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

Abstract 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 robus...

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Autores principales:	D. Virag, J. Homolak, I. Kodvanj, A. Babic Perhoc, A. Knezovic, J. Osmanovic Barilar, M. Salkovic-Petrisic
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/47f0f1b7d1e3432aaece9321a09ed270
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spelling	oai:doaj.org-article:47f0f1b7d1e3432aaece9321a09ed2702021-12-02T10:44:21ZRepurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA10.1038/s41598-021-82710-62045-2322https://doaj.org/article/47f0f1b7d1e3432aaece9321a09ed2702021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82710-6https://doaj.org/toc/2045-2322Abstract 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.D. ViragJ. HomolakI. KodvanjA. Babic PerhocA. KnezovicJ. Osmanovic BarilarM. Salkovic-PetrisicNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q D. Virag J. Homolak I. Kodvanj A. Babic Perhoc A. Knezovic J. Osmanovic Barilar M. Salkovic-Petrisic Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA
description	Abstract 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.
format	article
author	D. Virag J. Homolak I. Kodvanj A. Babic Perhoc A. Knezovic J. Osmanovic Barilar M. Salkovic-Petrisic
author_facet	D. Virag J. Homolak I. Kodvanj A. Babic Perhoc A. Knezovic J. Osmanovic Barilar M. Salkovic-Petrisic
author_sort	D. Virag
title	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_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_sort	repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for pasta
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/47f0f1b7d1e3432aaece9321a09ed270
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Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA

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