An open-source tool for automated analysis of breathing behaviors in common marmosets and rodents

Abstract

The respiratory system maintains homeostatic levels of oxygen (O2) and carbon dioxide (CO2) in the body through rapid and efficient regulation of breathing frequency and depth (tidal volume). The commonly used methods of analysing breathing data in behaving experimental animals are usually subjective, laborious, and time-consuming. To overcome these hurdles, we optimized an analysis toolkit for the unsupervised study of respiratory activities in animal subjects. Using this tool, we analyzed breathing behaviors of the common marmoset (Callithrix jacchus), a New World non-human primate model. Using Whole-body Plethysmography in room air as well as acute hypoxic (10% O2) and hypercapnic (6% CO2) conditions, we describe breathing behaviors in awake, freely behaving marmosets. Our data indicate that marmosets' exposure to acute hypoxia decreased metabolic rate and increased sigh rate. However, the hypoxic condition did not augment ventilation. Hypercapnia, on the other hand, increased both the frequency and depth (i.e., tidal volume) of breathing.

Brainstem astrocytes regulate breathing and may affect arousal state in rats

“…Plethysmography data were analyzed as described before [17], [24], [25]. Briefly, the respiratory cycle duration was calculated for each respiratory cycle for the first 40 minutes that the animals were placed in the plethysmography chamber.…”

“…Tidal volume (V T , dept of breathing) and minute ventilation (V E = f R x V T ) were measured as described before [17], [25]. Sighs were defined as peaks with amplitudes two times greater than the average amplitude of the previous four cycles and a respiratory cycle duration 50% greater than the average of the previous four cycles and confirmed manually as described before [17], [24], [25] and reported as the numbers per hour (hr -1 ) The frequency distribution of the instantaneous rate of respiratory-related events (including signing) in the 30-min assay period was analyzed and plotted after extracting high frequency sniffing. The most common breathing rate in each group defined as the dominant breathing frequency (i.e.…”

GoFish: A low-cost, open-source platform for closed-loop behavioural experiments on fish

“…To address this, we developed GoFish , a user-friendly platform for dynamic, fully-automated behavioural experiments on fish or other aquatic organisms. Our platform is inspired by present day behavioural, cognitive and neuroscience experiments that rely on open-source, community based, DIY-type solutions for running and developing new experimental paradigms, as well as for processing and analysing the resulting data streams (Akam et al, 2022; Aoki et al, 2015; Bishop et al, 2022; Buscher et al, 2020; Devarakonda et al, 2016; Geissmann et al, 2017; Guilbeault et al, 2021; Gurley, 2019; Kane et al, 2020; Kapanaiah et al, 2021; Lopes et al, 2021; Mathis et al, 2018; Oh et al, 2017; O’Leary et al, 2018; Pineño, 2014; Siegle et al, 2017; Swanson et al, 2021; Walter & Couzin, 2021).…”

“…To address this, we developed GoFish, a user-friendly platform for dynamic, fully-automated behavioural experiments on fish or other aquatic organisms. Our platform is inspired by present day behavioural, cognitive and neuroscience experiments that rely on open-source, community based, DIY-type solutions for running and developing new experimental paradigms, as well as for processing and analysing the resulting data streams (Akam et al, 2022;Aoki et al, 2015;Bishop et al, 2022;Buscher et al, 2020;Devarakonda et al, 2016;Geissmann et al, 2017;Guilbeault et al, 2021;Gurley, 2019;Kane et al, 2020;Kapanaiah et al, 2021;Mathis et al, 2018;Oh et al, 2017;O'Leary et al, 2018;Pineño, 2014;Siegle et al, 2017;Swanson et al, 2021;Walter & Couzin, 2021). Briefly, our system allows for the display of stimuli on a computer screen placed outside but adjacent to a tank, the detection of the subject's location in real-time through an overhanging camera, the programming of contingencies between fish movements and the delivery of food rewards, and the automatic recording of data in analysable format.…”