Biology subjects

Roche, D. G.

Publications and source records attributed to Roche, D. G..

5 recordsLinked to original sources

bioRxiv2026

TracktorLive: an integrated real-time object tracking and response system

Real-time tracking and automated response systems are essential for standardising experiments, reducing observer bias, and improving reproducibility in studies of movement and behaviour. However, existing solutions face significant challenges: AI-based tracking systems require expensive hardware and impose computational delays, creating challenges for closed-loop experiments; existing real-time tracking tools lack standardised implementations for response delivery; and steep learning curves limit accessibility for users without programming or computer vision expertise. Here, we introduce TracktorLive, an open-source Python package designed to overcome these challenges through concurrency and a modular, cassette-based architecture. TracktorLive leverages traditional computer vision techniques to perform image-based object detection without the need for expensive hardware or deep learning. By parallelizing object tracking and response delivery into separate, concurrent server and client processes, the software minimizes frame processing time, enabling rapid, real-time analysis and response delivery. User-friendly cassettes--portable code snippets that can be copy-pasted into scripts--enable users with minimal programming experience to implement complex workflows for use in experiments and practical applications. We demonstrate TracktorLives utility through several applications, including microcontroller-based stimulus delivery for location-dependent manipulations; conditional video recording that activates only during events of interest; kinematic-based response triggering using real-time velocity computations; and multi-cassette experimental designs combining multiple functionalities. Detailed tutorials are provided to familiarize users with TracktorLives operation and functionality, and a growing library of cassettes supports diverse applications for processing both real-time and pre-recorded video. We validated the software by comparing its response timing to human experimenters in a stimulus delivery task involving two fish species, where TracktorLive demonstrated consistently higher accuracy and lower variability, particularly for fast-moving subjects. Beyond experimental biology, TracktorLives unique architecture and versatility could support many different applications in fields ranging from neuroscience to wildlife management. As an open-source software combining accessibility, modularity, and computational efficiency, TracktorLive can help democratize real-time tracking and automated response systems across disciplines.

animal behavior and cognition↗

bioRxiv2023

How prior and p-value heuristics are used when interpreting data

Scientific conclusions are based on the ways that researchers interpret data, a process that is shaped by psychological and cultural factors. When researchers use shortcuts known as heuristics to interpret data, it can sometimes lead to errors. To test the use of heuristics, we surveyed 623 researchers in biology and asked them to interpret scatterplots that showed ambiguous relationships, altering only the labels on the graphs. Our manipulations tested the use of two heuristics based on major statistical frameworks: (1) the strong prior heuristic, where a relationship is viewed as stronger if it is expected a priori, following Bayesian statistics, and (2) the p-value heuristic, where a relationship is viewed as stronger if it is associated with a small p-value, following null hypothesis statistical testing. Our results show that both the strong prior and p-value heuristics are common. Surprisingly, the strong prior heuristic was more prevalent among inexperienced researchers, whereas its effect was diminished among the most experienced biologists in our survey. By contrast, we find that p-values cause researchers at all levels to report that an ambiguous graph shows a strong result. Together, these results suggest that experience in the sciences may diminish a researchers Bayesian intuitions, while reinforcing the use of p-values as a shortcut for effect size. Reform to data science training in STEM could help reduce researchers reliance on error-prone heuristics. Significance StatementScientific researchers must interpret data and statistical tests to draw conclusions. When researchers use shortcuts known as heuristics, it can sometimes lead to errors. To test how this occurs, we asked biologists to interpret graphs that showed an ambiguous relationship between two variables, and report whether the relationship was strong, weak, or absent. We altered features of the graph to test whether prior expectations or a statistic called the p-value could influence their interpretations. Our results indicate that both prior expectations and p-values can increase the probability that researchers will report that ambiguous data shows a strong result. These findings suggest that current training and research practices promote the use of error-prone shortcuts in decision-making.

scientific communication and education↗

bioRxiv2022

Increased parasite load is associated with reduced metabolic rates and escape responsiveness in pumpkinseed sunfish host

Wild animals have parasites that can compromise their physiological and/or behavioural performance. Yet, the extent to which parasite load is related to intraspecific variation in performance traits within wild populations remains relatively unexplored. We used pumpkinseed sunfish (Lepomis gibbosus) and their endoparasites as a model system to explore the effects of infection load on host aerobic metabolism and escape performance. Metabolic traits (standard and maximum metabolic rates, aerobic scope) and fast-start escape responses following a simulated aerial attack by a predator (responsiveness, response latency, and escape distance) were measured in fish from across a gradient of visible (i.e. trematodes causing black spot disease counted on fish surfaces) and non-visible (i.e. cestodes in fish abdominal cavity counted post-mortem) endoparasite infection. We found that a higher infection load of non-visible endoparasites was related to lower standard and maximum metabolic rates, but not aerobic scope in fish. Non-visible endoparasite infection load was also related to decreased responsiveness of the host to a simulated aerial attack. Visible endoparasites were not related to changes in metabolic traits nor fast-start escape responses. Our results suggest that infection with parasites that are inconspicuous to researchers can result in intraspecific variation in physiological and behavioral performance in wild populations, highlighting the need to more explicitly acknowledge and account for the role played by natural infections in studies of wild animal performance.

physiology↗

bioRxiv2018

Minimum Information for Reusable Arthropod Abundance Data (MIReAAD)

Introduction Introduction Discussion Conclusion References Arthropods play a dominant role in the dynamics of practically all natural and human-modified terrestrial ecosystems1-3, and have significant economic and health effects. For example, certain insects provide significant economic benefits (e.g. pollination) exceeding $57 billion a year to the United States alone4. Meanwhile, invasive insects cost an estimated $70 billion dollars per year globally5 and insect pests may reduce agricultural harvests by up to 16%, with an equal amount of further losses of harvested goods6. Particularly noteworthy is a subset of arthropods that are disease vectors, transmitting pathogens to and between animals as well as plan ...

ecology↗

bioRxiv2018

Tracktor: image-based automated tracking of animal movement and behaviour

1. Automated movement tracking is essential for high-throughput quantitative analyses of the behaviour and kinematics of organisms. Automated tracking also improves replicability by avoiding observer biases and allowing reproducible workflows. However, few automated tracking programs exist that are open access, open source, and capable of tracking unmarked organisms in noisy environments.\n\n2. Tracktor is an image-based tracking freeware designed to perform single-object tracking in noisy environments, or multi-object tracking in uniform environments while maintaining individual identities. Tracktor is code-based but requires no coding skills other than the user being able to specify tracking parameters in a designated location, much like in a graphical user interface (GUI). The installation and use of the software is fully detailed in a user manual.\n\n3. Through four examples of common tracking problems, we show that Tracktor is able to track a variety of animals in diverse conditions. The main strengths of Tracktor lie in its ability to track single individuals under noisy conditions (e.g. when the object shape is distorted), its robustness to perturbations (e.g. changes in lighting conditions during the experiment), and its capacity to track multiple individuals while maintaining their identities. Additionally, summary statistics and plots allow measuring and visualizing common metrics used in the analysis of animal movement (e.g. cumulative distance, speed, acceleration, activity, time spent in specific areas, distance to neighbour, etc.).\n\n4. Tracktor is a versatile, reliable, easy-to-use automated tracking software that is compatible with all operating systems and provides many features not available in other existing freeware. Access Tracktor and the complete user manual here: https://github.com/vivekhsridhar/tracktor

animal behavior and cognition↗