CalciSeg: A versatile approach for unsupervised segmentation of calcium imaging data.

Recent advances in calcium imaging, including the development of fast and sensitive genetically encoded indicators, high-resolution camera chips for wide-field imaging, and resonant scanning mirrors in laser scanning microscopy, have notably improved the temporal and spatial resolution of functional imaging analysis. Nonetheless, the variability of imaging approaches and brain structures challenges the development of versatile and reliable segmentation methods. Standard techniques, such as manual selection of regions of interest or machine learning solutions, often fall short due to either user bias, non-transferability among systems, or computational demand. To overcome these issues, we developed CalciSeg, a data-driven and reproducible approach for unsupervised functional calcium imaging data segmentation. CalciSeg addresses the challenges associated with brain structure variability and user bias by offering a computationally efficient solution for automatic image segmentation based on two parameters: regions' size limits and number of refinement iterations. We evaluated CalciSeg efficacy on datasets of varied complexity, different insect species (locusts, bees, and cockroaches), and imaging systems (wide-field, confocal, and multiphoton), showing the robustness and generality of our approach. Finally, the user-friendly nature and the open-source availability of CalciSeg facilitate the integration of this algorithm into existing analysis pipelines.

Convective mixing in porous media: a review of Darcy, pore-scale and Hele-Shaw studies.

Convection-driven porous media flows are common in industrial processes and in nature. The multiscale and multiphase character of these systems and the inherent nonlinear flow dynamics make convection in porous media a complex phenomenon. As a result, a combination of different complementary approaches, namely theory, simulations and experiments, have been deployed to elucidate the intricate physics of convection in porous media. In this work, we review recent findings on mixing in fluid-saturated porous media convection. We focus on the dissolution of a heavy fluid layer into a lighter one, and we consider different flow configurations. We present Darcy, pore-scale and Hele-Shaw investigations inspired by geophysical processes. While the results obtained for Darcy flows match the dissolution behaviour predicted theoretically, Hele-Shaw and pore-scale investigations reveal a different and tangled scenario in which finite-size effects play a key role. Finally, we present recent numerical and experimental developments and we highlight possible future research directions. The findings reviewed in this work will be crucial to make reliable predictions about the long-term behaviour of dissolution and mixing in engineering and natural processes, which are required to tackle societal challenges such as climate change mitigation and energy transition.

The TU Wien Turbulent Water Channel: Flow control loop and three-dimensional reconstruction of anisotropic particle dynamics.

A horizontal water channel facility was built to study particle dynamics in a turbulent flow. The channel is sufficiently long to produce fully developed turbulence at the test section, and the width-to-height ratio is sufficiently large to avoid the sidewall effect for a large proportion of the cross-section. The system was designed to study the dynamics of complex-shaped particles in wall-bounded turbulence, the characteristics of which can be finely controlled. A maximum bulk velocity of up to 0.8 m s-1 can be achieved, corresponding to a bulk Reynolds number of up to 7 × 104 (shear Reynolds number ≈1580), and flow parameters can be controlled within ±0.1%. The transparent channel design and aluminum structures allow easy optical access, which enables multiple laser and camera arrangements. With the current optical setup, a measurement volume of up to 54 × 14 × 54 mm3 can be imaged and reconstructed with six cameras from the top, bottom, and sides of the channel. Finally, the in-house developed reconstruction and tracking procedure allows us to measure the full motion of complex objects (i.e., shape reconstruction, translational, and rotational motions), and in this instance, it is applied to the case of microscopic, non-isotropic polyamide fibers.

Granger Causality Analysis of Transient Calcium Dynamics in the Honey Bee Antennal Lobe Network.

Odorant processing presents multiple parallels across animal species, and insects became relevant models for the study of olfactory coding because of the tractability of the underlying neural circuits. Within the insect brain, odorants are received by olfactory sensory neurons and processed by the antennal lobe network. Such a network comprises multiple nodes, named glomeruli, that receive sensory information and are interconnected by local interneurons participating in shaping the neural representation of an odorant. The study of functional connectivity between the nodes of a sensory network in vivo is a challenging task that requires simultaneous recording from multiple nodes at high temporal resolutions. Here, we followed the calcium dynamics of antennal lobe glomeruli and applied Granger causality analysis to assess the functional connectivity among network nodes in the presence and absence of an odorous stimulus. This approach revealed the existence of causal connectivity links between antennal lobe glomeruli in the absence of olfactory stimulation, while at odor arrival, the connectivity network's density increased and became stimulus-specific. Thus, such an analytical approach may provide a new tool for the investigation of neural network plasticity in vivo.

Neuroethology: Perceived danger inhibits the wanting system of bees.

A dopaminergic wanting system drives foraging in honey bees. A new study shows that encounters with the Asian hornet, a fierce bee predator, decrease brain dopamine levels and thus foraging. Stop signals, used to terminate the waggle dances of receivers, have the same effect, showing the power of bee communication.

A cognitive account of trace conditioning in insects.

Trace conditioning is a form of Pavlovian learning in which the conditioned stimulus (CS) and the unconditioned stimulus (US) are separated by a temporal gap. Insects learn trace associations of variable nature (appetitive, aversive) and involving CSs of different sensory modalities (olfactory, visual). The accessibility of the insect neural system in behaving animals allowed identifying neural processes driving trace conditioning: the existence of prolonged neural responses to the CS after stimulus offset and the anticipation of US responses during the free-stimulus gap. Specific brain structures, such as the mushroom bodies seem to be allocated to this learning form. Here, we posit that a further component facilitating trace conditioning in insects relates to neuromodulatory mechanisms underlying enhanced attention. We thus propose a model based on different types of mushroom-body neurons, which provides a cognitive account of trace conditioning in insects.

Efficient visual learning by bumble bees in virtual-reality conditions: Size does not matter.

Recent developments allowed establishing virtual-reality (VR) setups to study multiple aspects of visual learning in honey bees under controlled experimental conditions. Here, we adopted a VR environment to investigate the visual learning in the buff-tailed bumble bee Bombus terrestris. Based on responses to appetitive and aversive reinforcements used for conditioning, we show that bumble bees had the proper appetitive motivation to engage in the VR experiments and that they learned efficiently elemental color discriminations. In doing so, they reduced the latency to make a choice, increased the proportion of direct paths toward the virtual stimuli and walked faster toward them. Performance in a short-term retention test showed that bumble bees chose and fixated longer on the correct stimulus in the absence of reinforcement. Body size and weight, although variable across individuals, did not affect cognitive performances and had a mild impact on motor performances. Overall, we show that bumble bees are suitable experimental subjects for experiments on visual learning under VR conditions, which opens important perspectives for invasive studies on the neural and molecular bases of such learning given the robustness of these insects and the accessibility of their brain.

Food wanting is mediated by transient activation of dopaminergic signaling in the honey bee brain.

The biological bases of wanting have been characterized in mammals, but whether an equivalent wanting system exists in insects remains unknown. In this study, we focused on honey bees, which perform intensive foraging activities to satisfy colony needs, and sought to determine whether foragers leave the hive driven by specific expectations about reward and whether they recollect these expectations during their waggle dances. We monitored foraging and dance behavior and simultaneously quantified and interfered with biogenic amine signaling in the bee brain. We show that a dopamine-dependent wanting system is activated transiently in the bee brain by increased appetite and individual recollection of profitable food sources, both en route to the goal and during waggle dances. Our results show that insects share with mammals common neural mechanisms for encoding wanting of stimuli with positive hedonic value.

The short neuropeptide F regulates appetitive but not aversive responsiveness in a social insect.

The neuropeptide F (NPF) and its short version (sNPF) mediate food- and stress-related responses in solitary insects. In the honeybee, a social insect where food collection and defensive responses are socially regulated, only sNPF has an identified receptor. Here we increased artificially sNPF levels in honeybee foragers and studied the consequences of this manipulation in various forms of appetitive and aversive responsiveness. Increasing sNPF in partially fed bees turned them into the equivalent of starved animals, enhancing both their food consumption and responsiveness to appetitive gustatory and olfactory stimuli. Neural activity in the olfactory circuits of fed animals was reduced and could be rescued by sNPF treatment to the level of starved bees. In contrast, sNPF had no effect on responsiveness to nociceptive stimuli. Our results thus identify sNPF as a key modulator of hunger and food-related responses in bees, which are at the core of their foraging activities.

Short-range exposure to airborne virus transmission and current guidelines.

After the Spanish flu pandemic, it was apparent that airborne transmission was crucial to spreading virus contagion, and research responded by producing several fundamental works like the experiments of Duguid [J. P. Duguid, J. Hyg. 44, 6 (1946)] and the model of Wells [W. F. Wells, Am. J. Hyg. 20, 611-618 (1934)]. These seminal works have been pillars of past and current guidelines published by health organizations. However, in about one century, understanding of turbulent aerosol transport by jets and plumes has enormously progressed, and it is now time to use this body of developed knowledge. In this work, we use detailed experiments and accurate computationally intensive numerical simulations of droplet-laden turbulent puffs emitted during sneezes in a wide range of environmental conditions. We consider the same emission-number of drops, drop size distribution, and initial velocity-and we change environmental parameters such as temperature and humidity, and we observe strong variation in droplets' evaporation or condensation in accordance with their local temperature and humidity microenvironment. We assume that 3% of the initial droplet volume is made of nonvolatile matter. Our systematic analysis confirms that droplets' lifetime is always about one order of magnitude larger compared to previous predictions, in some cases up to 200 times. Finally, we have been able to produce original virus exposure maps, which can be a useful instrument for health scientists and practitioners to calibrate new guidelines to prevent short-range airborne disease transmission.

Social modulation of individual preferences in cockroaches.

In social species, decision-making is both influenced by, and in turn influences, the social context. This reciprocal feedback introduces coupling across scales, from the neural basis of sensing, to individual and collective decision-making. Here, we adopt an integrative approach investigating decision-making in dynamical social contexts. When choosing shelters, isolated cockroaches prefer vanillin-scented (food-associated) shelters over unscented ones, yet in groups, this preference is inverted. We demonstrate that this inversion can be replicated by replacing the full social context with social odors: presented alone food and social odors are attractive, yet when presented as a mixture they are avoided. Via antennal lobe calcium imaging, we show that neural activity in vanillin-responsive regions reduces as social odor concentration increases. Thus, we suggest that the mixture is evaluated as a distinct olfactory object with opposite valence, providing a mechanism that would naturally result in individuals avoiding what they perceive as recently exploited resources.

Olfactory coding in honeybees.

With less than a million neurons, the western honeybee Apis mellifera is capable of complex olfactory behaviors and provides an ideal model for investigating the neurophysiology of the olfactory circuit and the basis of olfactory perception and learning. Here, we review the most fundamental aspects of honeybee's olfaction: first, we discuss which odorants dominate its environment, and how bees use them to communicate and regulate colony homeostasis; then, we describe the neuroanatomy and the neurophysiology of the olfactory circuit; finally, we explore the cellular and molecular mechanisms leading to olfactory memory formation. The vastity of histological, neurophysiological, and behavioral data collected during the last century, together with new technological advancements, including genetic tools, confirm the honeybee as an attractive research model for understanding olfactory coding and learning.

Structural and transcriptional evidence of mechanotransduction in the Drosophila suzukii ovipositor.

Drosophila suzukii is an invasive pest that prefers to lay eggs in ripening fruits, whereas most closely related Drosophila species exclusively use rotten fruit as oviposition site. This behaviour is allowed by an enlarged and serrated ovipositor that can pierce intact fruit skin, and by multiple contact sensory systems (mechanosensation and taste) that detect the optimal egg-laying substrates. Here, we tested the hypothesis that bristles present in the D. suzukii ovipositor tip contribute to these sensory modalities. Analysis of the bristle ultrastructure revealed that four different types of cuticular elements (conical pegs type 1 and 2, chaetic and trichoid sensilla) are present on the tip of each ovipositor plate. All of them have a poreless shaft and are innervated at their base by a single neuron that ends in a distal tubular body, thus resembling mechanosensitive structures. Fluorescent labelling in D. suzukii and D. melanogaster revealed that pegs located on the ventral side of the ovipositor tip are innervated by a single neuron in both species. RNA-sequencing profiled gene expression, notably sensory receptor genes of the terminalia of D. suzukii and of three other Drosophila species with changes in their ovipositor structure (from serrated to blunt ovipositor: Drosophila subpulchrella, Drosophila biarmipes and D. melanogaster). Our results revealed few species-specific transcripts and an overlapping expression of candidate mechanosensitive genes as well as the presence of some chemoreceptor transcripts. These experimental evidences suggest a mechanosensitive function for the D. suzukii ovipositor, which might be crucial across Drosophila species independently from ovipositor shape.

Coding of odour and space in the hemimetabolous insect Periplaneta americana.

The general architecture of the olfactory system is highly conserved from insects to humans, but neuroanatomical and physiological differences can be observed across species. The American cockroach, inhabiting dark shelters with a rather stable olfactory landscape, is equipped with long antennae used for sampling the surrounding air-space for orientation and navigation. The antennae's exceptional length provides a wide spatial working range for odour detection; however, it is still largely unknown whether and how this is also used for mapping the structure of the olfactory environment. By selectively labelling antennal lobe projection neurons with a calcium-sensitive dye, we investigated the logic of olfactory coding in this hemimetabolous insect. We show that odour responses are stimulus specific and concentration dependent, and that structurally related odorants evoke physiologically similar responses. By using spatially confined stimuli, we show that proximal stimulations induce stronger and faster responses than distal ones. Spatially confined stimuli of the female pheromone periplanone B activate a subregion of the male macroglomerulus. Thus, we report that the combinatorial logic of odour coding deduced from holometabolous insects applies also to this hemimetabolous species. Furthermore, a fast decrease in sensitivity along the antenna, not supported by a proportionate decrease in sensillar density, suggests a neural architecture that strongly emphasizes neuronal inputs from the proximal portion of the antenna.

Neuronal Response Latencies Encode First Odor Identity Information across Subjects.

Odorants are coded in the primary olfactory processing centers by spatially and temporally distributed patterns of glomerular activity. Whereas the spatial distribution of odorant-induced responses is known to be conserved across individuals, the universality of its temporal structure is still debated. Via fast two-photon calcium imaging, we analyzed the early phase of neuronal responses in the form of the activity onset latencies in the antennal lobe projection neurons of honeybee foragers. We show that each odorant evokes a stimulus-specific response latency pattern across the glomerular coding space. Moreover, we investigate these early response features for the first time across animals, revealing that the order of glomerular firing onsets is conserved across individuals and allows them to reliably predict odorant identity, but not concentration. These results suggest that the neuronal response latencies provide the first available code for fast odor identification.SIGNIFICANCE STATEMENT Here, we studied early temporal coding in the primary olfactory processing centers of the honeybee brain by fast imaging of glomerular responses to different odorants across glomeruli and across individuals. Regarding the elusive role of rapid response dynamics in olfactory coding, we were able to clarify the following aspects: (1) the rank of glomerular activation is conserved across individuals, (2) its stimulus prediction accuracy is equal to that of the response amplitude code, and (3) it contains complementary information. Our findings suggest a substantial role of response latencies in odor identification, anticipating the static response amplitude code.

In Vivo Two-Photon Imaging of the Olfactory System in Insects.

This chapter describes how to apply two-photon neuroimaging to study the insect olfactory system in vivo. It provides a complete protocol for insect brain functional imaging, with some additional remarks on the acquisition of morphological information from the living brain. We discuss the most important choices to make when buying or building a two-photon laser-scanning microscope. We illustrate different possibilities of animal preparation and brain tissue labeling for in vivo imaging. Finally, we give an overview of the main methods of image data processing and analysis, followed by a short description of pioneering applications of this imaging modality.

Spatial Receptive Fields for Odor Localization.

Animals rely on olfaction to navigate through complex olfactory landscapes, but the mechanisms that allow an animal to encode the spatial structure of an odorous environment remain unclear. To acquire information about the spatial distribution of an odorant, animals may rely on bilateral olfactory organs and compare side differences of odor intensity and timing [1-6] or may perform spatial and temporal signal integration of subsequent samplings [7]. The American cockroach can efficiently locate a source of sex pheromone even after the removal of one antenna, suggesting that bilateral comparison is not a prerequisite for odor localization in this species [8, 9]. Cognate olfactory sensory neurons (OSNs) originating from different locations on the flagellum, but bearing the same olfactory receptor, converge onto the same glomerulus within the antennal lobe, which is thought to result in a loss of spatial information. Here, we identified 12 types of pheromone-responsive projection neurons (PNs), each with spatially tuned receptive field. The combination of (1) the antennotopic organization of OSNs terminals and (2) the stereotyped compartmentalization of PNs' dendritic arborization within the macroglomerulus (MG), allows encoding the spatial position of the pheromone. Furthermore, each PN type innervates a different compartment of the mushroom body, providing the means for encoding spatial olfactory information along the olfactory circuit. Finally, MG PNs exhibit both excitatory and inhibitory spatial receptive fields and modulate their responses based on changes in stimulus geometry. In conclusion, we propose a mechanism for encoding information on the spatial distribution of a pheromone, expanding both our understanding of odor coding and of the strategies insects adopt to localize a sexual mate.

Spatially resolved time-frequency analysis of odour coding in the insect antennal lobe.

Antennal lobes constitute the first neurophils in the insect brain involved in coding and processing of olfactory information. With their stereotyped functional and anatomical organization, they provide an accessible model with which to investigate information processing of an external stimulus in a neural network in vivo. Here, by combining functional calcium imaging with time-frequency analysis, we have been able to monitor the oscillatory components of neural activity upon olfactory stimulation. The aim of this study is to investigate the presence of stimulus-induced oscillatory patterns in the honeybee antennal lobe, and to analyse the distribution of those patterns across the antennal lobe glomeruli. Fast two-photon calcium imaging reveals the presence of low-frequency oscillations, the intensity of which is perturbed by an incoming stimulus. Moreover, analysis of the spatial arrangement of this activity indicates that it is not homogeneous throughout the antennal lobe. On the contrary, each glomerulus displays an odorant-specific time-frequency profile, and acts as a functional unit of the oscillatory activity. The presented approach allows simultaneous recording of complex activity patterns across several nodes of the antennal lobe, providing the means to better understand the network dynamics regulating olfactory coding and leading to perception.