Disentangling rodent behaviors to improve automated behavior recognition

Automated observation and analysis of behavior is important to facilitate progress in many fields of science. Recent developments in deep learning have enabled progress in object detection and tracking, but rodent behavior recognition struggles to exceed 75–80% accuracy for ethologically relevant behaviors. We investigate the main reasons why and distinguish three aspects of behavior dynamics that are difficult to automate. We isolate these aspects in an artificial dataset and reproduce effects with the state-of-the-art behavior recognition models. Having an endless amount of labeled training data with minimal input noise and representative dynamics will enable research to optimize behavior recognition architectures and get closer to human-like recognition performance for behaviors with challenging dynamics

CatWalk XT gait parameters: a review of reported parameters in pre-clinical studies of multiple central nervous system and peripheral nervous system disease models

Automated gait assessment tests are used in studies of disorders characterized by gait impairment. CatWalk XT is one of the first commercially available automated systems for analyzing the gait of rodents and is currently the most used system in peer-reviewed publications. This automated gait analysis system can generate a large number of gait parameters. However, this creates a new challenge in selecting relevant parameters that describe the changes within a particular disease model. Here, for the first time, we performed a multi-disorder review on published CatWalk XT data. We identify commonly reported CatWalk XT gait parameters derived from 91 peer-reviewed experimental studies in mice, covering six disorders of the central nervous system (CNS) and peripheral nervous system (PNS). The disorders modeled in mice were traumatic brain injury (TBI), stroke, sciatic nerve injury (SNI), spinal cord injury (SCI), Parkinson’s disease (PD), and ataxia. Our review consisted of parameter selection, clustering, categorization, statistical evaluation, and data visualization. It suggests that certain gait parameters serve as potential indicators of gait dysfunction across multiple disease models, while others are specific to particular models. The findings also suggest that the more site-specific the injury is, the fewer parameters are reported to characterize its gait abnormalities. This study strives to present a clearly organized picture of gait parameters used in each one of the different mouse models, potentially helping novel CatWalk XT users to apply this information to similar or related mouse models they are working on

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An Integrated System for the Automated Recording and Analysis of Insect Behavior in T-maze Arrays

Host-plant resistance to insects like thrips and aphids is a complex trait that is difficult to phenotype quickly and reliably. Here, we introduce novel hardware and software to facilitate insect choice assays and automate the acquisition and analysis of movement tracks. The hardware consists of an array of individual T-mazes allowing simultaneous release of up to 90 insect individuals from their individual cage below each T-maze with choice of two leaf disks under a video camera. Insect movement tracks are acquired with computer vision software (EthoVision) and analyzed with EthoAnalysis, a novel software package that allows for automated reporting of highly detailed behavior parameters and statistical analysis. To validate the benefits of the system we contrasted two Arabidopsis accessions that were previously analyzed for differential resistance to western flower thrips. Results of two trials with 40 T-mazes are reported and we show how we arrived at optimized settings for the different filters and statistics. The statistics are reported in terms of frequency, duration, distance and speed of behavior events, both as sum totals and event averages, and both for the total trial period and in time bins of 1 h. Also included are higher level analyses with subcategories like short-medium-long events and slow-medium-fast events. The time bins showed how some behavior elements are more descriptive of differences between the genotypes during the first hours, whereas others are constant or become more relevant at the end of an 8 h recording. The three overarching behavior categories, i.e., choice, movement, and halting, were automatically corrected for the percentage of time thrips were detected and 24 out of 38 statistics of behavior parameters differed by a factor 2–6 between the accessions. The analysis resulted in much larger contrasts in behavior traits than reported previously. Compared to leaf damage assays on whole plants or detached leaves that take a week or more to complete, results were obtained in 8 h, with more detail, fewer individuals and higher significance. The potential value of the new integrated system, named EntoLab, for discovery of genetic traits in plants and insects by high throughput screening of large populations is discussed

Reproducibility via coordinated standardization:A multi-center study in a Shank2 genetic rat model for Autism Spectrum Disorders

Inconsistent findings between laboratories are hampering scientific progress and are of increasing public concern. Differences in laboratory environment is a known factor contributing to poor reproducibility of findings between research sites, and well-controlled multisite efforts are an important next step to identify the relevant factors needed to reduce variation in study outcome between laboratories. Through harmonization of apparatus, test protocol, and aligned and non-aligned environmental variables, the present study shows that behavioral pharmacological responses in Shank2 knockout (KO) rats, a model of synaptic dysfunction relevant to autism spectrum disorders, were highly replicable across three research centers. All three sites reliably observed a hyperactive and repetitive behavioral phenotype in KO rats compared to their wild-type littermates as well as a dose-dependent phenotype attenuation following acute injections of a selective mGluR1 antagonist. These results show that reproducibility in preclinical studies can be obtained and emphasizes the need for high quality and rigorous methodologies in scientific research. Considering the observed external validity, the present study also suggests mGluR1 as potential target for the treatment of autism spectrum disorders

Automated image-based tracking and its application in ecology

The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers