Thomas Deneux

I lead the Computing and Data Science team. I develop tools and provide expertise for data analysis, statistics, machine learning, as well as data acquisition and optics.

I lead the innovation project "Naivia", developing an autonomous learning robot based on state-of-the art reinforcement learning methods. This weaves new interactions with the artificial intelligence community, and with technology transfer and business (engineer position available).

Learning robot project

Fig. 1: Learning robot project. (left) The AlphaBot robotic platform. (right) Neural network - based artificial intelligence.

I also launched the open-source project Xplor for the visualization of multi-dimensional data (Matlab and soon Python, engineer position available).


Fig. 2: Visualizing three different types of data using XPLOR: traces of neuronal activities, movies of brain activity, graphics of unemployment data.

My previous postdoctoral research included experimental studies of cortical dynamics in vivo and the development of data analysis methods, among them the MLspike algorithm for reconstruction of spiking activity from fluorescent calcium signals (Deneux et al. 2016). A summary can be found in the following presentation [PPT with movies, 130MB].

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Articles (16)


Benjamin Roland, Thomas Deneux, Kevin Franks, Brice Bathellier and Alexander Fleischmann, Odor identity coding by distributed ensembles of neurons in the mouse olfactory cortex, Elife 6: , (2017) [pdf] [PubMed]

Kazunori O'Hashi, Tomer Fekete, Thomas Deneux, Rina Hildesheim, Cees van Leeuwen and Amiram Grinvald, Interhemispheric Synchrony of Spontaneous Cortical States at the Cortical Column Level, Cerebral Cortex 13: 1-14, (2017) [PubMed]

Thomas Deneux and Amiram Grinvald, Milliseconds of sensory input abruptly modulate the dynamics of cortical states for seconds, Cerebral Cortex 27(9): 4549-4563, (2017) [pdf] [PubMed]

Isabelle Ferezou and Thomas Deneux, Review: How do spontaneous and sensory-evoked activities interact?, Neurophotonics 4(3): , (2017) [pdf] [PubMed]

Thomas Deneux, Thimothée Masquelier, Maria Bermudez, Guillaume Masson, Gustavo Deco and Ivo Vanzetta, Visual stimulation quenches global alpha range activity in awake primate V4: a case study, Neurophotonics 4(3): , (2017) [pdf] [PubMed]

Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolas Chenkov, Thomas McColgan, Artur Speiser, Jakob Macke, Srinivas Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth Harris, Ben Bolte, Timothy Machado, Dario Ringach, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Roman-Roson, Lucas Theis, Andreas Tolias and Matthias Bethge, Community-based benchmarking improves spike inference from two-photon calcium imaging data, bioRxiv : , (2017) [pdf]


Thomas Deneux, Alexandre Kempf, Aurélie Daret, Emmanuel Ponsot and Brice Bathellier, Temporal asymmetries in auditory coding and perception reflect multi-layered nonlinearities, Nature Communications 7: 12682, (2016) [pdf] [PubMed]

Thomas Deneux, Attila Kaszas, Gergely Szalay, Gergely Katona, Tamás Lakner, Amiram Grinvald, Bálazs Rózsa and Ivo Vanzetta, Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo, Nature Communications 7: , (2016) [pdf] [PubMed]


Thomas Deneux, Sylvain Takerkart, Amiram Grinvald, Guillaume Masson and Ivo Vanzetta, A processing work-flow for measuring erythrocytes velocity in extended vascular networks from wide field high-resolution optical imaging data, NeuroImage 59(3): 2569-2588, (2012) [pdf] [PubMed]


Thomas Deneux, Olivier Faugeras, Sylvain Takerkart, Guillaume Masson and Ivo Vanzetta, A new variational method for erythrocyte velocity estimation in wide-field imaging in vivo, IEEE Transactions on Medical Imaging 30(8): 1527-45, (2011) [pdf] [PubMed]


Thomas Deneux and Olivier Faugeras, EEG-fMRI fusion of paradigm-free activity using Kalman filtering, Neural Computation 22(4): 906-48, (2010) [pdf] [PubMed]


Mickaël Péchaud, Ivo Vanzetta, Thomas Deneux and Renaud Keriven, Sift-based sequence registration and flow-based cortical vessel segmentation applied to high resolution optical imaging data, Proceedings of the IEEE International Symposium on Biomedical Imaging : 720-723, (2008)


Thomas Deneux and Olivier Faugeras, Using nonlinear models in fMRI data analysis: model selection and activation detection, NeuroImage 32: 1669 – 1689, (2006) [pdf] [PubMed]

Thomas Deneux and Olivier Faugeras, EEG-fMRI fusion of non-triggered data using Kalman filtering, Proceedings of the IEEE International Symposium on Biomedical Imaging : 1068-1071, (2006) [pdf]

Ivo Vanzetta, Thomas Deneux, Guillaume Masson and Olivier Faugeras, Cerebral blood flow recorded at high sensitivity in two dimensions using high resolution optical imaging, Proceedings of the IEEE International Symposium on Biomedical Imaging : 1264-1267, (2006) [pdf]


Olivier Faugeras, Geoffray Adde, Guillaume Charpiat, Christophe Chefd'Hotel, Maureen Clerc, Thomas Deneux, Rachid Deriche, Gerardo Hermosillo, Renaud Keriven, Pierre Kornprost, Jan Kybic, Christophe Lenglet, Lucero Lopez-Perez, Théo Papadopoulo, Jean-Philippe Pons, Florent Segonne, Bertrand Thirion, David Tschumperlé, Thierry Viéville and Nicolas Wotawa, Variational, geometric, and statistical methods for modeling brain anatomy and function, NeuroImage 23: S46-S55, (2004) [PubMed]

Book Chapters (3)


Ivo Vanzetta, Thomas Deneux and Amiram Grinvald, High-Resolution Wide-Field Optical Imaging of Microvascular Characteristics: From the Neocortex to the Eye, In: Neurovascular Coupling Methods ( Mingrui ZhaoHongtao MaTheodore H. Schwartz) Springer 123-159, (2014)


Ivo Vanzetta, Thomas Deneux, Attila Kaszas, Gergely Katona and Bálazs Rózsa, Functional imaging using two-photon microscopy in living tissue, In: Visualization Techniques: From Immunohistochemistry to Magnetic Resonance Imaging (Emilio Badoer) Humana Press 129-164, (2012)


Thomas Deneux, EEG-fMRI Fusion: Adaptations of the Kalman Filter for Solving a High-Dimensional Spatio-Temporal Inverse Problem, In: Adaptive Filtering (Lino Garcia) InTech 233-258, (2011) [pdf]