B-SOiD, an open-source unsupervised algorithm for identification and fast prediction of behaviors.

Studying naturalistic animal behavior remains a difficult objective. Recent machine learning advances have enabled limb localization; however, extracting behaviors requires ascertaining the spatiotemporal patterns of these positions. To provide a link from poses to actions and their kinematics, we developed B-SOiD - an open-source, unsupervised algorithm that identifies behavior without user bias. By training a machine classifier on pose pattern statistics clustered using new methods, our approach achieves greatly improved processing speed and the ability to generalize across subjects or labs. Using a frameshift alignment paradigm, B-SOiD overcomes previous temporal resolution barriers. Using only a single, off-the-shelf camera, B-SOiD provides categories of sub-action for trained behaviors and kinematic measures of individual limb trajectories in any animal model. These behavioral and kinematic measures are difficult but critical to obtain, particularly in the study of rodent and other models of pain, OCD, and movement disorders.

Two open source designs for a low-cost operant chamber using Raspberry Pi™.

After almost a century of use and development, operant chambers remain a significant financial investment for scientists. Small powerful single-board computers such as the Raspberry Pi™ offer researchers a low-cost alternative to expensive operant chambers. In this paper, we describe two new operant chambers, one using nose-poke ports as operanda and another using a touchscreen. To validate the chamber designs, rats learned to perform both visual discrimination and delayed alternation tasks in each chamber. Designs and codes are open source and serve as a starting point for researchers to develop behavioral experiments or educational demonstrations.

The "House of Quality for Behavioral Science"-a user-centered tool to design behavioral interventions.

Within the behavioral field, a plethora of conceptual frameworks and tools have been developed to improve transition from efficacy to effectiveness trials; however, they are limited in their ability to support new, iterative intervention design decision-making methodologies beyond traditional randomized controlled trial design. Emerging theories suggest that researchers should employ engineering based user-centered design (UCD) methods to support more iterative intervention design decision-making in the behavioral field. We present, an adaptation of a UCD tool used in the engineering field-the Quality Function Deployment "House of Quality" correlation matrix, to support iterative intervention design decision-making and documentation for multicomponent behavioral interventions and factorial trial designs. We provide a detailed description of the adapted tool-"House of Quality for Behavioral Science", and a step-by-step use-case scenario to demonstrate the early identification of intervention flaws and prioritization of requirements. Four intervention design flaws were identified via the tool application. Completion of the relationship correlation matrix increased requirement ranking variance for the researcher (σ2 = 0.47 to 7.19) and participant (σ2 = 0.56 to 3.89) perspective. Requirement prioritization (ranking) was facilitated by factoring in the strength of the correlation between each perspective and corresponding importance. A correlational matrix tool such as the "House of Quality for Behavioral Science" may provide a structured, UCD approach that balances researcher and participant needs and identifies design flaws for pragmatic behavioral intervention design. This tool may support iterative design decision-making for multicomponent and factorial trial designs.

The Hillary Climber trumps manual testing: an automatic system for studying Drosophila climbing.

Climbing or negative geotaxis is an innate behavior of the fruit fly Drosophila melanogaster. There has been considerable interest in using this simple behavior to gain insights into the changes in brain function associated with aging, influence of drugs, mutated genes, and human neurological disorders. At present, most climbing tests are conducted manually and there is a lack of a simple and automatic device for repeatable and quantitative analysis of fly climbing behavior. Here we present an automatic fly climbing system, named the Hillary Climber (after Sir Edmund Hillary), that can replace the human manual tapping of vials with a mechanical tapping mechanism to provide more consistent force and reduce variability between the users and trials. Following tapping the HC records fly climbing, tracks the fly climbing path, and analyzes the velocity of individual flies and the percentage of successful climbers. The system is relatively simple to build, easy to operate, and efficient and reliable for climbing tests.

An experimental validation method for questioning techniques that assess sensitive issues.

Studies addressing sensitive issues often yield distorted prevalence estimates due to socially desirable responding. Several techniques have been proposed to reduce this bias, including indirect questioning, psychophysiological lie detection, and bogus pipeline procedures. However, the increase in resources required by these techniques is warranted only if there is a substantial increase in validity as compared to direct questions. Convincing demonstration of superior validity necessitates the availability of a criterion reflecting the "true" prevalence of a sensitive attribute. Unfortunately, such criteria are notoriously difficult to obtain, which is why validation studies often proceed indirectly by simply comparing estimates obtained with different methods. Comparative validation studies, however, provide weak evidence only since the exact increase in validity (if any) remains unknown. To remedy this problem, we propose a simple method that allows for measuring the "true" prevalence of a sensitive behavior experimentally. The basic idea is to elicit normatively problematic behavior in a way that ensures conclusive knowledge of the prevalence rate of this behavior. This prevalence measure can then serve as an external validation criterion in a second step. An empirical demonstration of this method is provided.

PandaEPL: a library for programming spatial navigation experiments.

Recent advances in neuroimaging and neural recording techniques have enabled researchers to make significant progress in understanding the neural mechanisms underlying human spatial navigation. Because these techniques generally require participants to remain stationary, computer-generated virtual environments are used. We introduce PandaEPL, a programming library for the Python language designed to simplify the creation of computer-controlled spatial-navigation experiments. PandaEPL is built on top of Panda3D, a modern open-source game engine. It allows users to construct three-dimensional environments that participants can navigate from a first-person perspective. Sound playback and recording and also joystick support are provided through the use of additional optional libraries. PandaEPL also handles many tasks common to all cognitive experiments, including managing configuration files, logging all internal and participant-generated events, and keeping track of the experiment state. We describe how PandaEPL compares with other software for building spatial-navigation experiments and walk the reader through the process of creating a fully functional experiment.

A cold radial maze for long-lasting spatial memory in mice.

Here we report the establishment of a novel spatial learning and memory test called the cold radial maze. It is specifically designed for mice, with all conditions tailored to their natural behaviors. The cold radial maze is a dry-land test with easy-to-measure variables that relies on a consistent motivation system and limits the moderately adverse experience to the duration of testing. Training on this maze produces a long-lasting, resistant, and reversible spatial memory in mice in a reproducible way, without introducing undesirable side effects typically produced in other spatial learning tests. This novel behavioral technique may prove useful in studying mouse models of memory impairment-associated human conditions.

A system utilizing radio frequency identification (RFID) technology to monitor individual rodent behavior in complex social settings.

Pre-clinical investigation of human CNS disorders relies heavily on mouse models. However these show low predictive validity for translational success to humans, partly due to the extensive use of rapid, high-throughput behavioral assays. Improved assays to monitor rodent behavior over longer time scales in a variety of contexts while still maintaining the efficiency of data collection associated with high-throughput assays are needed. We developed an apparatus that uses radio frequency identification device (RFID) technology to facilitate long-term automated monitoring of the behavior of mice in socially or structurally complex cage environments. Mice that were individually marked and implanted with transponders were placed in pairs in the apparatus, and their locations continuously tracked for 24 h. Video observation was used to validate the RFID readings. The apparatus and its associated software accurately tracked the locations of all mice, yielding information about each mouse's location over time, its diel activity patterns, and the amount of time it was in the same location as the other mouse in the pair. The information that can be efficiently collected in this apparatus has a variety of applications for pre-clinical research on human CNS disorders, for example major depressive disorder and autism spectrum disorder, in that it can be used to quantify validated endophenotypes or biomarkers of these disorders using rodent models. While the specific configuration of the apparatus described here was designed to answer particular experimental questions, it can be modified in various ways to accommodate different experimental designs.

A mechatronic platform for behavioral analysis on nonhuman primates.

In this work we present a new mechatronic platform for measuring behavior of nonhuman primates, allowing high reprogrammability and providing several possibilities of interactions. The platform is the result of a multidisciplinary design process, which has involved bio-engineers, developmental neuroscientists, primatologists, and roboticians to identify its main requirements and specifications. Although such a platform has been designed for the behavioral analysis of capuchin monkeys (Cebus apella), it can be used for behavioral studies on other nonhuman primates and children. First, a state-of-the-art principal approach used in nonhuman primate behavioral studies is reported. Second, the main advantages of the mechatronic approach are presented. In this section, the platform is described in all its parts and the possibility to use it for studies on learning mechanism based on intrinsic motivation discussed. Third, a pilot study on capuchin monkeys is provided and preliminary data are presented and discussed.

Box for interaction with objects (BIO): a new device to synchronize the presentation of objects with electrophysiological recordings.

Brain event-related potentials are a useful tool for investigating visual processing and action planning. This technique requires extremely accurate synchronization of stimulus delivery with recordings. The precision of the onset time of visual stimulus delivery is a major challenge when attempting to use real, three-dimensional objects as stimuli. Here, we present an innovative device, the "box for interaction with objects" (BIO), that is designed to synchronize the presentation of objects with electroencephalographic (EEG) recordings. To reach the required resolution of stimulus-onset timing, the BIO system features an interface with reflective glass and light-emitting diodes (LEDs). When the LEDs inside the BIO are turned on, the object inside becomes visible, and a synchronizing pulse is sent to the recording systems. The BIO was tested in a motivational study that focused on visual and motor event-related potentials. EEG signals were recorded during the presentation of an emotion-laden object that could be grasped and brought close to the participant's chest. BIO successfully synchronized the appearance of a three-dimensional object with EEG recordings, which would allow for an analysis of visual and motor event-related potentials in the same experiment. The BIO device, through a high-quality psychophysiological approach, offers a new perspective for the study of the motivational factors that drive actions toward relevant stimuli.

SenseCam: a wearable camera that stimulates and rehabilitates autobiographical memory.

SenseCam is a wearable digital camera that captures an electronic record of the wearer's day. It does this by automatically recording a series of still images through its wide-angle lens, and simultaneously capturing a log of data from a number of built-in electronic sensors. Subsequently reviewing a sequence of images appears to provide a powerful autobiographical memory cue. A preliminary evaluation of SenseCam with a patient diagnosed with severe memory impairment was extremely positive; periodic review of images of events recorded by SenseCam resulted in significant recall of those events. Following this, a great deal of work has been undertaken to explore this phenomenon and there are early indications that SenseCam technology may be beneficial to a variety of patients with physical and mental health problems, and is valuable as a tool for investigating normal memory through behavioural and neuroimaging means. Elsewhere, it is becoming clear that judicious use of SenseCam could significantly impact the study of human behaviour. Meanwhile, research and development of the technology itself continues with the aim of providing robust hardware and software tools to meet the needs of clinicians, patients, carers, and researchers. In this paper we describe the history of SenseCam, and the design and operation of the SenseCam device and the associated viewing software, and we discuss some of the ongoing research questions being addressed with the help of SenseCam.

From foraging to operant conditioning: a new computer-controlled Skinner box to study free-flying nectar gathering behavior in bees.

The experimental study of nectar foraging behavior in free-flying bees requires the use of automated devices to control solution delivery and measure dependent variables associated with nectar gathering. We describe a new computer-controlled artificial flower and provide calibration data to measure the precision of the apparatus. Our device is similar to a "Skinner box" and we present data of an experiment where various amounts of a 50% sugar solution are presented randomly to individual bees. These data show large individual variations among subjects across several dependent variables. Finally, we discuss possible applications of our device to problems in behavioral sciences.

Chronic infusion of PCP via osmotic mini-pumps: a new rodent model of cognitive deficit in schizophrenia characterized by impaired attentional set-shifting (ID/ED) performance.

The identification of animal disease-like models for cognitive symptoms in schizophrenia is of central importance to the successful development of pharmacological therapies for psychosis resulting in a functional outcome in patients. Executive function is one of the most severely affected cognitive domains in schizophrenia that remains inadequately treated by existing therapies. The rat attentional set-shifting (or intra-dimensional-extra-dimensional (ID/ED)) task has been developed to test executive function in rodents and successful translation of pre-clinical data into the clinical setting now depends on the identification of a predictive animal disease-like model. The present study investigates whether a continuous 14-day mini-pump infusion of the non-competitive NMDA receptor antagonist phencyclidine (PCP) leads to a deficit in the ID/ED task, and subsequently evaluates the effect of modafinil in this model. Lister hooded rats were implanted subcutaneously with osmotic mini-pumps containing saline or PCP (15 mg/kg/day) for 14 days followed by a 7-day drug-free recovery phase. Rats were then tested in the ID/ED task following an acute injection of either vehicle or modafinil. PCP-treated animals displayed a selective deficit at the ED shift stage resembling that observed in schizophrenic patients. This deficit was reversed by an acute injection of modafinil. The PCP-induced impairment and its reinstatement by modafinil are quantitatively and qualitatively similar to that described earlier by our group following sub-chronic intraperitoneal PCP administration, indicative that sub-chronic PCP infusion via osmotic mini-pumps may represent an attractive alternative to the systemic administration protocols generally employed to date.

Hippocampal-dependent familiar area map supports corrective re-orientation following navigational error during pigeon homing: a GPS-tracking study.

It is hypothesized that a central role of the vertebrate hippocampal formation (HF) in behavior is the learning and operation of a map-like representation of familiar landmarks and landscape features. One critical property of a map is that it should enable an individual to re-orient towards a goal location following a navigational error. To test this prediction on a spatial scale consistent with their naturally occurring behavior, control and HF-lesioned homing pigeons were trained from two locations and then subsequently released, while carrying portable GPS-tracking devices, following a phase-shift treatment. Analyses revealed that the HF-lesioned pigeons were less successful than control pigeons in re-orienting homewards following the phase-shift-induced error in their initial orientation. Furthermore, the observation that HF-lesioned pigeons were found to routinely ignore a land-sea landscape boundary when returning home from one of the release sites suggests that coarse landscape features may be an underappreciated source of navigational information for homing pigeons. The data demonstrate that, on a scale of tens of kilometers, homing pigeons are able to learn a hippocampal-dependent, map-like representation of familiar landmarks/landscape features that can support corrective re-orientation following a navigational error.

Automated behavioral analysis of limbs' activity in the forced swim test.

The forced swim test in rodents has been widely used to evaluate potential effectiveness of antidepressant medications since it was described in 1977 by Porsolt. In this test, a rodent is placed in a water container, and its immobility time is measured. The immobility time indicates the level of inactivity, interpreted as 'hopelessness', and has been shown to decrease when the rodent is treated with antidepressant medications. The simple measure of immobility time does not take into account intermediate behaviors during testing (ranging from total immobility to extensive 'struggling' behavior) and does not show normal Gaussian distribution in tested groups of rats. We have previously developed a software allowing an observer to assign scores to the full range of intermediate behaviors by continuously reporting the motion of the limbs using a joystick. Based on the joystick score, we have now developed an automatic tool that uses computer vision algorithm (CVA) to analyze specifically the motion of the limbs and generate an objective, reproducible and automated score. In the current study we have analyzed data obtained during the swim test using the traditional immobility time, the joystick analysis and the new CVA method to test the distribution of scores in a group of 20 rats. In addition, we tested the effects of various medications using these different scoring methods. The CVA method has been validated and positively correlated with the joystick score. Data obtained using the CVA method is objective, reproducible, and significantly reduces the time required for human analysis.

A new touchscreen test of pattern separation: effect of hippocampal lesions.

Researchers are becoming increasingly interested in the role of the hippocampus in pattern separation, a process which keeps items distinct in memory. In this study, we develop and test a new automated touchscreen-based method for studying pattern separation in rodents. Rats were trained to discriminate locations on a computer screen that varied in their similarity, that is, their distance apart on the screen. Animals with lesions of the dorsal hippocampus were impaired when the locations discriminated were close together but not when they were far apart, indicating impaired pattern separation. This test provides an automated test of pattern separation, which adds to an expanding battery of cognitive tests that can be carried out using the touchscreen testing method.

A computer-assisted odorized hole-board for testing olfactory perception in mice.

The present paper describes a behavioral setup, designed and built in our laboratory, allowing the systematic and automatic recording of performances in a large number of olfactory behavioral tests. This computerized monitoring system has the capability of measuring different aspects of olfactory function in mice using different paradigms including threshold evaluation, generalization tasks, habituation/dishabituation, olfactory associative learning, short-term olfactory memory with or without a spatial component, and olfactory preferences. In this paper, we first describe the hole-board apparatus and its software and then give the experimental results obtained using this system. We demonstrate that one single, easy-to-run experimental setup is a powerful tool for the study of olfactory behavior in mice that has many advantages and broad applications.

Observer agreement for timed-event sequential data: a comparison of time-based and event-based algorithms.

Observer agreement is often regarded as the sine qua non of observational research. Cohen's kappa is a widely used index and is appropriate when discrete entities-such as a turn-of-talk or a demarcated time interval-are presented to pairs of observers to code. kappa-like statistics and agreement matrices are also used for the timed-event sequential data produced when observers first segment and then code events detected in the stream of behavior, noting onset and offset times. Such kappas are of two kinds: time-based and event-based. Available for download is a computer program (OASTES; Observer Agreement for Simulated Timed Event Sequences) that simulates the coding of observers of a stated accuracy and then computes agreement statistics for two time-based kappas (with and without tolerance) and three event-based kappas (one implemented in The Observer, one in INTERACT, and one in GSEQ). On the basis of simulation results presented here, and due to the somewhat different information provided by each, the reporting of both a time-based and an event-based kappa is recommended.

The footfault test as a screening tool in the 6-hydroxydopamine rat model of Parkinson's disease.

The administration of 6-hydroxydopamine (6-OHDA) into the nigrostriatal pathway is a rat model of Parkinson's disease (PD). The footfault test is a behavioural task in which rodents have their motor functions assessed. Here, we observed that unilaterally 6-OHDA-lesioned animals show a context-induced ipsilateral rotational behaviour when placed on the footfault apparatus for 3 min and this may be used as index to detect lesioned animals. Our results showed a sensitivity and specificity of 100% for lesions higher than 94% and 64%, respectively (ROC curve: AUC=0.988). A binary logistic regression model showed an expB=1.116 (95% CI, 1.007-1.236) and C=-9.081+/-4.554 (p=0.046) using the nigral tyrosine hidroxylase immunocontent as standard (each unit represents a 10%-lesion extension). Additionally, the footfault test was more sensitive than apomorphine challenging at 1mg/kg when these tests were carried out days apart and it was less sensitive than methylphenidate at 40 mg/kg (sign test, p<0.05). Therefore, the footfault test may be very useful in the PD animal model for screening animals since it is fast and simple and it does not require a drug to induce rotational activity.

A novel method for precisely timed stimulation of mouse whiskers in a freely moving preparation: application for delivery of the conditioned stimulus in trace eyeblink conditioning.

The somatosensory whisker pathway has been a useful system for increasing our understanding of experience-induced plasticity. However, precisely timed whisker activation in the awake freely moving mouse has been very difficult. This manuscript describes a method for construction of a whisker stimulator that can be attached to a freely moving mouse. The stimulator was used to activate the whiskers in a time-sensitive forebrain-dependent task, trace eyeblink conditioning. After repeatedly pairing whisker stimulation with delivery of a mild periorbital shock following a stimulus-free trace interval, trace-conditioned mice were able to learn the association. This study demonstrates the potential for using the whisker stimulator in time-sensitive behavioral tasks, such as trace eyeblink conditioning, thus enhancing our ability to examine experience-induced neuronal plasticity in the somatosensory whisker pathway in awake behaving rodents.