Automated recording of home cage activity and temperature of individual rats housed in social groups: The Rodent Big Brother project

AI-powered home cage system for real-time tracking and analysis of rodent behavior

Researchers in animal behavior and neuroscience devote considerable time to observing rodents behavior and physiological responses, with AI monitoring systems reducing personnel workload. This study presents the RodentWatch (RW) system, which leverages deep learning to automatically identify experimental animal behaviors in home cage environments. A single multifunctional camera and edge device are installed inside the animal's home cage, allowing continuous real-time monitoring of the animal's behavior, position, and body temperature for extended periods. We investigated identifying the drinking and resting behaviors of rats, with recognition accuracy enhanced through contextual object labeling and modified non-maximum suppression (NMS) schemes. Two tests-a light cycle change test and a sucrose preference test-were conducted to evaluate the usability of this system in rat behavioral experiments. This system enables notable advancements in image-based behavior recognition for living rodents.

Added Value of Sensor-Based Behavioural Monitoring in an Infectious Disease Study with Sheep Infected with Toxoplasma gondii

Sensor technologies are increasingly used to monitor laboratory animal behaviour. The aim of this study was to investigate the added value of using accelerometers and video to monitor the activity and drinking behaviour of three rams from 5 days before to 22 days after inoculation with Toxoplasma gondii. We computed the activity from accelerometer data as the vectorial dynamic body acceleration (VDBA). In addition, we assessed individual drinking behaviour from video, using frame differencing above the drinker to identify drinking bouts, and Aruco markers for individual identification. Four days after inoculation, rams developed fever and activity decreased. The daytime VDBA from days 4 to 10 was 60-80% of that before inoculation. Animal caretakers scored rams as lethargic on days 5 and 6 and, for one ram, also on the morning of day 7. Video analysis showed that each ram decreased its number of visits to the drinker, as well as its time spent at the drinker, by up to 50%. The fever and corresponding sickness behaviours lasted until day 10. Overall, while we recognize the limited conclusiveness due to the small number of animals, the sensor technologies provided continuous, individual, detailed, and objective data and offered additional insights as compared to routine observations. We recommend the wider implementation of such technologies in animal disease trials to refine experiments and guarantee the quality of experimental results.

Development of a 3D tracking system for multiple marmosets under free-moving conditions

Assessment of social interactions and behavioral changes in nonhuman primates is useful for understanding brain function changes during life events and pathogenesis of neurological diseases. The common marmoset (Callithrix jacchus), which lives in a nuclear family like humans, is a useful model, but longitudinal automated behavioral observation of multiple animals has not been achieved. Here, we developed a Full Monitoring and Animal Identification (FulMAI) system for longitudinal detection of three-dimensional (3D) trajectories of each individual in multiple marmosets under free-moving conditions by combining video tracking, Light Detection and Ranging, and deep learning. Using this system, identification of each animal was more than 97% accurate. Location preferences and inter-individual distance could be calculated, and deep learning could detect grooming behavior. The FulMAI system allows us to analyze the natural behavior of individuals in a family over their lifetime and understand how behavior changes due to life events together with other data.

MouseVUER: video based open-source system for laboratory mouse home-cage monitoring

Video monitoring of mice in the home-cage reveals behavior profiles without the disruptions caused by specialized test setups and makes it possible to quantify changes in behavior patterns continually over long time frames. Several commercial home-cage monitoring systems are available with varying costs and capabilities; however there are currently no open-source systems for home-cage monitoring. We present an open-source system for top-down video monitoring of research mice in a slightly modified home-cage. The system is designed for integration with Allentown NexGen ventilated racks and allows unobstructed view of up to three mice, but can also be operated outside the rack. The system has an easy to duplicate and assemble home-cage design along with a video acquisition solution. The system utilizes a depth video camera, and we demonstrate the robustness of depth video for home-cage mice monitoring. For researchers without access to Allentown NexGen ventilated racks, we provide designs and assembly instructions for a standalone non-ventilated rack solution that holds three systems for more compact and efficient housing. We make all the design files, along with detailed assembly and installation instructions, available on the project webpage ( https://github.com/NIH-CIT-OIR-SPIS/MouseVUER ).

Tracking individual broilers on video in terms of time and distance

Tracking group-housed individual broilers using video can provide valuable information on their health, welfare, and performance, allowing breeders to identify novel or indicator traits that aid genetic improvement. However, their similar appearances make tracking individual broilers in a group-housed setting challenging. This study aimed to analyze broiler tracking on video (number of ID-switches, tracking time and distance) and examined potential tracking errors (ID-losses - location, proximity, kinematics) in an experimental pen to enable broiler locomotion phenotyping. This comprehensive analysis provided insights into the potential and challenges of tracking group-housed broilers on video with regards to phenotyping broiler locomotion. Thirty-nine broilers, of which 35 noncolor marked, were housed in an experimental pen (1.80 × 2.61 m), and only data at 18 d of age were used. A YOLOv7-tiny model was trained (n = 140), validated (n = 30), and tested (n = 30) on 200 annotated frames to detect the broilers. On the test set, YOLOv7-tiny had a precision, recall, and average precision (@0.5 - Intersection over Union threshold) of 0.99. A multi-object tracker (SORT) was implemented and evaluated on ground-truth trajectories of thirteen white broilers based on 136 min of video data (1-min intervals). The number of ID-switches varied from 5 to 20 (mean: 9.92) per ground-truth trajectory, tracking times ranged from 1 (by definition) to 51 min (mean: 12.36), and tracking distances ranged from 0.01 to 17.07 meters (mean: 1.89) per tracklet. Tracking errors primarily occurred when broilers were occluded by the drinker, and relatively frequently when broilers were in close proximity (within 10 cm), with velocity and acceleration appearing to have a lesser impact on tracking errors. The study establishes a 'baseline' for future research and identified the potential and challenges of tracking group-housed individual broilers. The results highlighted the importance of addressing ID-switches, identified potential tracking algorithm improvements, and emphasized the need for an external animal identification system to enable objective, simultaneous and semi-continuous locomotion phenotyping of group-housed individual broilers.

Towards substitution of invasive telemetry: An integrated home cage concept for unobtrusive monitoring of objective physiological parameters in rodents

This study presents a novel concept for a smart home cage design, tools, and software used to monitor the physiological parameters of mice and rats in animal-based experiments. The proposed system focuses on monitoring key clinical parameters, including heart rate, respiratory rate, and body temperature, and can also assess activity and circadian rhythm. As the basis of the smart home cage system, an in-depth analysis of the requirements was performed, including camera positioning, imaging system types, resolution, frame rates, external illumination, video acquisition, data storage, and synchronization. Two different camera perspectives were considered, and specific camera models, including two near-infrared and two thermal cameras, were selected to meet the requirements. The developed specifications, hardware models, and software are freely available via GitHub. During the first testing phase, the system demonstrated the potential of extracting vital parameters such as respiratory and heart rate. This technology has the potential to reduce the need for implantable sensors while providing reliable and accurate physiological data, leading to refinement and improvement in laboratory animal care.

PiE: an open-source pipeline for home cage behavioral analysis

Over the last two decades a growing number of neuroscience labs are conducting behavioral assays in rodents. The equipment used to collect this behavioral data must effectively limit environmental and experimenter disruptions, to avoid confounding behavior data. Proprietary behavior boxes are expensive, offer limited compatible sensors, and constrain analysis with closed-source hardware and software. Here, we introduce PiE, an open-source, end-to-end, user-configurable, scalable, and inexpensive behavior assay system. The PiE system includes the custom-built behavior box to hold a home cage, as well as software enabling continuous video recording and individual behavior box environmental control. To limit experimental disruptions, the PiE system allows the control and monitoring of all aspects of a behavioral experiment using a remote web browser, including real-time video feeds. To allow experiments to scale up, the PiE system provides a web interface where any number of boxes can be controlled, and video data easily synchronized to a remote location. For the scoring of behavior video data, the PiE system includes a standalone desktop application that streamlines the blinded manual scoring of large datasets with a focus on quality control and assay flexibility. The PiE system is ideal for all types of behavior assays in which video is recorded. Users are free to use individual components of this setup independently, or to use the entire pipeline from data collection to analysis. Alpha testers have included scientists without prior coding experience. An example pipeline is demonstrated with the PiE system enabling the user to record home cage maternal behavior assays, synchronize the resulting data, conduct blinded scoring, and import the data into R for data visualization and analysis.

Bouts of rest and physical activity in C57BL/6J mice

The objective was to exploit the raw data output from a scalable home cage (type IIL IVC) monitoring (HCM) system (DVC®), to characterize pattern of undisrupted rest and physical activity (PA) of C57BL/6J mice. The system's tracking algorithm show that mice in isolation spend 67% of the time in bouts of long rest (≥40s). Sixteen percent is physical activity (PA), split between local movements (6%) and locomotion (10%). Decomposition revealed that a day contains ˜7100 discrete bouts of short and long rest, local and locomotor movements. Mice travel ˜330m per day, mainly during the dark hours, while travelling speed is similar through the light-dark cycle. Locomotor bouts are usually <0.2m and <1% are >1m. Tracking revealed also fits of abnormal behaviour. The starting positions of the bouts showed no preference for the rear over the front of the cage floor, while there was a strong bias for the peripheral (75%) over the central floor area. The composition of bouts has a characteristic circadian pattern, however, intrusive husbandry routines increased bout fragmentation by ˜40%. Extracting electrode activations density (EAD) from the raw data yielded results close to those obtained with the tracking algorithm, with 81% of time in rest (<1 EAD s-1) and 19% in PA. Periods ≥40 s of file when no movement occurs and there is no EAD may correspond to periods of sleep (˜59% of file time). We confirm that EAD correlates closely with movement distance (rs>0.95) and the data agreed in ˜97% of the file time. Thus, albeit EAD being less informative it may serve as a proxy for PA and rest, enabling monitoring group housed mice. The data show that increasing density from one female to two males, and further to three male or female mice had the same effect size on EAD (˜2). In contrast, the EAD deviated significantly from this stepwise increase with 4 mice per cage, suggesting a crowdedness stress inducing sex specific adaptations. We conclude that informative metrics on rest and PA can be automatically extracted from the raw data flow in near-real time (< 1 hrs). As discussed, these metrics relay useful longitudinal information to those that use or care for the animals.

Socially Integrated Polysubstance (SIP) system: An open-source solution for continuous monitoring of polysubstance fluid intake in group housed mice

Despite impressive results from neuroscience research using rodent models, there is a paucity of successful translation from preclinical findings to effective pharmacological interventions for treatment of substance use disorder (SUD) in humans. One potential reason for lack of translation from animal models is difficulty in accurately replicating the lived experience of people who use drugs. Aspects of substance use in humans that are often not modeled in animal research include but are not limited to 1) voluntary timing and frequency of substance intake, 2) social environment during substance use, and 3) access to multiple substances and multiple concentrations of each substance. Critically, existing commercial equipment that allows for social housing and voluntary polysubstance use (e.g., home cage monitoring system) is prohibitively expensive and no open-source solutions exist. With these goals in mind, here we detail development of the Socially Integrated Polysubstance (SIP) system, an open-source and lower cost solution that allows for group housed rodents to self-administer multiple substances with continuous monitoring and measurement. In our current setup, each SIP cage contains four drinking stations, and each station is equipped with a RFID sensor and sipper tube connected to a unique fluid reservoir. Using this system, we can track which animal (implanted with unique RFID transponder) visits which drinking location and the amount they drink during each visit (in 20 ul increments). Using four flavors of Kool-Aid, here we demonstrate that the SIP system is reliable and accurate with high temporal resolution for long term monitoring of substance intake and behavior tracking in a social environment. The SIP cage system is a first step towards designing an accessible and flexible rodent model of substance use that more closely resembles the experience of people who use drugs.

2000-2023 over two decades of ICH S7A: has the time come for a revamp?

The ICH S7A guideline on safety pharmacology studies released over 20 years ago largely achieved its objective "to help protect clinical trial participants and patients receiving marketed products from potential adverse effects of pharmaceuticals". Although, Phase I clinical trials are generally very safe, the incidence and severity of adverse events, the safety related attrition and product withdrawal remain elevated during late-stage clinical development and post approval, a proportion of which can be attributed at least in part to safety pharmacology related issues. Considering the latest scientific and technological advancements in drug safety science, the paradigm shift of the drug discovery and development process and the continuously evolving regulatory landscape, we recommend revisiting, adapting and evolving the ICH S7A guideline. This might offer opportunities i) to select and progress optimized drugs with increased confidence in success, ii) to refine and adapt the clinical monitoring at all stages of clinical development resulting in an optimized benefit/risk assessment, iii) to increase likelihood of regulatory acceptance in a way compatible with an expedited and streamlined drug discovery and development process to benefit patients and iv) to avoid the unnecessary use of animals in 'tick-the-box' studies and encourage alternative approaches. As presented in the article, several options could be envisioned to revisit and adapt the ICH S7A taking into consideration several key features.

Passive radio frequency identification and video tracking for the determination of location and movement of broilers

Phenotypes on individual animals are required for breeding programs to be able to select for traits. However, phenotyping individual animals can be difficult and time-consuming, especially for traits related to health, welfare, and performance. Individual broiler behavior could serve as a proxy for these traits when recorded automatically and reliably on many animals. Sensors could record individual broiler behavior, yet different sensors can differ in their assessment. In this study a comparison was made between a passive radio frequency identification (RFID) system (grid of antennas underneath the pen) and video tracking for the determination of location and movement of 3 color-marked broilers at d 18. Furthermore, a systems comparison of derived behavioral metrics such as space usage, locomotion activity and apparent feeding and drinking behavior was made. Color-marked broilers simplified the computer vision task for YOLOv5 to detect, track, and identify the animals. Animal locations derived from the RFID-system and based on video were largely in agreement. Most location differences (77.5%) were within the mean radius of the antennas' enclosing circle (≤128 px, 28.15 cm), and 95.3% of the differences were within a one antenna difference (≤256 px, 56.30 cm). Animal movement was not always registered by the RFID-system whereas video was sensitive to detection noise and the animal's behavior (e.g., pecking). The method used to determine location and the systems' sensitivities to movement led to differences in behavioral metrics. Behavioral metrics derived from video are likely more accurate than RFID-system derived behavioral metrics. However, at present, only the RFID-system can provide individual identification for non-color marked broilers. A combination of verifiable and detailed video with the unique identification of RFID could make it possible to identify, describe, and quantify a wide range of individual broiler behaviors.

Measuring Locomotor Activity and Behavioral Aspects of Rodents Living in the Home-Cage

Automatization and technological advances have led to a larger number of methods and systems to monitor and measure locomotor activity and more specific behavior of a wide variety of animal species in various environmental conditions in laboratory settings. In rodents, the majority of these systems require the animals to be temporarily taken away from their home-cage into separate observation cage environments which requires manual handling and consequently evokes distress for the animal and may alter behavioral responses. An automated high-throughput approach can overcome this problem. Therefore, this review describes existing automated methods and technologies which enable the measurement of locomotor activity and behavioral aspects of rodents in their most meaningful and stress-free laboratory environment: the home-cage. In line with the Directive 2010/63/EU and the 3R principles (replacement, reduction, refinement), this review furthermore assesses their suitability and potential for group-housed conditions as a refinement strategy, highlighting their current technological and practical limitations. It covers electrical capacitance technology and radio-frequency identification (RFID), which focus mainly on voluntary locomotor activity in both single and multiple rodents, respectively. Infrared beams and force plates expand the detection beyond locomotor activity toward basic behavioral traits but discover their full potential in individually housed rodents only. Despite the great premises of these approaches in terms of behavioral pattern recognition, more sophisticated methods, such as (RFID-assisted) video tracking technology need to be applied to enable the automated analysis of advanced behavioral aspects of individual animals in social housing conditions.

O mouse, where art thou? The Mouse Position Surveillance System (MoPSS)-an RFID-based tracking system

Existing methods for analysis of home cage-based preference tests are either time-consuming, not suitable for group management, expensive, and/or based on proprietary equipment that is not freely available. To correct this, we developed an automated system for group-housed mice based on radio frequency identification: the Mouse Position Surveillance System (MoPSS). The system uses an Arduino microcontroller with compatible components; it is affordable and easy to rebuild for every laboratory because it uses free and open-source software and open-source hardware with the RFID readers as the only proprietary component. The MoPSS was validated using female C57BL/6J mice and manual video comparison. It proved to be accurate even for fast-moving mice (up to 100% accuracy after logical reconstruction), and is already implemented in several studies in our laboratory. Here, we provide the complete construction description as well as the validation data and the results of an example experiment. This tracking system will allow group-based preference testing with individually identified mice to be carried out in a convenient manner. This facilitation of preference tests creates the foundation for better housing conditions from the animals' perspective.

Long-Term Effects of Low-Intensity Blast Non-Inertial Brain Injury on Anxiety-Like Behaviors in Mice: Home-Cage Monitoring Assessments

Mild traumatic brain injury induced by low-intensity blast (LIB) exposure poses concerns in military personnel. Using an open-field, non-inertial blast model and assessments by conventional behavioral tests, our previous studies revealed early-phase anxiety-like behaviors in LIB-exposed mice. However, the impact of LIB upon long-term anxiety-like behaviors requires clarification. This study applied a highly sensitive automated home-cage monitoring (HCM) system, which minimized human intervention and environmental changes, to assess anxiety-like responses in mice 3 months after LIB exposure. Initial assessment of 72-h spontaneous activities in a natural cage condition over multiple light and dark phases showed altered sheltering behaviors. LIB-exposed mice exhibited a subtle, but significantly decreased, duration of short shelter visits as compared to sham controls. Other measured responses between LIB-exposed mice and sham controls were insignificant. When behavioral assessments were performed in a challenged condition using an aversive spotlight, LIB-exposed mice demonstrated a significantly higher frequency of movements of shorter distance and duration per movement. Taken together, these findings demonstrated the presence of chronic anxiety-like behaviors assessed by the HCM system under both natural and challenged conditions in mice occurring post-LIB exposure. This model thus provides a platform to test for screening and interventions on anxiety disorders occurring after LIB non-inertial brain injury.

Use of subcutaneous transponders to monitor body temperature in laboratory rats

Implantable radiofrequency transponders may be adequate for the characterization of hazardous chemicals targeting body temperature control in experimental animals when colonic probes and automated monitoring systems based on intraperitoneal transmitters are not available, installable or applicable for any reason. In this work, we summarize a series of experiments showing the implantation protocol and utility of rice-grain size transponders to monitor subcutaneous temperature (T_sc) after exposure to pharmacological or toxicological treatments targeting body temperature control in laboratory rats. In addition, to explore the responsiveness of this thermometric system, the influence of physiological activity on T_sc readings was examined by monitoring T_sc after a motor exercise in a RotaRod system. Moreover, we characterized the effects of acute oral administration of the pyrethroid insecticide permethrin (PRM) in corn oil (1 mL/kg) on T_sc. PRM has been previously reported to cause dose-related increases in core temperature after administering oral doses ≥75 mg/kg, with peak effects at 2-4 h in adult rats. We monitored T_sc at 30 min intervals over a 4 h period after exposure to PRM (40-160 mg/kg). PRM caused a moderate increase in T_sc starting at ~3.5 h. Overall, T_sc assays showed minimal animal stress (if any) and rapid animal recovery from transponder implantation, simplicity to collect data, convenient testing room space requirements, and a competitive global cost per animal examined. However, various experimental factors may greatly influence the variability within and between individuals, some of which can be controlled by carefully setting up experimental conditions.

Scalable and modular wireless-network infrastructure for large-scale behavioural neuroscience

The use of rodents to acquire understanding of the function of neural circuits and of the physiological, genetic and developmental underpinnings of behaviour has been constrained by limitations in the scalability, automation and high-throughput operation of implanted wireless neural devices. Here we report scalable and modular hardware and software infrastructure for setting up and operating remotely programmable miniaturized wireless networks leveraging Bluetooth Low Energy for the study of the long-term behaviour of large groups of rodents. The integrated system allows for automated, scheduled and real-time experimentation via the simultaneous and independent use of multiple neural devices and equipment within and across laboratories. By measuring the locomotion, feeding, arousal and social behaviours of groups of mice or rats, we show that the system allows for bidirectional data transfer from readily available hardware, and that it can be used with programmable pharmacological or optogenetic stimulation. Scalable and modular wireless-network infrastructure should facilitate the remote operation of fully automated large-scale and long-term closed-loop experiments for the study of neural circuits and animal behaviour.

Refining Procedures within Regulatory Toxicology Studies: Improving Animal Welfare and Data

Simple Summary

Before any new medicine can be administered to humans, or new chemical marketed, some tests using animals such as fish, mice, rats, rabbits, dogs, or monkeys are performed in order to satisfy the legal requirements of international regulatory and government agencies. These assess the potential for harmful side effects in humans or species found in the environment and to explore how the compound is processed within the body. The housing conditions and procedures performed (such as dosing of compounds and removal of small blood samples) are designed to minimize any pain, suffering, distress, or lasting harm that may be experienced by the animals. These refinements improve animal welfare but can also improve the data quality. Examples of new processes, technologies, or equipment that have been introduced within some UK facilities are shared in this article and provide opportunities to benefit many more animals undergoing testing across the world in the future.

Abstract

During the development of potential new medicines or agrochemicals, an assessment of the safety profile to humans and environmental species is conducted using a range of different in silico and in vitro techniques in conjunction with metabolism and toxicity studies using animals. The required studies are outlined within international regulatory guidelines which acknowledge and support the application of the 3Rs to reduce the number of animals used or to refine the procedures performed when these studies are deemed to be necessary. The continued development of new technologies and adoption of best-practice approaches to laboratory animal housing and study procedures has generated a series of refinements that can be incorporated into animal studies throughout the package. These refinements benefit the welfare of fish, mice, rats, rabbits, dogs, minipigs, and non-human primates (NHPs) whilst maintaining or improving data quality within general toxicology, metabolism, and other studies and can also bring efficiencies to processes that benefit study costs and timings. Examples are shared which cover the following topics: social housing of dogs and NHPs, surgical refinements in the rat bile duct cannulation model for collection of data for metabolism studies, whether fasting is really required prior to clinical pathology sampling, and the use of microsampling for toxicokinetics.

Developing Recommendations for Cumulative Endpoints and Lifetime Use for Research Animals

Research animals are important for scientific advancement, and therefore, their long-term welfare needs to be monitored to not only minimize suffering, but to provide positive affective states and experiences. Currently, there is limited guidance in countries around the world on cumulative and experimental endpoints. This paper aims to explore current opinions and institutional strategies regarding cumulative use and endpoints through a scoping survey and review of current regulations and welfare assessment tools, and ultimately to provide recommendations for assessment of cumulative and lifetime use of research animals. The survey found that only 36% of respondents indicated that their institution had cumulative use endpoint policies in place, but these policies may be informal and/or vary by species. Most respondents supported more specific guidelines but expressed concerns about formal policies that may limit their ability to make case-by-case decisions. The wide diversity in how research animals are used makes it difficult for specific policies to be implemented. Endpoint decisions should be made in an objective manner using standardized welfare assessment tools. Future research should focus on robust, efficient welfare assessment tools that can be used to support planning and recommendations for cumulative endpoints and lifetime use of research and teaching animals.

Spontaneous, Voluntary, and Affective Behaviours in Rat Models of Pathological Pain

In pain patients affective and motivational reactions as well as impairment of daily life activities dominate the clinical picture. In contrast, many rodent pain models have been established on the basis of mechanical hypersensitivity testing. Up to today most rodent studies on pain still rely on reflexive withdrawal responses only. This discrepancy has likely contributed to the low predictive power of preclinical pain models for novel therapies. Here, we used a behavioural test array for rats to behaviourally evaluate five aetiologically distinct pain models consisting of inflammatory-, postsurgical-, cephalic-, neuropathic- and chemotherapy-induced pain. We assessed paralleling clinical expressions and comorbidities of chronic pain with an array of behavioural tests to assess anxiety, social interaction, distress, depression, and voluntary/spontaneous behaviours. Pharmacological treatment of the distinct pain conditions was performed with pathology-specific and clinically efficacious analgesics as gabapentin, sumatriptan, naproxen, and codeine. We found that rats differed in their manifestation of symptoms depending on the pain model and that pathology-specific analgesics also reduced the associated behavioural parameters. Based on all behavioural test performed, we screened for tests that can discriminate experimental groups on the basis of reflexive as well as non-sensory, affective parameters. Together, we propose a set of non-evoked behaviours with a comparable predictive power to mechanical threshold testing for each pain model.

Biomonitoring and Digital Data Technology as an Opportunity for Enhancing Animal Study Translation

The failure of animal studies to translate to effective clinical therapeutics has driven efforts to identify underlying cause and develop solutions that improve the reproducibility and translatability of preclinical research. Common issues revolve around study design, analysis, and reporting as well as standardization between preclinical and clinical endpoints. To address these needs, recent advancements in digital technology, including biomonitoring of digital biomarkers, development of software systems and database technologies, as well as application of artificial intelligence to preclinical datasets can be used to increase the translational relevance of preclinical animal research. In this review, we will describe how a number of innovative digital technologies are being applied to overcome recurring challenges in study design, execution, and data sharing as well as improving scientific outcome measures. Examples of how these technologies are applied to specific therapeutic areas are provided. Digital technologies can enhance the quality of preclinical research and encourage scientific collaboration, thus accelerating the development of novel therapeutics.

Automation of training and testing motor and related tasks in pre-clinical behavioural and rehabilitative neuroscience

Testing and training animals in motor and related tasks is a cornerstone of pre-clinical behavioural and rehabilitative neuroscience. Yet manually testing and training animals in these tasks is time consuming and analyses are often subjective. Consequently, there have been many recent advances in automating both the administration and analyses of animal behavioural training and testing. This review is an in-depth appraisal of the history of, and recent developments in, the automation of animal behavioural assays used in neuroscience. We describe the use of common locomotor and non-locomotor tasks used for motor training and testing before and after nervous system injury. This includes a discussion of how these tasks help us to understand the underlying mechanisms of neurological repair and the utility of some tasks for the delivery of rehabilitative training to enhance recovery. We propose two general approaches to automation: automating the physical administration of behavioural tasks (i.e., devices used to facilitate task training, rehabilitative training, and motor testing) and leveraging the use of machine learning in behaviour analysis to generate large volumes of unbiased and comprehensive data. The advantages and disadvantages of automating various motor tasks as well as the limitations of machine learning analyses are examined. In closing, we provide a critical appraisal of the current state of automation in animal behavioural neuroscience and a prospective on some of the advances in machine learning we believe will dramatically enhance the usefulness of these approaches for behavioural neuroscientists.

Motility Profile of Captive-Bred Marmosets Revealed by a Long-Term In-Cage Monitoring System

A quantitative evaluation of motility is crucial for studies employing experimental animals. Here, we describe the development of an in-cage motility monitoring method for new world monkeys using off-the-shelf components, and demonstrate its capability for long-term operation (e.g., a year). Based on this novel system, we characterized the motility of the common marmoset over different time scales (seconds, hours, days, and weeks). Monitoring of seven young animals belonging to two different age groups (sub-adult and young-adult) over a 231-day period revealed: (1) strictly diurnal activity (97.3% of movement during daytime), (2) short-cycle (∼20 s) transition in activity, and (3) bimodal diurnal activity including a "siesta" break. Additionally, while the mean duration of short-cycle activity, net daily activity, and diurnal activity changed over the course of development, 24-h periodicity remained constant. Finally, the method allowed for detection of progressive motility deterioration in a transgenic marmoset. Motility measurement offers a convenient way to characterize developmental and pathological changes in animals, as well as an economical and labor-free means for long-term evaluation in a wide range of basic and translational studies.

Intensive longitudinal characterization of multidimensional biobehavioral dynamics in laboratory rats

Rats have been used as animal models for human diseases for more than a century, yet a systematic understanding of basal biobehavioral phenotypes of laboratory rats is still missing. In this study, we utilize wireless tracking technology and videography, collect and analyze more than 130 billion data points to fill this gap, and characterize the evolution of behavior and physiology of group-housed male and female rats (n = 114) of the most commonly used strains (Lister Hooded, Long-Evans, Sprague-Dawley, and Wistar) throughout their development. The resulting intensive longitudinal data suggest the existence of strain and sex differences and bi-stable developmental states. Under standard laboratory 12-h light/12-h dark conditions, our study found the presence of multiple oscillations such as circatidal-like rhythms in locomotor activity. The overall findings further suggest that frequent movement along cage walls or thigmotaxic activity may be a physical feature of motion in constrained spaces, critically affecting the interpretation of basal behavior of rats in cages.

Major oscillations in spontaneous home-cage activity in C57BL/6 mice housed under constant conditions

The mouse is the most important mammalian model in life science research and the behavior of the mouse is a key read-out of experimental interventions and genetic manipulations. To serve this purpose a solid understanding of the mouse normal behavior is a prerequisite. Using 14-19 months of cumulative 24/7 home-cage activity recorded with a non-intrusive technique, evidence is here provided for a highly significant circannual oscillation in spontaneous activity (1-2 SD of the mean, on average 65% higher during peak of highs than lows; P = 7E-50) of male and female C57BL/6 mice held under constant conditions. The periodicity of this hitherto not recognized oscillation is in the range of 2-4 months (average estimate was 97 days across cohorts of cages). It off-sets responses to environmental stimuli and co-varies with the feeding behavior but does not significantly alter the preference for being active during the dark hours. The absence of coordination of this rhythmicity between cages with mice or seasons of the year suggest that the oscillation of physical activity is generated by a free-running intrinsic oscillator devoid of external timer. Due to the magnitude of this rhythmic variation it may be a serious confounder in experiments on mice if left unrecognized.

Differences in fatigue-like behavior in the lipopolysaccharide and poly I:C inflammatory animal models

Central fatigue is a condition associated with impairment of the central nervous system often leading to the manifestation of a range of debilitating symptoms. Fatigue can be a consequence of systemic inflammation following an infection. Administration of lipopolysaccharide (LPS) and polyriboinosinic:polyribocytidlic (poly I:C) to animals can induce systemic inflammation by mimicking a bacterial or viral infection respectively and therefore have been used as models of fatigue. We evaluated a range of phenotypic behaviors exhibited in the LPS and poly I:C animal models to assess whether they adequately replicate fatigue symptomology in humans. In addition to standard observation- and intervention-based behavioral assessments, we used powerful in-cage monitoring technology to quantify rodent behavior without external interference. LPS and poly I:C treated Sprague Dawley rats displayed 'sickness behaviors' of elevated temperature, weight loss and reduced activity in the open field test and with in-cage monitoring within 24 h post-treatment, but only LPS-treated rats displayed these behaviors beyond these acute timepoints. Once sickness behavior diminished, LPS-treated rats exhibited an increase in reward-seeking and motivation behaviors. Overall, these results suggest that the LPS animal model produces an extensive and sustained fatigue-like phenotype, whereas the poly I:C model only produced acute effects. Our results suggest that the LPS animal model is a more suitable candidate for further studies on central fatigue-like behavior.

Automated and Continuous Monitoring of Animal Welfare through Digital Alerting

A primary goal in preclinical animal research is respectful and responsible care aimed toward minimizing stress and discomfort while enhancing collection of accurate and reproducible scientific data. Researchers use hands-on clinical observations and measurements as part of routine husbandry procedures or study protocols to monitor animal welfare. Although frequent assessments ensure the timely identification of animals with declining health, increased handling can result in additional stress on the animal and increased study variability. We investigated whether automated alerting regarding changes in behavior and physiology can complement existing welfare assessments to improve the identification of animals in pain or distress. Using historical data collected from a diverse range of therapeutic models, we developed algorithms that detect changes in motion and breathing rate frequently associated with sick animals but rare in healthy controls. To avoid introducing selec- tion bias, we evaluated the performance of these algorithms by using retrospective analysis of all studies occurring over a 31-d period in our vivarium. Analyses revealed that the majority of the automated alerts occurred prior to or simultaneously with technicians' observations of declining health in animals. Additional analyses performed across the entire duration of 2 studies (animal models of rapid aging and lung metastasis) demonstrated the sensitivity, accuracy, and utility of automated alerting for detecting unhealthy subjects and those eligible for humane endpoints. The percentage of alerts per total subject days ranged between 0% and 24%, depending on the animal model. Automated alerting effectively complements standard clinical observations to enhance animal welfare and promote responsible scientific advancement.

Temporal dissociation of phencyclidine: Induced locomotor and social alterations in rats using an automated homecage monitoring system - implications for the 3Rs and preclinical drug discovery

BACKGROUND

Rodent behavioural assays are widely used to delineate the mechanisms of psychiatric disorders and predict the efficacy of drug candidates. Conventional behavioural paradigms are restricted to short time windows and involve transferring animals from the homecage to unfamiliar apparatus which induces stress. Additionally, factors including environmental perturbations, handling and the presence of an experimenter can impact behaviour and confound data interpretation. To improve welfare and reproducibility these issues must be resolved. Automated homecage monitoring offers a more ethologically relevant approach with reduced experimenter bias.

AIM

To evaluate the effectiveness of an automated homecage system at detecting locomotor and social alterations induced by phencyclidine (PCP) in group-housed rats. PCP is an N-methyl-D-aspartate (NMDA) receptor antagonist commonly utilised to model aspects of schizophrenia.

METHODS

Rats housed in groups of three were implanted with radio frequency identification (RFID) tags. Each homecage was placed over a RFID reader baseplate for the automated monitoring of the social and locomotor activity of each individual rat. For all rats, we acquired homecage data for 24 h following administration of both saline and PCP (2.5 mg/kg).

RESULTS

PCP resulted in significantly increased distance travelled from 15 to 60 min post injection. Furthermore, PCP significantly enhanced time spent isolated from cage mates and this asociality occured from 60 to 105 min post treatment.

CONCLUSIONS

Unlike conventional assays, in-cage monitoring captures the temporal duration of drug effects on multiple behaviours in the same group of animals. This approach could benefit psychiatric preclinical drug discovery through improved welfare and increased between-laboratory replicability.

Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and repeat or build upon the work of other researchers. The ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) were developed in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. Despite widespread endorsement by the scientific community, the impact of ARRIVE on the transparency of reporting in animal research publications has been limited. We have revised the ARRIVE guidelines to update them and facilitate their use in practice. The revised guidelines are published alongside this paper. This explanation and elaboration document was developed as part of the revision. It provides further information about each of the 21 items in ARRIVE 2.0, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples of good reporting from the published literature. This document also covers advice and best practice in the design and conduct of animal studies to support researchers in improving standards from the start of the experimental design process through to publication.

Assessing the Activity of Individual Group-Housed Broilers Throughout Life using a Passive Radio Frequency Identification System-A Validation Study

Individual data are valuable for assessing the health, welfare and performance of broilers. In particular, data on the first few days of life are needed to study the predictive value of traits recorded early in life for later life performance. However, broilers are generally kept in groups, which hampers individual identification and monitoring of animals. Sensor technologies may aid in identifying and monitoring individual animals. In this study, a passive radio frequency identification (RFID) system was implemented to record broiler activity, in combination with traditional video recordings. The two main objectives were (1) to validate the output of the RFID system by comparing it to the recorded locations on video, and (2) to assess whether the number of antennas visited per unit time could serve as a measure of activity, by comparing it to the distance recorded on video and to the distance moved as recorded using a validated ultra-wideband (UWB) tracking system. The locations recorded by the RFID system exactly matched the video in 62.5% of the cases, and in 99.2% of the cases when allowing for a deviation of one antenna grid cell. There were moderately strong Spearman rank correlations between the distance recorded with the RFID system and the distance recorded from video (r_s = 0.82) and between UWB and RFID (r_s = 0.70) in approximately one-hour recordings, indicating that the RFID system can adequately track relative individual broiler activity, i.e., the activity level of a broiler in comparison to its group members. As the RFID tags are small and lightweight, the RFID system is well suited for monitoring the individual activity of group-housed broilers throughout life.

INSPIRE: A European training network to foster research and training in cardiovascular safety pharmacology

Safety pharmacology is an essential part of drug development aiming to identify, evaluate and investigate undesirable pharmacodynamic properties of a drug primarily prior to clinical trials. In particular, cardiovascular adverse drug reactions (ADR) have halted many drug development programs. Safety pharmacology has successfully implemented a screening strategy to detect cardiovascular liabilities, but there is room for further refinement. In this setting, we present the INSPIRE project, a European Training Network in safety pharmacology for Early Stage Researchers (ESRs), funded by the European Commission's H2020-MSCA-ITN programme. INSPIRE has recruited 15 ESR fellows that will conduct an individual PhD-research project for a period of 36 months. INSPIRE aims to be complementary to ongoing research initiatives. With this as a goal, an inventory of collaborative research initiatives in safety pharmacology was created and the ESR projects have been designed to be complementary to this roadmap. Overall, INSPIRE aims to improve cardiovascular safety evaluation, either by investigating technological innovations or by adding mechanistic insight in emerging safety concerns, as observed in the field of cardio-oncology. Finally, in addition to its hands-on research pillar, INSPIRE will organize a number of summer schools and workshops that will be open to the wider community as well. In summary, INSPIRE aims to foster both research and training in safety pharmacology and hopes to inspire the future generation of safety scientists.

Stress in groups: Lessons from non-traditional rodent species and housing models

A major feature of life in groups is that individuals experience social stressors of varying intensity and type. Social stress can have profound effects on health, social behavior, and ongoing relationships. Relationships can also buffer the experience of exogenous stressors. Social stress has most commonly been investigated in dyadic contexts in mice and rats that produce intense stress. Here we review findings from studies of diverse rodents and non-traditional group housing paradigms, focusing on laboratory studies of mice and rats housed in visible burrow systems, prairie and meadow voles, and mole-rats. We argue that the use of methods informed by the natural ecology of rodent species provides novel insights into the relationship between social stress, behavior and physiology. In particular, we describe how this ethologically inspired approach reveals how individuals vary in their experience of and response to social stress, and how ecological and social contexts impact the effects of stress. Social stress induces adaptive changes, as well as long-term disruptive effects on behavior and physiology.

Repeatability analysis improves the reliability of behavioral data

Reliability of data has become a major concern in the course of the reproducibility crisis. Especially when studying animal behavior, confounding factors such as novelty of the test apparatus can lead to a wide variability of data which may mask treatment effects and consequently lead to misinterpretation. Habituation to the test situation is a common practice to circumvent novelty induced increases in variance and to improve the reliability of the respective measurements. However, there is a lack of published empirical knowledge regarding reasonable habituation procedures and a method validation seems to be overdue. This study aimed at setting up a simple strategy to increase reliability of behavioral data measured in a familiar test apparatus. Therefore, exemplary data from mice tested in an Open Field (OF) arena were used to elucidate the potential of habituation and how reliability of measures can be confirmed by means of a repeatability analysis using the software R. On seven consecutive days, male C57BL/6J, BALB/cJ and 129S1/SvImJ mice were tested in an OF arena once daily and individual mouse behavior was recorded. A repeatability analysis was conducted with regard to repeated trials of habituation. Our data analysis revealed that monitoring animal behavior during habituation is important to determine when individual differences of the measurements are stable. Repeatability values from distance travelled and average activity increased over the habituation period, revealing that around 60% of the variance of the data can be explained by individual differences between mice. The first day of habituation was significantly different from the following 6 days. A three-day habituation period appeared to be sufficient in this study. Overall, these results emphasize the importance of habituation and in depth analysis of habituation data to define the correct starting point of the experiment for improving the reliability and reproducibility of experimental data.

Novel Activity Detection Algorithm to Characterize Spontaneous Stepping During Multimodal Spinal Neuromodulation After Mid-Thoracic Spinal Cord Injury in Rats

A mid-thoracic spinal cord injury (SCI) severely impairs activation of the lower limb sensorimotor spinal networks, leading to paralysis. Various neuromodulatory techniques including electrical and pharmacological activation of the spinal networks have been successful in restoring locomotor function after SCI. We hypothesized that the combination of self-training in a natural environment with epidural stimulation (ES), quipazine (Quip), and strychnine (Strych) would result in greater activity in a cage environment after paralysis compared to either intervention alone. To assess this, we developed a method measuring and characterizing the chronic EMG recordings from tibialis anterior (TA) and soleus (Sol) muscles while rats were freely moving in their home cages. We then assessed the relationship between the change in recorded activity over time and motor-evoked potentials (MEPs) in animals receiving treatments. We found that the combination of ES, Quip, and Strych (sqES) generated the greatest level of recovery followed by ES + Quip (qES) while ES + Strych (sES) and ES alone showed least improvement in recorded activity. Further, we observed an exponential relationship between late response (LR) component of the MEPs and spontaneously generated step-like activity. Our data demonstrate the feasibility and potential importance of quantitatively monitoring mechanistic factors linked to activity-dependence in response to combinatorial interventions compared to individual therapies after SCI.

Assessing Affective State in Laboratory Rodents to Promote Animal Welfare-What Is the Progress in Applied Refinement Research?

An animal's capacity to suffer is a prerequisite for any animal welfare concern, and the minimization of suffering is a key aim of refinement research. In contrast to the traditional focus on avoiding or reducing negative welfare states, modern animal welfare concepts highlight the importance of promoting positive welfare states in laboratory animals. Reliable assessments of affective states, as well as the knowledge of how to elicit positive affective states, are central to this concept. Important achievements have been made to assess pain and other negative affective states in animals in the last decades, but it is only recently that the neurobiology of positive emotions in humans and animals has been gaining more interest. Thereby, the need for promotion of positive affective states for laboratory animals is gaining more acceptance, and methods allowing the assessment of affective states in animals have been increasingly introduced. In this overview article, we present common and emerging methods to assess affective states in laboratory rodents. We focus on the implementation of these methods into applied refinement research to identify achieved progress as well as the future potential of these tools to improve animal welfare in animal-based research.

Low-cost solution for rodent home-cage behaviour monitoring

In the current research on measuring complex behaviours/phenotyping in rodents, most of the experimental design requires the experimenter to remove the animal from its home-cage environment and place it in an unfamiliar apparatus (novel environment). This interaction may influence behaviour, general well-being, and the metabolism of the animal, affecting the phenotypic outcome even if the data collection method is automated. Most of the commercially available solutions for home-cage monitoring are expensive and usually lack the flexibility to be incorporated with existing home-cages. Here we present a low-cost solution for monitoring home-cage behaviour of rodents that can be easily incorporated to practically any available rodent home-cage. To demonstrate the use of our system, we reliably predict the sleep/wake state of mice in their home-cage using only video. We validate these results using hippocampal local field potential (LFP) and electromyography (EMG) data. Our approach provides a low-cost flexible methodology for high-throughput studies of sleep, circadian rhythm and rodent behaviour with minimal experimenter interference.

Studies on long term behavioural changes in group-housed rat models of brain and spinal cord injury using an automated home cage recording system

BACKGROUND

Neurotrauma patients face major neurological sequelae. The failure in the preclinical-to-clinical translation of candidate therapies could be due to poor evaluation of rodent behaviours after neurotrauma.

NEW METHOD

A home cage automated system was used to study the long term behaviour of individual rats with traumatic brain injury (TBI), spinal cord injury (SCI) and non-CNS injured controls, whilst group-housed in their home cages. Naïve rats were used as baseline controls. Automated locomotor activity and body temperature recordings were carried out 24 h /day for 3 days/week during 12 weeks post-injury. Behavioural patterns, including aggression, rearing, grooming, feeding and drinking were analysed from automated video recordings during week 1, 6 and 12.

RESULTS

SCI animals showed a lower locomotor activity compared to TBI or control animals during light and dark phases. TBI animals showed a higher aggression during the dark phase in the first week post-injury compared to SCI or control animals. Individual grooming and rearing were reduced in SCI animals compared to TBI and control animals in the first week post-injury during the dark phase. No differences in drinking or feeding were detected between groups. Locomotor activity did not differ between naïve male and female rats, but body temperature differ between light and dark phases for both.

STANDARD METHODS

Injury severity was compared to standard SCI and TBI behaviour scores (BBB and mNSS, respectively) and histological analysis.

CONCLUSIONS

This study demonstrates the practical benefits of using a non-intrusive automated home cage recording system to observe long term individual behaviour of group-housed SCI and TBI rats.

Replacement, Refinement, and Reduction in Animal Studies With Biohazardous Agents

Animal models are critical to the advancement of our knowledge of infectious disease pathogenesis, diagnostics, therapeutics, and prevention strategies. The use of animal models requires thoughtful consideration for their well-being, as infections can significantly impact the general health of an animal and impair their welfare. Application of the 3Rs—replacement, refinement, and reduction—to animal models using biohazardous agents can improve the scientific merit and animal welfare. Replacement of animal models can use in vitro techniques such as cell culture systems, mathematical models, and engineered tissues or invertebrate animal hosts such as amoeba, worms, fruit flies, and cockroaches. Refinements can use a variety of techniques to more closely monitor the course of disease. These include the use of biomarkers, body temperature, behavioral observations, and clinical scoring systems. Reduction is possible using advanced technologies such as in vivo telemetry and imaging, allowing longitudinal assessment of animals during the course of disease. While there is no single method to universally replace, refine, or reduce animal models, the alternatives and techniques discussed are broadly applicable and they should be considered when infectious disease animal models are developed.

Maternal immune activation: reporting guidelines to improve the rigor, reproducibility, and transparency of the model

The 2017 American College of Neuropychopharmacology (ACNP) conference hosted a Study Group on 4 December 2017, Establishing best practice guidelines to improve the rigor, reproducibility, and transparency of the maternal immune activation (MIA) animal model of neurodevelopmental abnormalities. The goals of this session were to (a) evaluate the current literature and establish a consensus on best practices to be implemented in MIA studies, (b) identify remaining research gaps warranting additional data collection and lend to the development of evidence-based best practice design, and (c) inform the MIA research community of these findings. During this session, there was a detailed discussion on the importance of validating immunogen doses and standardizing the general design (e.g., species, immunogenic compound used, housing) of our MIA models both within and across laboratories. The consensus of the study group was that data does not currently exist to support specific evidence-based model selection or methodological recommendations due to lack of consistency in reporting, and that this issue extends to other inflammatory models of neurodevelopmental abnormalities. This launched a call to establish a reporting checklist focusing on validation, implementation, and transparency modeled on the ARRIVE Guidelines and CONSORT (scientific reporting guidelines for animal and clinical research, respectively). Here we provide a summary of the discussions in addition to a suggested checklist of reporting guidelines needed to improve the rigor and reproducibility of this valuable translational model, which can be adapted and applied to other animal models as well.

Automated monitoring of mouse feeding and body weight for continuous health assessment

Routine health assessment of laboratory rodents can be improved using automated home cage monitoring. Continuous, non-stressful, objective assessment of rodents unaware that they are being watched, including during their active dark period, reveals behavioural and physiological changes otherwise invisible to human caretakers. We developed an automated feeder that tracks feed intake, body weight, and physical appearance of individual radio frequency identification-tagged mice in social home cages. Here, we experimentally induce illness via lipopolysaccharide challenge and show that this automated tracking apparatus reveals sickness behaviour (reduced food intake) as early as 2-4 hours after lipopolysaccharide injection, whereas human observers conducting routine health checks fail to detect a significant difference between sick mice and saline-injected controls. Continuous automated monitoring additionally reveals pronounced circadian rhythms in both feed intake and body weight. Automated home cage monitoring is a non-invasive, reliable mode of health surveillance allowing caretakers to more efficiently detect and respond to early signs of illness in laboratory rodent populations.

Pharmacological validation of individual animal locomotion, temperature and behavioural analysis in group-housed rats using a novel automated home cage analysis system: A comparison with the modified Irwin test

BACKGROUND

The ActualHCA™ system continuously monitors the activity, temperature and behavior of group-housed rats without invasive surgery. The system was validated to detect the contrasting effects of sedative and stimulant test agents (chlorpromazine, clonidine and amphetamine), and compared with the modified Irwin test (mIT) with rectal temperature measurements.

METHODS

Six male Han Wistar rats per group were used to assess each test agent and vehicle controls in separate ActualHCA™ recordings and mIT. The mIT was undertaken at 15, 30 mins, 1, 2, 4 and 24 h post-dose. ActualHCA™ recorded continuously for 24 h post-dose under 3 experimental conditions: dosed during light phase, dark phase, and light phase with a scheduled cage change at the time of peak effects determined by mIT.

RESULTS

ActualHCA™ detected an increase stimulated activity from the cage change at 1-2 h post-dose which was obliterated by chlorpromazine and clonidine. Amphetamine increased activity up to 4 h post-dose in all conditions. Temperature from ActualHCA™ was affected by all test agents in all conditions. The mIT showed effects on all 3 test agents up to 4 h post-dose, with maximal effects at 1-2 h post-dose. The maximal effects on temperature from ActualHCA™ differed from mIT. Delayed effects on activity were detected by ActualHCA™, but not on mIT.

CONCLUSIONS

Continuous monitoring has the advantage of capturing effects over time that may be missed with manual tests using pre-determined time points. This automated behavioural system does not replace the need for conventional methods but could be implemented simultaneously to improve our understanding of behavioural pharmacology.