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    Emmanouil Froudarakis

    Additional Info

    • email address This email address is being protected from spambots. You need JavaScript enabled to view it.
    • position title Group Leader
    • Communication Details

      Institute of Molecular Biology and Biotechnology (IMBB)
      Foundation for Research and Technology - Hellas (FORTH)
      Nikolaou Plastira 100
      GR-70013, Heraklion, Crete, Greece

      Phone : +30 2810 391230 (office)
      Phone : +30 2810 391057 (lab)

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    Open positions

    Post-Doc position
    We are looking for a highly motivated and skilled postdoc to acquire large neural recordings during animal behavior and develop and apply computational models on these neuronal data. In a collaboration with labs from the US and Germany, the candidate will have several opportunities to train on specific techniques abroad.
     
    The ideal candidate has a PhD in machine learning, neuroscience, math, electrical engineering, or related fields, and a strong background in mathematics, statistics, programming with prior experience in working on neural data.


    PhD positions
    We are looking for highly motivated PhD students to work on recording neural data across multiple cortical areas, large scale behavioral training of animals and analyzing neuronal recordings. In a collaboration with labs from the US and Germany, the candidates will have several opportunities to train on specific techniques abroad.

    The ideal candidate should have a master’s degree in neuroscience, electrical engineering, computer science, math, psychology or related fields. Previous experience with programing or neural recordings, or behavioral training not necessary but advantageous.


    MSc rotations
    MSc students are encouraged to apply for a rotation!

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    Publications

    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.

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    What are we interested in?
    The brain tries to build an internal model of the environment based on information from multiple sensory systems, in order to guide future actions. Every day, we see thousands of unique objects with many different shapes, colors, sizes and textures. Each one of these objects can generate a virtually infinite number of different images on our retinas, depending on the conditions we view it under. In spite of this extraordinary variability, our brain can recognize objects in a fraction of a second and without any apparent effort. To accomplish this computationally challenging task, a large part of our brain is dedicated to processing all the available information from the environment and extracting and isolating object identities. Fundamentally, we want to understand how different circuits in cortical areas coordinate to perform this complicated computation.

    What methods do we use in our research?
    We use a combination of computational, behavioral, electrophysiological, two-photon and widefield imaging, and optogenetic techniques. We train mice to perform object discrimination tasks that require multiple kinds of sensory information. Importantly, we study the neural responses of awake animals to sensory stimuli both during passive tasks, and during behavior. Finally, we use computational models, to understand how the activities of large number of neurons generate invariant object representations, and to try to infer how different circuit architectures might underly this ability. The models give us greater insight into potential mechanistic interpretations and guide our next experiments.

    What are some of the questions we are studying?

    Mouse object recognition: Even though mice are considered nocturnal animals, there have been plenty of studies showing that mice can perform complicated visual tasks. However, due to the difficulties in training these animals on complicated tasks, there has been limited research in this area. A first step is to try to answer the question: “What are the visual object recognition capabilities of mice?” Can we develop tasks and objects that are easy for these animals to learn? How do the animals use this information to navigate? With the help of our high-throughput behavioral home-cage training system that runs on low-cost Raspberry Pi’s we can overcome the limitations of training individual animals and explore the parameter space for difficult tasks. Additionally, this automatic training method provides a good screening method for various cognitive deficits.

    Object representations across the visual hierarchy: One of the primary areas of research in our lab is to identify the visual areas that are critical for object recognition. How do the neural representations evolve across the visual hierarchy and how do cortical circuits across these areas interact? Does visual experience alter these representations? How are representations of multiple objects multiplexed across populations of neurons?

    Multimodal object recognition: Objects can elicit a plethora of sensory stimulation that may involve one or more senses; for example, a cat in the world has visual, olfactory, auditory, and somatosensory features.  Our brains have evolved to be able to assign these diverse features correctly to a single object base on constancy and correlation in the sensory input. Despite the fact that this is a central characteristic of our ability to identify objects, most studies on object recognition do not use such a rich stimulus set of information or include the dynamics of real existing objects. We are using multisensory information (olfactory, visual, auditory) to define objects that animals have to discriminate, and we are investigating the cortical areas and neural activity that are necessary to integrate these sensations into a single representation of an object.

     

    Collaborators

    Andreas S. Tolias (Professor, Baylor College of Medicine Houston, TX US)
    Jacob Reimer (Assistant Professor, Baylor College of Medicine, Houston TX US)
    Dorina Papageorgiou (Assistant Professor, Baylor College of Medicine, Houston TX US)
    Philipp Berens (Professor, University of Tübingen, Germany)
    Alex Ecker (Professor, University of Göttingen, Germany)
    Fabian Sinz (Group Leader, University of Tübingen, Germany)

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    Nikol Androulaki

    Additional Info

    • email address This email address is being protected from spambots. You need JavaScript enabled to view it.
    • position title BSc Student
    • Communication Details

      University of Crete
      School of Sciences
      Faculty of Medicine
      P.O. Box 2208, Heraklion, Crete, Greece

      Phone : +30 2810 394548

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    Christina Efraimoglou

    Additional Info

    • email address This email address is being protected from spambots. You need JavaScript enabled to view it.
    • position title MSc Student
    • Communication Details

      University of Crete
      School of Sciences
      Faculty of Medicine
      P.O. Box 2208, Heraklion, Crete, Greece

      Phone : +30 2810 394548

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    Konstantinos Axarlis

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    • email address This email address is being protected from spambots. You need JavaScript enabled to view it.
    • position title MSc Student
    • Communication Details

      University of Crete
      School of Sciences
      Faculty of Medicine
      P.O. Box 2208, Heraklion, Crete, Greece

      Phone : +30 2810 394548

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    Ioanna Lapi

    Additional Info

    • email address This email address is being protected from spambots. You need JavaScript enabled to view it.
    • position title MSc Student
    • Communication Details

      University of Crete
      School of Sciences
      Faculty of Medicine
      P.O. Box 2208, Heraklion, Crete, Greece

      Phone : +30 2810 394548

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    Ioanna Pantazi

    Additional Info

    • email address This email address is being protected from spambots. You need JavaScript enabled to view it.
    • position title PhD Student
    • Communication Details

      University of Crete
      School of Sciences
      Faculty of Medicine
      P.O. Box 2208, Heraklion, Crete, Greece

      Phone : +30 2810 394548

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