Design of complex neuroscience experiments using mixed-integer linear programming

Slivkoff, Storm; Gallant, Jack L.

doi:10.1016/j.neuron.2021.02.019

Cited by 5 publications

(1 citation statement)

References 87 publications

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“…Most importantly, the key distinction of PRT is the ability to be customized for tracking different types of rodents (varied coat color or species) in different experimental settings. As more and more in depth questions are being asked, the complexity of experimental designs have also increased (Basso et al, 2021; Slivkoff and Gallant, 2021). Investigators will need readily adaptable tools for their experimental design involving rodents of different size and coat colors in different environments.…”

Section: Discussionmentioning

confidence: 99%

PyRodentTracks: flexible computer vision and RFID based system for multiple rodent tracking and behavioral assessment

Fong

Jury

et al. 2022

Preprint

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PyRodentTracks (PRT) is a scalable and customizable computer vision and RFID-based system for multiple rodent tracking and behavior assessment that can be set up within minutes in any user-defined arena at minimal cost. PRT is composed of the online Raspberry Pi-based video and RFID acquisition and the subsequent offline analysis tools. The system is capable of tracking up to 6 mice in experiments ranging from minutes to days. PRT maintained a minimum of 88% detections tracked with an overall accuracy >85% when compared to manual validation of videos containing 1-4 mice in a modified home-cage. As expected, chronic recording in home-cage revealed diurnal activity patterns. Moreover, it was observed that novel non-cagemate mice pairs exhibit more similarity in travel trajectory patterns over a 10-minute period in the openfield than cagemates. Therefore, shared features within travel trajectories between animals may be a measure of sociability that has not been previously reported. Moreover, PRT can interface with open-source packages such as Deeplabcut and Traja for pose estimation and travel trajectory analysis, respectively. In combination with Traja, PRT resolved motor deficits exhibited in stroke animals. Overall, we present an affordable, open-sourced, and customizable/scalable rodent-specific behavior recording and analysis system.

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Section: Discussionmentioning

confidence: 99%