Bayesian Algorithmic Decoding of Acceleration and Speed Software (BADASS)
An important question in neuroscience is how the brain encodes the environment and the self, and how accurate these codes are. Bayesian decoding techniques have been used to determine the position of an animal based on neuron spike rate in the brain’s hippocampus. In this software package, Bayesian...
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| Published in | Software impacts Vol. 10; p. 100125 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier B.V
01.11.2021
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| Online Access | Get full text |
| ISSN | 2665-9638 2665-9638 |
| DOI | 10.1016/j.simpa.2021.100125 |
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| Abstract | An important question in neuroscience is how the brain encodes the environment and the self, and how accurate these codes are. Bayesian decoding techniques have been used to determine the position of an animal based on neuron spike rate in the brain’s hippocampus. In this software package, Bayesian Algorithmic Decoding of Acceleration and Speed Software (BADASS), we expand on existing decoding algorithms to decode speed and acceleration using cell spiking. BADASS can be used to determine the extent of speed and acceleration coding in different brain regions during movement, as well as during periods of memory consolidation and planning.
•Spike rate of neurons in the brain can be used to decode information about an animal.•Speed/acceleration are represented in brain areas, including lateral septum and entorhinal cortex.•This software (BADASS) allows for Bayesian decoding of speed and acceleration.•BADASS can also be used to determine if speed/acceleration coding precedes or follows movement. |
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| AbstractList | An important question in neuroscience is how the brain encodes the environment and the self, and how accurate these codes are. Bayesian decoding techniques have been used to determine the position of an animal based on neuron spike rate in the brain’s hippocampus. In this software package, Bayesian Algorithmic Decoding of Acceleration and Speed Software (BADASS), we expand on existing decoding algorithms to decode speed and acceleration using cell spiking. BADASS can be used to determine the extent of speed and acceleration coding in different brain regions during movement, as well as during periods of memory consolidation and planning.
•Spike rate of neurons in the brain can be used to decode information about an animal.•Speed/acceleration are represented in brain areas, including lateral septum and entorhinal cortex.•This software (BADASS) allows for Bayesian decoding of speed and acceleration.•BADASS can also be used to determine if speed/acceleration coding precedes or follows movement. |
| ArticleNumber | 100125 |
| Author | Wirtshafter, Hannah S. Wilson, Matthew A. |
| Author_xml | – sequence: 1 givenname: Hannah S. orcidid: 0000-0003-4684-7074 surname: Wirtshafter fullname: Wirtshafter, Hannah S. email: hsw@mit.edu, hsw@northwestern.edu organization: Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA – sequence: 2 givenname: Matthew A. surname: Wilson fullname: Wilson, Matthew A. organization: Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA |
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| Cites_doi | 10.1523/JNEUROSCI.2862-08.2008 10.1016/j.cub.2019.07.089 10.1523/JNEUROSCI.3414-13.2014 10.1038/nn.2344 10.1515/REVNEURO.2004.15.2.89 10.1016/0006-8993(71)90358-1 10.1523/JNEUROSCI.23-04-01535.2003 10.1016/j.neubiorev.2021.03.029 10.1093/cercor/bht020 10.1016/S0896-6273(01)00186-6 10.1152/jn.00512.2013 10.1126/science.8036517 10.1038/nrn3888 10.1016/j.neuron.2006.06.032 10.1038/nature14622 10.1152/jn.1998.79.2.1017 10.1016/S0896-6273(00)80773-4 10.1523/JNEUROSCI.14-12-07235.1994 10.1523/JNEUROSCI.1450-18.2019 10.1002/hipo.22453 10.1038/nn1825 10.1152/jn.00068.2006 10.21769/BioProtoc.3947 10.1126/science.1235338 10.1016/j.neuron.2009.07.027 10.1146/annurev.neuro.29.051605.112854 10.1016/j.cub.2018.09.037 10.1126/science.1250444 10.1038/nrn3827 |
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| Keywords | Place cells Neuroscience Entorhinal cortex Replay Lateral septum Grid cells Bayesian probability Decoding Hippocampus |
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