Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.03.03.641160

CHROMAS: A Computational Pipeline to Track Chromatophores and Analyze their Dynamics

Ukrow, J.·Renard, M. D. M.·Moghimi, M.·Laurent, G.
View original source ↗Export metadata ↓

Abstract

Cephalopod chromatophores are small dermal neuromuscular organs, each consisting of a pigment-containing cell and 10-20 surrounding radial muscles. Their expansions and contractions, controlled and coordinated by the brain, are used to modify the animals appearance during camouflaging and signaling. Building up on tools developed by this lab, we propose a flexible computational pipeline to track and analyse chromatophore dynamics from high-resolution videos of behaving cephalopods. This suite of functions, which we call CHROMAS, segments and classifies individual chromatophores, compensates for animal movements and skin deformations, thus enabling precise and parallel measurements of chromatophore dynamics and long-term tracking over development. A high-resolution tool for the analysis of chromatophore deformations during behavior reveals details of their motor control and thus, their likely innervation. When applied to many chromatophores simultaneously and combined with statistical and clustering tools, this analysis reveals the complex and distributed nature of the chromatophore motor units. We apply CHROMAS to the skins of the bobtail squid Euprymna berryi and the European cuttlefish Sepia officinalis, illustrating its performance with species with widely different chromatophore densities and patterning behaviors. More generally, CHROMAS offers many flexible and easily reconfigured tools to quantify the dynamics of pixelated biological patterns.

Explore related subjects

animal behavior and cognitionPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ukrow, J., Renard, M. D. M., Moghimi, M., Laurent, G.. 2025-03-07. CHROMAS: A Computational Pipeline to Track Chromatophores and Analyze their Dynamics. https://doi.org/10.1101/2025.03.03.641160

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A comparison of female competitive traits: Female aggression peaks at nest building but female song spans multiple contexts in a temperate songbird

Female-female competition is increasingly recognized as a key driver of female ornamentation, including birdsong, which often functions in intrasexual competition. However, the specific resources females use elaborate traits to compete for remain unclear. In addition, few studies have simultaneously investigated the use of multiple competitive traits in females, despite growing independent interest in these traits (e.g., female song and aggression). We investigated the competitive contexts of female song, aggression and calling behavior in northern house wrens (Troglodytes aedon) to determine which resources females compete for across the breeding season. We simulated conspecific territorial intrusions using female song at three breeding stages representing different contexts: arrival (mate and territory acquisition), nest building (nest site and breeding status defense), and egg laying (brood defense). We tested whether female song and physical aggression varied as reproductive resources shifted across the breeding cycle. Females were significantly more aggressive during nest building, showing 5.8 times greater odds of a higher-intensity aggressive response during nest building compared to arrival. Female song output was similar across early stages but declined during egg laying, though this was not statistically significant after correction for multiple comparisons and individuals varied substantially in overall singing propensity. Non-song vocalizations varied by call type and breeding stage. Calls associated with aggression occurred most frequently during nest building, consistent with peak physical aggression responses. Together, these results identify nest building as the stage of highest female aggression, consistent with heightened competition over nest cavities and associated breeding status in this cavity-nesting species. In contrast, female song occurred across all stages and appears to function in multiple competitive contexts. This study provides evidence for context and mode-specific female signaling in a temperate songbird and highlights that females strategically use aggression, calls, and song to mediate social conflict across breeding contexts.

animal behavior and cognition↗
bioRxiv2026

Tracking human foragers and their prey reveals adaptive predator-prey dynamics

Hunting for mobile prey is thought to have played a key role in hominin evolution, by providing high-quality nutrition that supported the development of the exceptionally large human brain. However, human-prey dynamics remain poorly understood because studies have not yet tracked human foragers and their prey simultaneously. Here, we employ high resolution tracking of groups of human foragers (ice-fishers) and their prey (fish shoals) to study human-prey dynamics. Our results show that foragers adaptively combined personal and social information in deciding where to forage and for how long, closely matching the prey distribution. Prey responded dynamically to human exploitation, showing increased attraction to fishing activity, alongside decreased biting probability. Furthermore, we found that foragers adaptively relied on memory, preferentially returning to areas with high prey presence, particularly when their current return rate was low. Our results show how human foragers overcome the challenges of extracting invisible, mobile and reactive prey by tightly tuning patch-selection, patch-leaving and patch-return decisions to the distribution and behaviour of their prey.

animal behavior and cognition↗
bioRxiv2026

4-Dimensional Chess: Acoustic Localisation Reveals Nested Spatio-temporal Strategies in an Arboreal Communication Network

1. Adaptive behavioural strategies require animals to simultaneously navigate social and ecological domains across multiple spatial and temporal scales. Although drones and computer vision have recently transformed the study of wild animal societies, many nocturnal species and those occupying structurally complex habitats remain inaccessible to these approaches, limiting our understanding of behaviour in natural settings. 2. We aimed to determine how behavioural strategies are organised across nested spatial and temporal scales within a wild communication network. 3. We used three-dimensional acoustic localisation and source separation to track individual male Hyperolius sp. A, a nocturnal African reed frog, within a natural rainforest chorus and quantify patterns of site fidelity, movement, spatial organisation, and call-timing interactions. 4. Males exhibited significant site fidelity across nights, while chorus spatial structure varied with local caller density. Within nights, individuals followed a stereotyped behavioural sequence, descending from elevated arboreal refugia before settling into lower calling positions near breeding sites. At finer temporal scales, call-timing interactions varied according to both local competitor density and the proximity of neighbouring rivals. 5. These findings demonstrate that behavioural strategies emerge across nested spatial and temporal scales and that long-term spatial positioning, short-term movement decisions, and moment-to-moment signalling interactions are tightly linked within natural communication networks. More broadly, acoustic localisation provides a powerful framework for studying behaviour in species and habitats that remain difficult to observe using conventional approaches.

animal behavior and cognition↗