imbb logo for mobile
Emmanouil Froudarakis

Emmanouil Froudarakis

IMBB Group Leader (Assistant Professor Grade)
Email address
This email address is being protected from spambots. You need JavaScript enabled to view it.
Lab web page

Our lab investigates how cortical circuits across different brain areas interact to form multimodal object representations that can guide behavior. Natural scenes contain large number of objects, 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 (transformation-invariant) object representations. If we understood how brains achieve this extraordinary ability at the algorithmic level, this would represent a significant advance in our understanding of cortical computation. To address this question, we combine advanced imaging techniques for recording neural activity with high-throughput behavioral training and computational modeling to study how the activity of large neuronal populations across different cortical regions  enables behaving animals to identify and isolate objects in different contexts.

Froudarakis E, Fahey PG, Reimer J, Smirnakis SM, Tehovnik EJ, Tolias AS. (2019) The Visual Cortex in Context. Annu Rev Vis Sci. 5:317–339.

Liu G, Froudarakis E, Patel JM, Kochukov MY, Pekarek B, Hunt PJ, Patel M, Ung K, Fu CH, Jo J, Lee HK, Tolias AS, Arenkiel BR. (2019) Target specific functions of EPL interneurons in olfactory circuits. Nat Commun. 10:3369.
Walker EY, Sinz FH, Froudarakis E, Fahey PG, Muhammad T, Ecker AS, Cobos E, Reimer J, Pitkow X, Tolias AS. (2018) Inception in visual cortex: in vivo-silico loops reveal most exciting images. bioRxiv:506956.
Reimer J, Froudarakis E, Cadwell CR, Yatsenko D, Denfield GH, Tolias AS. (2014) Pupil Fluctuations Track Fast Switching of Cortical States during Quiet Wakefulness. Neuron 84:355–362.

Froudarakis E, Berens P, Ecker AS, Cotton RJ, Sinz FH, Yatsenko D, Saggau P, Bethge M, Tolias AS. (2014) Population code in mouse V1 facilitates readout of natural scenes through increased sparseness. Nat Neurosci. 17:851–857.

Froudarakis, E., Fahey, P.G., Reimer, J., Smirnakis, S.M., Tehovnik, E.J., and Tolias, A.S. 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. Target specific functions of EPL interneurons in olfactory circuits. Nature Communications 10, 1–14. (2019)

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.. How well do deep neural networks trained on object recognition characterize the mouse visual system? Neural Information Processing Systems (2019)

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. Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas. Nat Commun 10, 1–12. (2019)

Baker, C., Froudarakis, E., Yatsenko, D., Tolias, A.S., and Rosenbaum, R. Inference of Synaptic Connectivity and External Variability in Neural Microcircuits. BioRxiv 650069. (2019)

Walker E.Y., Sinz F.H., Froudarakis E., Fahey P.G., Muhammad T., Ecker A.S., Cobos E., Reimer J., Pitkow X., Tolias A.S.  Inception in visual cortex: in vivo-silico loops reveal most exciting images bioRxiv:506956 (2018)

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

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)

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., Roson M.R, Theis L., Tolias A.S., Bethge M. (2018). Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. PLOS Comput. Biol. 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. (2007b). 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. (2007a). Distinct neuronal circuits mediate experience-dependent, non-associative osmotactic responses in Drosophila. Mol. Cell. Neurosci. 34, 378–389.