordiner, K., Saggau, P., Tolias, A.S., et al. (2017). Developmental broadening of inhibitory sensory maps. Nat. Neurosci. 20, 189–199.
• Theis, L., Berens, P., Froudarakis, E., Reimer, J., Román Rosón, M., Baden, T., Euler, T., Tolias, A.S., and Bethge, M. (2016). Benchmarking Spike Rate Inference in Population Calcium Imaging. Neuron 90, 471–482.
• Jiang, X., Shen, S., Sinz, F., Reimer, J., Cadwell, C.R., Berens, P., Ecker, A.S., Patel, S., Denfield, G.H., Froudarakis, E., et al. (2016). Response to Comment on “Principles of connectivity among morphologically defined cell types in adult neocortex.” Science 353, 1108–1108.
• Yatsenko, D., Josić, K., Ecker, A.S., Froudarakis, E., Cotton, R.J., and Tolias, A.S. (2015). Improved Estimation and Interpretation of Correlations in Neural Circuits. PLOS Comput. Biol. 11, e1004083.
• Reimer, J., Froudarakis, E., Cadwell, C.R., Yatsenko, D., Denfield, G.H., and Tolias, A.S. (2014). Pupil Fluctuations Track Fast Switching of Cortical States during Quiet Wakefulness. Neuron 84, 355–362.
• Froudarakis, E., Berens, P., Ecker, A.S., Cotton, R.J., Sinz, F.H., Yatsenko, D., Saggau, P., Bethge, M., and Tolias, A.S. (2014). Population code in mouse V1 facilitates readout of natural scenes through increased sparseness. Nat. Neurosci. 17, 851–857.
• Cotton, R.J., Froudarakis, E., Storer, P., Saggau, P., and Tolias, A.S. (2013). Three-dimensional mapping of microcircuit correlation structure. Front. Neural Circuits 7.
• Acevedo, S.F.*, Froudarakis, E.I.*, Kanellopoulos, A.*, and Skoulakis, E.M.C. (2007). Protection from premature habituation requires functional mushroom bodies in Drosophila. Learn. Mem. Cold Spring Harb. N 14, 376–384.
• Acevedo, S.F., Froudarakis, E.I., Tsiorva, A.-A., and Skoulakis, E.M.C. (2007). Distinct neuronal circuits mediate experience-dependent, non-associative osmotactic responses in Drosophila. Mol. Cell. Neurosci. 34, 378–389.

B. Conference Proceedings (peer reviewed)
• Ustyuzhaninov, I., Cadena, S.A., Froudarakis, E., Fahey, P.G., Walker, E.Y., Cobos, E., Reimer, J., Sinz, F.H., Tolias, A.S., Bethge, M., and Ecker, A.S. (2020). Rotation-invariant clustering of neuronal responses in primary visual cortex. Eighth International Conference on Learning Representations 2020
• Cadena, S.A., Sinz, F.H., Muhammad, T., Froudarakis, E., Cobos, E., Walker, E.Y., Reimer, J., Bethge, M., Tolias, A., and Ecker, A.S. (2019). How well do deep neural networks trained on object recognition characterize the mouse visual system? In NeurIPS Neuro AI Workshop.
• Sinz, H. F., Ecker, A., Fahey, G. P., Walker, Y. E., Cobos, E., Froudarakis, E., Yatsenko, D., Pitkow, X., Reimer, J., Tolias, A.S. (2018). Stimulus domain transfer in recurrent models for large scale cortical population prediction on video. Neural Information Processing Systems

C. Preprints (not peer-reviewed)
• Franke, K., Karantzas, N., Willeke, K., Diamantaki, M., Ramakrishnan, K., Elumalai, P., Restivo, K., Fahey, P., Nealley, C., Shinn, T., Garcia, G., Patel, S., Ecker, A., Walker, E.Y., Froudarakis, E., Sanborn, S., Sinz, F.H., Tolias, A. (2025). Dual-feature selectivity enables bidirectional coding in visual cortical neurons. bioRxiv 2025.07.16.665209.
• Papageorgiou, T.D., Webb, J., Allam, A., Rohren, E.M., Sturgis, E.M., Hutcheson, K., Heilbronner, S.R., Froudarakis, E. (2025). Individualized fMRI neuromodulation enhances swallow and tongue motor and sensory control: an intervention targeted for radiation-induced cranial neuropathy following head and neck cancer. bioRxiv 2025.04.30.651533.
• Macrina, T., Lee, K., Lu, R., Turner, N.L., Wu, J., Popovych, S., Silversmith, W., Kemnitz, N., Bae, J.A., Castro, M.A., Dorkenwald, S., Halageri, A., Jia, Z., Jordan, C., Li, K., Mitchell, E., Mondal, S.S., Mu, S., Nehoran, B., Wong, W., Yu, S., Bodor, A.L., Brittain, D., Buchanan, J., Bumbarger, D.J., Cobos, E., Collman, F., Elabbady, L., Fahey, P.G., Froudarakis, E., Kapner, D., Kinn, S., Mahalingam, G., Papadopoulos, S., Patel, S., Schneider-Mizell, C.M., Sinz, F.H., Takeno, M., Torres, R., Yin, W., Pitkow, X., Reimer, J., Tolias, A.S., Reid, R.C., Costa, N.M. da, and Seung, H.S. (2021). Petascale neural circuit reconstruction: automated methods. bioRxiv 2021.08.04.455162.
• Froudarakis, E., Cohen, U., Diamantaki, M., Walker, E.Y., Reimer, J., Berens, P., Sompolinsky, H., and Tolias, A.S. (2020). Object manifold geometry across the mouse cortical visual hierarchy. bioRxiv, 2020.08.20.258798.
• Zhou, P., Reimer, J., Zhou, D., Pasarkar, A., Kinsella, I., Froudarakis, E., Yatsenko, D.V., Fahey, P.G., Bodor, A., Buchanan, J., et al. (2020). EASE: EM-Assiste Source Extraction from calcium imaging data. bioRxiv, 2020.03.25.007468.
• Fahey, P.G., Muhammad, T., Smith, C., Froudarakis, E., Cobos, E., Fu, J., Walker, E.Y., Yatsenko, D., Sinz, F.H., Reimer, J., et al. (2019). A global map of orientation tuning in mouse visual cortex. bioRxiv, 745323.
• Ecker A.S., Sinz F.H., Froudarakis E., Fahey P.G., Cadena S.A., Walker E.Y., Cobos E., Reimer J., Tolias A.S., Bethge M. A rotation-equivariant convolutional neural network model of primary visual cortex ArXiv:1809.10504 (2018)

Member of Federation of European Neuroscience Societies
Member of Hellenic Society for Neuroscience
Member of International Brain Research Organization