How to cite SpyKING CIRCUS


If you are using SpyKING CIRCUS for your project, please cite us

  • Yger P., Spampinato, G.L.B, Esposito E., Lefebvre B., Deny S., Gardella C., Stimberg M., Jetter F., Zeck G. Picaud S., Duebel J., Marre O., A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo, eLife 2018;7:e34518

Publications refering to SpyKING CIRCUS

Here is a non exhaustive list of papers using SpyKING CIRCUS. Do not hesitate to send us a mail in order update this list, the more the merrier


  • Macé E., Montaldo G., Trenholm S., Cowan C., rignall A., Urban A., Roska B., Whole-Brain Functional Ultrasound Imaging Reveals Brain Modules for Visuomotor Integration, Neuron, 5:1241-1251
  • Aydın C., Couto J., Giugliano M., Farrow K., Bonin V., Locomotion modulates specific functional cell types in the mouse visual thalamus, Nature Communications, 4882 (2018)
  • Belkhiri M., Kvitsiani D., D.sort: template based automatic spike sorting tool, BioRxiv, 10.1101/423913
  • Nadian M. H., Karimimehr S., Doostmohammadi J., Ghazizadeh A., Lashgari R., A fully automated spike sorting algorithm using t-distributed neighbor embedding and density based clustering, BioRxiv, 10.1101/418913
  • Ferrari U., Deny S., Chalk M., Tkacik G., Marre O., Mora T, Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons, BioRxiv, 10.1101/243816
  • Jin M., Beck J. M, Glickfeld L., Neuronal adaptation reveals a suboptimal decoding of orientation tuned populations in the mouse visual cortex, BioRxiv, 10.1101/433722
  • Jin M., Glickfeld L., Contribution of sensory encoding to measured bias, BioRxiv, 10.1101/444430
  • Lazarevich I., Prokin I., Gutkin B., Neural activity classification with machine learning models trained on interspike interval series data, arXiv, 1810.03855
  • Radosevic M., Willumsen A., Petersen P. C., Linden H., Vestergaard M., Berg R. W. Decoupling of timescales reveals sparse convergent CPG network in the adult spinal cord, BiorXiv, 402917
  • Chaure F, Rey HG, Quian Quiroga R, A novel and fully automatic spike sorting implementation with variable number of features, J Neurophysiol. 10.1152/jn.00339.2018
  • Ravello C., Perrinet L. U, Escobar M.-J., Palacios A. G, Speed-Selectivity in Retinal Ganglion Cells is Modulated by the Complexity of the Visual Stimulus, BioRxiv, 350330
  • Wouters J, Kloosterman F., Bertrand A, Towards online spike sorting for high-density neural probes using discriminative template matching with suppression of interfering spikes, Journal of Neural Engineering, 1741-2552
  • Vilarchao M. E., Estebanez L., Shulz D. E., Férezou I., Supra-barrel Distribution of Directional Tuning for Global Motion in the Mouse Somatosensory Cortex, Cell Reports 22, 3534–3547
  • Barth A. M., Domonkos A., Fernandez-Ruiz A., Freund T.F., Varga V., Hippocampal Network Dynamics during Rearing Episodes, Cell Reports, 23(6):1706-1715
  • Steinmetz N. A., Koch C., Harris K.D., Carandini M., Challenges and opportunities for large-scale electrophysiology with Neuropixels probes, Current Opinion in Neurobiology, Volume 50, 92-100
  • Stern M., Bolding K. A. , Abbott L. F., Franks K. M, A transformation from temporal to ensemble coding in a model of piriform cortex, eLife, 10.7554/eLife.34831
  • Bolding K. A., Franks K. M. , Recurrent cortical circuits implement concentration-invariant odor coding, Science, 361(6407)
  • Escobar M.-J., Otero M., Reyes C., Herzog R., Araya J., Ibaceta C., Palacios A. G., Functional Asymmetries between Central and Peripheral Retinal Ganglion Cells in a Diurnal Rodent, BioRxiv, 277814
  • Wouters J., Kloosterman F., Bertrand A., Data-driven multi-channel filter design with peak-interference suppression for threshold-based spike sorting in high-density neural probes, IEEE International Conference on Acoustics, Speech and Signal processing (ICASSP)


  • Paninski L., Cunningham J., Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience, BioRxiv, 196949
  • Lee J., Carlson D., Shokri H., Yao W., Goetz G., Hagen E., Batty E., Chichilnisky E.J., Einevoll G., Paninski L., YASS: Yet Another Spike Sorter, BioRxiv, 151928
  • Shan K. Q., Lubenov E. V., Siapas A. G., Model-based spike sorting with a mixture of drifting t-distributions, Journal of Neuroscience Methods, 288, 82-98
  • Deny S., Ferrari U., Mace E., Yger P., Caplette R., Picaud S., Tkacik G., Marre O., Multiplexed computations in retinal ganglion cells of a single type, Nature Communications 10.1038/s41467-017-02159-y
  • Chung, J. E., Magland, J. F., Barnett, A. H., Tolosa, V. M., Tooker, A. C., Lee, K. Y., … & Greengard, L. F. A Fully Automated Approach to Spike Sorting, Neuron, 95(6), 1381-1394
  • Mena, G. E., Grosberg, L. E., Madugula, S., Hottowy, P., Litke, A., Cunningham, J., … & Paninski, L. Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays, PLOS Computational Biology, 13(11), e1005842.
  • Mokri Y., Salazar R.F, Goodell2 B., Baker J., Gray C.M. and Yen S., Sorting Overlapping Spike Waveforms from Electrode and Tetrode Recordings, Front. Neuroinform.
  • Wilson C.D., Serrano G. O., Koulakov A. A., Rinberg D., A primacy code for odor identity, Nature Communication, 1477
  • Ferrari U., Gardella C., Marre O., Mora T., Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding, eNeuro, ENEURO.0166-17.2017
  • Denman, D. J., Siegle, J. H., Koch, C., Reid, R. C., & Blanche, T. J. Spatial organization of chromatic pathways in the mouse dorsal lateral geniculate nucleus, Journal of Neuroscience, 37(5), 1102-1116.


  • Dimitriadis, G., Neto, J., & Kampff, A. T-SNE visualization of large-scale neural recordings, bioRxiv, 087395.
  • Yger P., Spampinato, G.L.B, Esposito E., Lefebvre B., Deny S., Gardella C., Stimberg M., Jetter F., Zeck G. Picaud S., Duebel J., Marre O., Fast and accurate spike sorting in vitro and in vivo for up to thousands of electrodes, bioRxiv, 67843