References

ima

Imagen. https://imagen.pyviz.org.

BGTB04

James C Beck, Edwin Gilland, David W Tank, and Robert Baker. Quantifying the ontogeny of optokinetic and vestibuloocular behaviors in zebrafish, medaka, and goldfish. Journal of neurophysiology, 92(6):3546–3561, 2004.

Bra00

G. Bradski. The OpenCV Library. Dr. Dobb’s Journal of Software Tools, 2000.

BV97

David H Brainard and Spatial Vision. The psychophysics toolbox. Spatial vision, 10:433–436, 1997.

BLD+18

Alessio Paolo Buccino, Mikkel Elle Lepperod, Svenn-Arne Dragly, Philipp Dominik Hafliger, Marianne Fyhn, and Torkel Hafting. Open source modules for tracking animal behavior and closed-loop stimulation based on open ephys and bonsai. bioRxiv, pages 340141, 2018.

BOMalley00

S.A. Budick and D.M. O’Malley. Locomotor repertoire of the larval zebrafish: swimming, turning and prey capture. Journal of Experimental Biology, 203(17):2565–2579, 2000. URL: http://jeb.biologists.org/content/203/17/2565, arXiv:http://jeb.biologists.org/content/203/17/2565.full.pdf.

Cha18

André Maia Chagas. Haves and have nots must find a better way: the case for open scientific hardware. PLoS biology, 16(9):e3000014, 2018.

CK17

Davide Ciliberti and Fabian Kloosterman. Falcon: a highly flexible open-source software for closed-loop neuroscience. Journal of neural engineering, 14(4):045004, 2017.

DvDLA18

Florian A Dehmelt, Adam von Daranyi, Claire Leyden, and Aristides B Arrenberg. Evoking and tracking zebrafish eye movement in multiple larvae with zebeyetrack. Nature protocols, pages 1, 2018.

Hae19

Martin Haesemeyer. Haesemeyer/zebratrack: initial release. January 2019. URL: https://doi.org/10.5281/zenodo.2539837, doi:10.5281/zenodo.2539837.

HADE13

Kuo-Hua Huang, Misha B Ahrens, Timothy W Dunn, and Florian Engert. Spinal projection neurons control turning behaviors in zebrafish. Current Biology, 23(16):1566–1573, 2013.

IPA+16

Eldar Insafutdinov, Leonid Pishchulin, Bjoern Andres, Mykhaylo Andriluka, and Bernt Schiele. Deepercut: a deeper, stronger, and faster multi-person pose estimation model. Lecture Notes in Computer Science, pages 34–50, 2016. URL: http://dx.doi.org/10.1007/978-3-319-46466-4_3, doi:10.1007/978-3-319-46466-4_3.

KKM+17

Andreas M Kist, Laura D Knogler, Daniil A Markov, Tugce Yildizoglu, and Ruben Portugues. Whole-brain imaging using genetically encoded activity sensors in vertebrates. In Decoding Neural Circuit Structure and Function, pages 321–341. Springer, 2017.

LBFrazao+15

Gonçalo Lopes, Niccolò Bonacchi, João Frazão, Joana P Neto, Bassam V Atallah, Sofia Soares, Luís Moreira, Sara Matias, Pavel M Itskov, Patrícia A Correia, and others. Bonsai: an event-based framework for processing and controlling data streams. Frontiers in neuroinformatics, 9:7, 2015.

MMC+18

Alexander Mathis, Pranav Mamidanna, Kevin M. Cury, Taiga Abe, Venkatesh N. Murthy, Mackenzie W. Mathis, and Matthias Bethge. Deeplabcut: markerless pose estimation of user-defined body parts with deep learning. Nature Neuroscience, 2018. URL: https://www.nature.com/articles/s41593-018-0209-y.

MW18

Alexander Mathis and Richard A. Warren. On the inference speed and video-compression robustness of deeplabcut. bioRxiv, 2018. URL: https://www.biorxiv.org/content/early/2018/10/30/457242, arXiv:https://www.biorxiv.org/content/early/2018/10/30/457242.full.pdf, doi:10.1101/457242.

MSSW13

Olivier Mirat, Jenna Renée Sternberg, Kristen E Severi, and Claire Wyart. Zebrazoom: an automated program for high-throughput behavioral analysis and categorization. Frontiers in neural circuits, 7:107, 2013.

OKS+08

Michael B Orger, Adam R Kampff, Kristen E Severi, Johann H Bollmann, and Florian Engert. Control of visually guided behavior by distinct populations of spinal projection neurons. Nature neuroscience, 11(3):327, 2008.

Pei07

Jonathan W Peirce. Psychopy—psychophysics software in python. Journal of neuroscience methods, 162(1-2):8–13, 2007.

PE09

Ruben Portugues and Florian Engert. The neural basis of visual behaviors in the larval zebrafish. Current opinion in neurobiology, 19(6):644–647, 2009.

PE11

Ruben Portugues and Florian Engert. Adaptive locomotor behavior in larval zebrafish. Frontiers in systems neuroscience, 5:72, 2011.

PFEO14

Ruben Portugues, Claudia E Feierstein, Florian Engert, and Michael B Orger. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron, 81(6):1328–1343, 2014.

PerezEVPH+14

Alfonso Pérez-Escudero, Julián Vicente-Page, Robert C Hinz, Sara Arganda, and Gonzalo G De Polavieja. Idtracker: tracking individuals in a group by automatic identification of unmarked animals. Nature methods, 11(7):743, 2014.

WDB+17

Sébastien Wolf, Alexis M Dubreuil, Tommaso Bertoni, Urs Lucas Böhm, Volker Bormuth, Raphaël Candelier, Sophia Karpenko, David GC Hildebrand, Isaac H Bianco, Rémi Monasson, and others. Sensorimotor computation underlying phototaxis in zebrafish. Nature Communications, 8(1):651, 2017.