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Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA

Widely available low-cost electronics encourage the development of open-source tools for neuroscientific research. In recent years, many neuroscientists recognized the open science movement for its potential to stimulate and encourage science that is less focused on money, and more on robustness, va...

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Autores principales: Virag, D., Homolak, J., Kodvanj, I., Babic Perhoc, A., Knezovic, A., Osmanovic Barilar, J., Salkovic-Petrisic, M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7858584/
https://www.ncbi.nlm.nih.gov/pubmed/33536528
http://dx.doi.org/10.1038/s41598-021-82710-6
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author Virag, D.
Homolak, J.
Kodvanj, I.
Babic Perhoc, A.
Knezovic, A.
Osmanovic Barilar, J.
Salkovic-Petrisic, M.
author_facet Virag, D.
Homolak, J.
Kodvanj, I.
Babic Perhoc, A.
Knezovic, A.
Osmanovic Barilar, J.
Salkovic-Petrisic, M.
author_sort Virag, D.
collection PubMed
description Widely available low-cost electronics encourage the development of open-source tools for neuroscientific research. In recent years, many neuroscientists recognized the open science movement for its potential to stimulate and encourage science that is less focused on money, and more on robustness, validity, questioning and understanding. Here, we wanted to contribute to this global community by creating a research platform based on a common digital kitchen scale. This everyday ordinary kitchen tool is sometimes used in neuroscience research in various ways; however, its use is limited by sampling rate and inability to store and analyze data. To tackle this problem we developed a Platform for Acoustic STArtle or PASTA. This robust and simple platform enables users to obtain data from kitchen scale load cells at a high sampling rate, store it and analyze it. Here, we used it to analyze acoustic startle and prepulse inhibition sensorimotor gating in rats treated intracerebroventricularly with streptozotocin, but the system can be easily modified and upgraded for other purposes. In accordance with open science principles, we shared complete hardware design with instructions. Furthermore, we also disclose our software codes written for PASTA data acquisition (C++, Arduino) and acoustic startle experimental protocol (Python) and analysis (ratPASTA R package—R-based Awesome Toolbox for PASTA, and pastaWRAP—Python wrapper package for ratPASTA). To further encourage the development of our PASTA platform we demonstrate its sensitivity by using PASTA-gathered data to extract breathing patterns during rat freezing behavior in our experimental protocol.
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spelling pubmed-78585842021-02-04 Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA Virag, D. Homolak, J. Kodvanj, I. Babic Perhoc, A. Knezovic, A. Osmanovic Barilar, J. Salkovic-Petrisic, M. Sci Rep Article Widely available low-cost electronics encourage the development of open-source tools for neuroscientific research. In recent years, many neuroscientists recognized the open science movement for its potential to stimulate and encourage science that is less focused on money, and more on robustness, validity, questioning and understanding. Here, we wanted to contribute to this global community by creating a research platform based on a common digital kitchen scale. This everyday ordinary kitchen tool is sometimes used in neuroscience research in various ways; however, its use is limited by sampling rate and inability to store and analyze data. To tackle this problem we developed a Platform for Acoustic STArtle or PASTA. This robust and simple platform enables users to obtain data from kitchen scale load cells at a high sampling rate, store it and analyze it. Here, we used it to analyze acoustic startle and prepulse inhibition sensorimotor gating in rats treated intracerebroventricularly with streptozotocin, but the system can be easily modified and upgraded for other purposes. In accordance with open science principles, we shared complete hardware design with instructions. Furthermore, we also disclose our software codes written for PASTA data acquisition (C++, Arduino) and acoustic startle experimental protocol (Python) and analysis (ratPASTA R package—R-based Awesome Toolbox for PASTA, and pastaWRAP—Python wrapper package for ratPASTA). To further encourage the development of our PASTA platform we demonstrate its sensitivity by using PASTA-gathered data to extract breathing patterns during rat freezing behavior in our experimental protocol. Nature Publishing Group UK 2021-02-03 /pmc/articles/PMC7858584/ /pubmed/33536528 http://dx.doi.org/10.1038/s41598-021-82710-6 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Virag, D.
Homolak, J.
Kodvanj, I.
Babic Perhoc, A.
Knezovic, A.
Osmanovic Barilar, J.
Salkovic-Petrisic, M.
Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
title Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
title_full Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
title_fullStr Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
title_full_unstemmed Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
title_short Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
title_sort repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for pasta
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7858584/
https://www.ncbi.nlm.nih.gov/pubmed/33536528
http://dx.doi.org/10.1038/s41598-021-82710-6
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