rBat 0.1.1

Toolkit for preprocessing rat time-spatial data and quantifying their (artificially induced) OCD-like behaviour.

rBat

Repo for the rBat package — behavioural quantification algorithms & preprocessing methods.

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Important Links

• Source Code: https://github.com/brandonc-edu/rBat
• Bug Reports: https://github.com/brandonc-edu/rBat/issues

Capabilities

It provides:

• Objects to replicate test environments for purposes of tracking rat movement.
• Functions to calculate summary measures — quantifications of the rat's OCD-like behaviour.
• Preprocessing methods to smooth time-spatial data and segment it into episodes of movement types (lingering, progression, etc.)
• API Interfaces to assist in preprocessing and summary measure calcuations.

Testing

rBat requires pytest to test the summary measure and preprocessing algorithms.

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Credits

Brandon Carrasco & Daniel Locke - Original Developers of rBat Package Inoday Yadav & Jamie Wong - Tested rBat package functionality Dr. Henry Szechtman & Dr. Anna Dvorkin-Gheva - Supervisors & Consultants for Desired Functionality

Implementations Based Upon

Summary Measures

Szechtman, H., Sulis, W., & Eilam, D. (1998). Quinpirole induces compulsive checking behavior in rats: a potential animal model of obsessive-compulsive disorder (OCD). Behavioral neuroscience, 112(6), 1475–1485. https://doi.org/10.1037//0735-7044.112.6.1475

Dvorkin, A., Perreault, M. L., & Szechtman, H. (2006). Development and temporal organization of compulsive checking induced by repeated injections of the dopamine agonist quinpirole in an animal model of obsessive-compulsive disorder. Behavioural brain research, 169(2), 303–311. https://doi.org/10.1016/j.bbr.2006.01.024

Dvorkin, A., Culver, K. E., & Szechtman, H. (2006). Differential effects of clorgyline on sensitization to quinpirole in rats tested in small and large environments. Psychopharmacology, 186(4), 534–543. https://doi.org/10.1007/s00213-006-0377-4

Tucci, M. C., Dvorkin-Gheva, A., Johnson, E., Cheon, P., Taji, L., Agarwal, A., Foster, J., & Szechtman, H. (2014). Performance of compulsive behavior in rats is not a unitary phenomenon - validation of separate functional components in compulsive checking behavior. The European journal of neuroscience, 40(6), 2971–2979. https://doi.org/10.1111/ejn.12652

Preprocessing

Hen, I., Sakov, A., Kafkafi, N., Golani, I., & Benjamini, Y. (2004). The dynamics of spatial behavior: how can robust smoothing techniques help?. Journal of neuroscience methods, 133(1-2), 161–172. https://doi.org/10.1016/j.jneumeth.2003.10.013

Drai, D., Benjamini, Y., & Golani, I. (2000). Statistical discrimination of natural modes of motion in rat exploratory behavior. Journal of neuroscience methods, 96(2), 119–131. https://doi.org/10.1016/s0165-0270(99)00194-6

Additional implementation details gleaned from: https://www.tau.ac.il/~ilan99/see/help/