Citations
=========

How to cite SpyKING CIRCUS
--------------------------

.. note::

    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

2020
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* Magland J. et al, *SpikeForest: reproducible web-facing ground-truth validation of automated neural spike sorters*, bioRxiv, 900688

* Park I. Y., et al. *Deep Learning-Based Template Matching Spike Classification for Extracellular Recordings*, Applied Sciences 10.1 (2020): 301

* Cantu D. A., et al. *EZcalcium: Open Source Toolbox for Analysis of Calcium Imaging Data*, bioRxiv, 893198

2019
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* Frazzini V. et al., *In vivo interictal signatures of human periventricular heterotopia*, bioRxiv, 816173

* Abbasi A et al., *Sensorimotor neuronal learning requires cortical topography*, bioRxiv 873794

* González-Palomares E. et al., *Enhanced representation of natural sound sequences in the ventral auditory midbrain*, bioRxiv 846485

* Chong E. et al., *Manipulating synthetic optogenetic odors reveals the coding logic of olfactory perception*, bioRxiv 841916

* Bolding K. et al., *Robust odor coding across states in piriform cortex requires recurrent circuitry: evidence for pattern completion in an associative network*, bioRxiv 694331

* Szőnyi1 A. et al., *Median raphe controls acquisition of negative experience in the mouse*, Science Vol 366, Issue 6469

* Buccino A. P. and Einevoll G. T., *MEArec: a fast and customizable testbench simulator for ground-truth extracellular spiking activity*, bioRxiv, 691642

* Wouters J., Kloosterman F., et Bertrand, A., *SHYBRID: A graphical tool for generating hybrid ground-truth spiking data for evaluating spike sorting performance*, bioRxiv, 734061

* Boi F., Perentos N., Lecomte A., Schwesig G., Zordan S., Sirota A. et Angotzi, G. N., *Multi-shanks SiNAPS Active Pixel Sensor CMOSprobe: 1024 simultaneously recording channels for high-density intracortical brain mapping*, bioRxiv, 749911

* Weineck K., García-Rosales F. & Hechavarría, J. C., *Fronto-striatal oscillations predict vocal output in bats*, bioRxiv, 724112

* Bolding K. A., Nagappan S., Han B.-X., Wang F., Franks K. M., *Pattern recovery by recurrent circuits in piriform cortex*, biooRxiv 694331; doi: https://doi.org/10.1101/694331

* Reinhard K., Li C., Do Q., Burke E., Heynderickx S., Farrow K.,*A projection specific logic to sampling visual inputs in mouse superior colliculus*, bioRxiv 272914; doi: https://doi.org/10.1101/272914

* Fiáth R., et al., *Fine-scale mapping of cortical laminar activity during sleep slow oscillations using high-density linear silicon probes*, Journal of neuroscience methods 316: 58-70

* Heiney K., et al. *µSpikeHunter: An advanced computational tool for the analysis of neuronal communication and action potential propagation in microfluidic platforms*, Scientific reports 9.1: 5777

* Angotzi, Gian Nicola, et al. *SiNAPS: An implantable active pixel sensor CMOS-probe for simultaneous large-scale neural recordings*, Biosensors and Bioelectronics 126: 355-364.

* Williams, Alex H., et al. *Discovering precise temporal patterns in large-scale neural recordings through robust and interpretable time warping*, bioRxiv: 661165

* Hennig, M. H., Hurwitz C., Sorbaro M., *Scaling Spike Detection and Sorting for Next-Generation Electrophysiology*, In Vitro Neuronal Networks. Springer, Cham 171-184.

* Carlson D., and Lawrence C., *Continuing progress of spike sorting in the era of big data*, Current opinion in neurobiology 55: 90-96

* Souza B. C., Lopes-dos-Santos V., Bacelo J., Tort A. B., *Spike sorting with Gaussian mixture models*, Scientific reports, 9(1), 3627

* Gardella C., Marre O., Mora T., *Modeling the correlated activity of neural populations: A review*, Neural computation, 31(2), 233-269.

* Dai J., Zhang P., Sun H., Qiao X., Zhao Y., Ma J., Wang, C., *Reliability of motor and sensory neural decoding by threshold crossings for intracortical brain–machine interface*, Journal of neural engineering.

* Despouy E., Curot J., Denuelle M., Deudon M., Sol J. C., Lotterie J. A., Valton L., *Neuronal spiking activity highlights a gradient of epileptogenicity in human tuberous sclerosis lesions*, Clinical Neurophysiology, 130(4), 537-547.

* Wouters J., Kloosterman F., Bertrand A., *A data-driven regularization approach for template matching in spike sorting with high-density neural probes*, In Proceedings of IEEE EMBC. IEEE.

* Weingärtner S., Chen X., Akçakaya M., Moore T., *Robust Online Spike Recovery for High-Density Electrode Recordings using Convolutional Compressed Sensing*. In 2019 9th International IEEE/EMBS Conference on Neural Engineering (NER) (pp. 1015-1020). IEEE.

* Sorochynskyi O., Deny S., Marre O., Ferrari U., *From serial to parallel: predicting synchronous firing of large neural populations from sequential recordings*, bioRxiv, 560656.

* Mahmud, M., Vassanelli, S., *Open-Source Tools for Processing and Analysis of In Vitro Extracellular Neuronal Signals. In In Vitro Neuronal Networks* (pp. 233-250). Springer, Cham.

* Wouters J., Kloosterman F., Bertrand A., *Signal-to-peak-interference ratio maximization with automatic interference weighting for threshold-based spike sorting of high-density neural probe data*, In International IEEE/EMBS Conference on Neural Engineering:[proceedings]. International IEEE EMBS Conference on Neural Engineering. IEEE.

2018
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* Parikh R., *Large-scale neuron cell classification of single-channel and multi-channel extracellularrecordings in the anterior lateral motor cortex*, bioRxiv 445700; doi: https://doi.org/10.1101/445700

* 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)

2017
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* 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.


2016
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* 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


