A 2D virtual reality system for visual goal-driven navigation in zebrafish larvae

Exploring the use of deep learning models for accurate tracking of 3D zebrafish trajectories

Zebrafish are ideal model organisms for various fields of biological research, including genetics, neural transmission patterns, disease and drug testing, and heart disease studies, because of their unique ability to regenerate cardiac muscle. Tracking zebrafish trajectories is essential for understanding their behavior, physiological states, and disease associations. While 2D tracking methods are limited, 3D tracking provides more accurate descriptions of their movements, leading to a comprehensive understanding of their behavior. In this study, we used deep learning models to track the 3D movements of zebrafish. Videos were captured by two custom-made cameras, and 21,360 images were labeled for the dataset. The YOLOv7 model was trained using hyperparameter tuning, with the top- and side-view camera models trained using the v7x.pt and v7.pt weights, respectively, over 300 iterations with 10,680 data points each. The models achieved impressive results, with an accuracy of 98.7% and a recall of 98.1% based on the test set. The collected data were also used to generate dynamic 3D trajectories. Based on a test set with 3,632 3D coordinates, the final model detected 173.11% more coordinates than the initial model. Compared to the ground truth, the maximum and minimum errors decreased by 97.39% and 86.36%, respectively, and the average error decreased by 90.5%.This study presents a feasible 3D tracking method for zebrafish trajectories. The results can be used for further analysis of movement-related behavioral data, contributing to experimental research utilizing zebrafish.

High-resolution tracking of unconfined zebrafish behavior reveals stimulatory and anxiolytic effects of psilocybin

Serotonergic psychedelics are emerging therapeutics for psychiatric disorders, yet their underlying mechanisms of action in the brain remain largely elusive. Here, we developed a wide-field behavioral tracking system for larval zebrafish and investigated the effects of psilocybin, a psychedelic serotonin receptor agonist. Machine learning analyses of precise body kinematics identified latent behavioral states reflecting spontaneous exploration, visually-driven rapid swimming, and irregular swim patterns following stress exposure. Using this method, we found that acute psilocybin treatment has two behavioral effects: [i] facilitation of spontaneous exploration ("stimulatory") and [ii] prevention of irregular swim patterns following stress exposure ("anxiolytic"). These effects differed from the effect of acute SSRI treatment and were rather similar to the effect of ketamine treatment. Neural activity imaging in the dorsal raphe nucleus suggested that psilocybin inhibits serotonergic neurons by activating local GABAergic neurons, consistent with psychedelic-induced suppression of serotonergic neurons in mammals. These findings pave the way for using larval zebrafish to elucidate neural mechanisms underlying the behavioral effects of serotonergic psychedelics.

Diving into the zebrafish brain: exploring neuroscience frontiers with genetic tools, imaging techniques, and behavioral insights

The zebrafish (Danio rerio) is increasingly used in neuroscience research. Zebrafish are relatively easy to maintain, and their high fecundity makes them suitable for high-throughput experiments. Their small, transparent embryos and larvae allow for easy microscopic imaging of the developing brain. Zebrafish also share a high degree of genetic similarity with humans, and are amenable to genetic manipulation techniques, such as gene knockdown, knockout, or knock-in, which allows researchers to study the role of specific genes relevant to human brain development, function, and disease. Zebrafish can also serve as a model for behavioral studies, including locomotion, learning, and social interactions. In this review, we present state-of-the-art methods to study the brain function in zebrafish, including genetic tools for labeling single neurons and neuronal circuits, live imaging of neural activity, synaptic dynamics and protein interactions in the zebrafish brain, optogenetic manipulation, and the use of virtual reality technology for behavioral testing. We highlight the potential of zebrafish for neuroscience research, especially regarding brain development, neuronal circuits, and genetic-based disorders and discuss its certain limitations as a model.

Efficacy of customized crown-level position jig in measuring peri-implant crestal bone level on periapical radiographs: An in vitro study

Background/purpose

Accuracy of using implant length on periapical radiographs as calibration reference for measurements has not been verified. This study aimed to verify the measurements of peri-implant crestal bone level (piCBL) on periapical radiographs taken by the paralleling technique and using the implant length for calibration; and to propose a customized crownlevel position (CLP) jig to improve the measurement accuracy of piCBL.

Materials and methods

A typodont installed an implant and a screw-retained crown at maxillary central incisor was used. To simulate piCBL, a metal post was placed near the implant at the same height of implant platform. The CLP jig was designed and 3-dimensionally printed out to allow implant projected orthogonally on periapical film. Thirty periapical radiographs were taken using paralleling technique with and without the jig by three examiners. The implant axis and implant length on radiographs were acquired by image segmentation. The discrepancy of piCBL determination (ΔD) from these measurements were compared and further analyzed when using the implant length for calibration.

Results

The piCBL measurement errors were smaller when the jig was used for all examiners (P < 0.001). The inter-rater differences were insignificant. After calibration, ΔD with and without jig were 0.09 (0.07-0.11) and 0.43 (0.38-0.49) mm, respectively.

Conclusion

Conventional long-cone paralleling technique using true implant length for calibration demonstrated imprecise piCBL measurement on periapical radiographs. Transferring the implant axis to the CLP jig allowed orthogonal projection of radiography which provided reliable measurements of piCBL with an accuracy of less than 0.1 mm.

Radial astrocyte synchronization modulates the visual system during behavioral-state transitions

Glial cells support the function of neurons. Recent evidence shows that astrocytes are also involved in brain computations. To explore whether and how their excitable nature affects brain computations and motor behaviors, we used two-photon Ca2+ imaging of zebrafish larvae expressing GCaMP in both neurons and radial astrocytes (RAs). We found that in the optic tectum, RAs synchronize their Ca2+ transients immediately after the end of an escape behavior. Using optogenetics, ablations, and a genetically encoded norepinephrine sensor, we observed that RA synchronous Ca2+ events are mediated by the locus coeruleus (LC)-norepinephrine circuit. RA synchronization did not induce direct excitation or inhibition of tectal neurons. Nevertheless, it modulated the direction selectivity and the long-distance functional correlations among neurons. This mechanism supports freezing behavior following a switch to an alerted state. These results show that LC-mediated neuro-glial interactions modulate the visual system during transitions between behavioral states.

Unlocking the Potential of Zebrafish Research with Artificial Intelligence: Advancements in Tracking, Processing, and Visualization

Zebrafish have become a widely accepted model organism for biomedical research due to their strong cortisol stress response, behavioral strain differences, and sensitivity to both drug treatments and predators. However, experimental zebrafish studies generate substantial data that must be analyzed through objective, accurate, and repeatable analysis methods. Recently, advancements in artificial intelligence (AI) have enabled automated tracking, image recognition, and data analysis, leading to more efficient and insightful investigations. In this review, we examine key AI applications in zebrafish research, including behavior analysis, genomics, and neuroscience. With the development of deep learning technology, AI algorithms have been used to precisely analyze and identify images of zebrafish, enabling automated testing and analysis. By applying AI algorithms in genomics research, researchers have elucidated the relationship between genes and biology, providing a better basis for the development of disease treatments and gene therapies. Additionally, the development of more effective neuroscience tools could help researchers better understand the complex neural networks in the zebrafish brain. In the future, further advancements in AI technology are expected to enable more extensive and in-depth medical research applications in zebrafish, improving our understanding of this important animal model. This review highlights the potential of AI technology in achieving the full potential of zebrafish research by enabling researchers to efficiently track, process, and visualize the outcomes of their experiments.

Effects of developmental exposure to neurotoxic algal metabolites on predator-prey interactions in larval Pimephales promelas

Harmful algal blooms are a growing environmental concern in aquatic systems. Although it is known that some of the secondary metabolites produced by cyanobacteria can alter predator-prey dynamics in aquatic communities by reducing foraging and/or predator evasion success, the mechanisms underpinning such responses are largely unknown. In this study, we examined the effects of a potent algal neurotoxin, β-N-methylamino-L-alanine (BMAA), on the development and behavior of larval Fathead Minnows, Pimephales promelas, during predator-prey interactions. We exposed eggs and larvae to environmentally relevant concentrations of BMAA for 21 days, then tested subjects in prey-capture and predator-evasion assays designed to isolate the effects of exposure at sequential points of the stimulus-response pathway. Exposure was associated with changes in the ability of larvae to detect and respond to environmental stimuli (i.e., a live prey item and a simulated vibrational predator), as well as changes in behavior and locomotor performance during the response. Our findings suggest that chronic exposure to neurodegenerative cyanotoxins could alter the outcomes of predator-prey interactions in natural systems by impairing an animal's ability to perceive, process, and respond to relevant biotic stimuli.

A Model of Discovery: The Role of Imaging Established and Emerging Non-mammalian Models in Neuroscience

Rodents have been the dominant animal models in neurobiology and neurological disease research over the past 60 years. The prevalent use of rats and mice in neuroscience research has been driven by several key attributes including their organ physiology being more similar to humans, the availability of a broad variety of behavioral tests and genetic tools, and widely accessible reagents. However, despite the many advances in understanding neurobiology that have been achieved using rodent models, there remain key limitations in the questions that can be addressed in these and other mammalian models. In particular, in vivo imaging in mammals at the cell-resolution level remains technically difficult and demands large investments in time and cost. The simpler nervous systems of many non-mammalian models allow for precise mapping of circuits and even the whole brain with impressive subcellular resolution. The types of non-mammalian neuroscience models available spans vertebrates and non-vertebrates, so that an appropriate model for most cell biological questions in neurodegenerative disease likely exists. A push to diversify the models used in neuroscience research could help address current gaps in knowledge, complement existing rodent-based bodies of work, and bring new insight into our understanding of human disease. Moreover, there are inherent aspects of many non-mammalian models such as lifespan and tissue transparency that can make them specifically advantageous for neuroscience studies. Crispr/Cas9 gene editing and decreased cost of genome sequencing combined with advances in optical microscopy enhances the utility of new animal models to address specific questions. This review seeks to synthesize current knowledge of established and emerging non-mammalian model organisms with advances in cellular-resolution in vivo imaging techniques to suggest new approaches to understand neurodegeneration and neurobiological processes. We will summarize current tools and in vivo imaging approaches at the single cell scale that could help lead to increased consideration of non-mammalian models in neuroscience research.

Clinical and prognostic values of urinary alpha1-microglobulin as a tubular marker in acute heart failure

BACKGROUND

Although urinary alpha-1-microglobulin has been used as a marker of tubular dysfunction, its clinical and prognostic values in patients with acute heart failure have not been validated.

METHODS

We analyzed 623 patients (74 ± 13 years old, 60.0% male) with acute heart failure in whom urinary alpha-1-microglobulin (A1MG) levels were measured as tubular markers at the time of admission. The primary endpoint was all-cause mortality.

RESULTS

The median levels of urinary alpha-1-microglobulin with and without correction for urinary creatinine concentration were 8.80 (interquartile range: 4.20-17.7) mg/dL and 12.9 (5.92-30.7) mg/gCr, respectively. Urinary A1MG levels were significantly correlated with all of beta-2-microglobulin (r = 0.77), N-acetyl-β-D-glucosaminidase (r = 0.51), and estimated glomerular filtration rate (r = -0.42); however, alpha-1-microglobulin was most often predicted using beta-2-microglobulin or N-acetyl-β-D-glucosaminidase. During the 488-day (interquartile range: 185-938 days) follow-up, 141 deaths occurred. Higher A1MG levels were associated with higher mortality even after adjustment for other covariates. Only A1MG, but not beta-2-microglobulin or N-acetyl-β-D-glucosaminidase, yielded incremental prognostic information in addition to the preexisting prognostic factors (net-reclassification improvement: 0.254, P = 0.023; integrated discrimination improvement: 0.015, P = 0.028).

CONCLUSIONS

In patients hospitalized due to acute heart failure, urinary alpha-1-microglobulin was a marker of tubular dysfunction. High alpha-1-microglobulin was associated with all-cause mortality independent of glomerular function and was a better predictor of mortality than urinary beta-2-microglobulin.

BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis

We present BonZeb-a suite of modular Bonsai packages which allow high-resolution zebrafish tracking with dynamic visual feedback. Bonsai is an increasingly popular software platform that is accelerating the standardization of experimental protocols within the neurosciences due to its speed, flexibility, and minimal programming overhead. BonZeb can be implemented into novel and existing Bonsai workflows for online behavioral tracking and offline tracking with batch processing. We demonstrate that BonZeb can run a variety of experimental configurations used for gaining insights into the neural mechanisms of zebrafish behavior. BonZeb supports head-fixed closed-loop and free-swimming virtual open-loop assays as well as multi-animal tracking, optogenetic stimulation, and calcium imaging during behavior. The combined performance, ease of use and versatility of BonZeb opens new experimental avenues for researchers seeking high-resolution behavioral tracking of larval zebrafish.

FastTrack: An open-source software for tracking varying numbers of deformable objects

Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical systems spanning a wide range of length scales and developed a general-purpose, optimized, open-source, cross-platform, easy to install and use, self-updating software called FastTrack. It can handle a changing number of deformable objects in a region of interest, and is particularly suitable for animal and cell tracking in two-dimensions. Furthermore, we introduce the probability of incursions as a new measure of a movie’s trackability that doesn’t require the knowledge of ground truth trajectories, since it is resilient to small amounts of errors and can be computed on the basis of an ad hoc tracking. We also leveraged the versatility and speed of FastTrack to implement an iterative algorithm determining a set of nearly-optimized tracking parameters—yet further reducing the amount of human intervention—and demonstrate that FastTrack can be used to explore the space of tracking parameters to optimize the number of swaps for a batch of similar movies. A benchmark shows that FastTrack is orders of magnitude faster than state-of-the-art tracking algorithms, with a comparable tracking accuracy. The source code is available under the GNU GPLv3 at https://github.com/FastTrackOrg/FastTrack and pre-compiled binaries for Windows, Mac and Linux are available at http://www.fasttrack.sh.

Many researchers and engineers face the challenge of tracking objects from very different systems across several fields of research. We observed that despite this diversity the core of the tracking task is very general and can be formalized. We thus introduce the notion of incursions—i.e. to what extent an object can enter a neighbor’s space—which can be defined on a statistical basis and captures the interplay between the acquisition rate, the objects’ dynamics and the geometrical characteristics of the scene, including density. To validate this approach, we compiled a dataset from various fields of Physics, Biology and human activities to serve as a benchmark for general-purpose tracking softwares. This dataset is open and accepts new submissions. We also developped a software called FastTrack that is able to track most of the movies in the dataset by proposing standard image processing tools and state-of-the-art implementation of the matching algorithm, which is at the core of the tracking task. Besides, it is open-source, simple to install and use and has an ergonomic interface to obtain fast and reliable results. FastTrack is particularly convenient for small-scale research projects, typically when the development of a dedicated software is overkill.

Fish as a model in social neuroscience: conservation and diversity in the social brain network

Mechanisms for fish social behaviours involve a social brain network (SBN) which is evolutionarily conserved among vertebrates. However, considerable diversity is observed in the actual behaviour patterns amongst nearly 30000 fish species. The huge variation found in socio-sexual behaviours and strategies is likely generated by a morphologically and genetically well-conserved small forebrain system. Hence, teleost fish provide a useful model to study the fundamental mechanisms underlying social brain functions. Herein we review the foundations underlying fish social behaviours including sensory, hormonal, molecular and neuroanatomical features. Gonadotropin-releasing hormone neurons clearly play important roles, but the participation of vasotocin and isotocin is also highlighted. Genetic investigations of developing fish brain have revealed the molecular complexity of neural development of the SBN. In addition to straightforward social behaviours such as sex and aggression, new experiments have revealed higher order and unique phenomena such as social eavesdropping and social buffering in fish. Finally, observations interpreted as 'collective cognition' in fish can likely be explained by careful observation of sensory determinants and analyses using the dynamics of quantitative scaling. Understanding of the functions of the SBN in fish provide clues for understanding the origin and evolution of higher social functions in vertebrates.

Visual acuity in the flying snake, Chrysopelea paradisi

Visual control during high-speed aerial locomotion requires a visual system adapted for such behaviors. Flying snakes (genus: Chrysopelea) are capable of gliding at speeds up to 11 m s-1 and perform visual assessments before take-off. Determining nuances of control requires a closed-loop experimental system, such as immersive virtual arenas. To characterize vision in the flying snake Chrysopelea paradisi, we used digitally reconstructed models of the head to determine a 3D field of vision. We also used optokinetic drum experiments and compared slowphase optokinetic nystagmus (OKN) speeds to calculate visual acuity and conducted preliminary experiments to determine whether snakes would respond to closed-loop virtual stimuli. Visual characterization showed that C. paradisi likely has a large field of view (308.5 ± 6.5° azimuthal range), with a considerable binocular region (33.0 ± 11.0° azimuthal width) that extends overhead. Their visual systems are broadly tuned and motion-sensitive, with peak OKN response gains of 0.50 ± 0.11 seen at 46.06 ± 11.08 Hz, and a low spatial acuity, with peak gain of 0.92 ± 0.41 seen at 2.89 ± 0.16 cpd (cycles per degree). These characteristics were used to inform settings in an immersive virtual arena, including framerate, brightness, and stimulus size. In turn, the immersive virtual arena was used to reproduce the optokinetic drum experiments. We elicited OKN in open-loop experiments, with a mean gain of 0.21 ± 0.9 seen at 0.019 ± 6x10-5 cpd and 1.79 ± 0.01 Hz. In closed-loop experiments, snakes did not exhibit OKN, but held the image fixed, indicating visual stabilization. These results demonstrate for that C. paradisi responds to visual stimuli in a digital virtual arena. The accessibility and adaptability of the virtual setup make it suitable for future studies of visual control in snakes and other animals in an unconstrained setting.

Learning steers the ontogeny of an efficient hunting sequence in zebrafish larvae

Goal-directed behaviors may be poorly coordinated in young animals but, with age and experience, behavior progressively adapts to efficiently exploit the animal’s ecological niche. How experience impinges on the developing neural circuits of behavior is an open question. We have conducted a detailed study of the effects of experience on the ontogeny of hunting behavior in larval zebrafish. We report that larvae with prior experience of live prey consume considerably more prey than naive larvae. This is mainly due to increased capture success and a modest increase in hunt rate. We demonstrate that the initial turn to prey and the final capture manoeuvre of the hunting sequence were jointly modified by experience and that modification of these components predicted capture success. Our findings establish an ethologically relevant paradigm in zebrafish for studying how the brain is shaped by experience to drive the ontogeny of efficient behavior.

Fovea-like Photoreceptor Specializations Underlie Single UV Cone Driven Prey-Capture Behavior in Zebrafish

In the eye, the function of same-type photoreceptors must be regionally adjusted to process a highly asymmetrical natural visual world. Here, we show that UV cones in the larval zebrafish area temporalis are specifically tuned for UV-bright prey capture in their upper frontal visual field, which may use the signal from a single cone at a time. For this, UV-photon detection probability is regionally boosted more than 10-fold. Next, in vivo two-photon imaging, transcriptomics, and computational modeling reveal that these cones use an elevated baseline of synaptic calcium to facilitate the encoding of bright objects, which in turn results from expressional tuning of phototransduction genes. Moreover, the light-driven synaptic calcium signal is regionally slowed by interactions with horizontal cells and later accentuated at the level of glutamate release driving retinal networks. These regional differences tally with variations between peripheral and foveal cones in primates and hint at a common mechanistic origin.

Effects of mixed reality head-mounted glasses during 90 minutes of mental and manual tasks on cognitive and physiological functions

Background

We evaluated the effects of a mixed reality (MR) head-mounted deviceon some cognitiveand physiological functions during 90 min tasks in an attempt to determine their safety for workers.

Methods

A total of 12 volunteers performed 90-min intellectual and manual tasks with and without MR glasses. Balance, Stroop, and memory tests were conducted before, during and after these tasks. Heart rate and electromyographic activity of some muscles were recorded. A survey was used to determine subjective fatigue, pain, or discomfort.

Results

Balance, heart rate, rate of perceived exertion, memory, and attention were unaffected by wearing MR glasses. Electromyographic activity increased with MR glasses for deltoid, biceps brachii, and soleus muscles. Few subjects reported discomfort, pain, or visual fatigue with MR glasses. Some participants reported they lost the notion of time and reality.

Discussion

Accordingly, we concluded that the MR glasses under investigation (Hololens) can be used safely. An appropriate setup and familiarization are needed to optimize use.

Ablation of a Neuronal Population Using a Two-photon Laser and Its Assessment Using Calcium Imaging and Behavioral Recording in Zebrafish Larvae

To identify the role of a subpopulation of neurons in behavior, it is essential to test the consequences of blocking its activity in living animals. Laser ablation of neurons is an effective method for this purpose when neurons are selectively labeled with fluorescent probes. In the present study, protocols for laser ablating a subpopulation of neurons using a two-photon microscope and testing of its functional and behavioral consequences are described. In this study, prey capture behavior in zebrafish larvae is used as a study model. The pretecto-hypothalamic circuit is known to underlie this visually-driven prey catching behavior. Zebrafish pretectum were laser-ablated, and neuronal activity in the inferior lobe of the hypothalamus (ILH; the target of the pretectal projection) was examined. Prey capture behavior after pretectal ablation was also tested.

Integrative whole-brain neuroscience in larval zebrafish

Due to their small size and transparency, zebrafish larvae are amenable to a range of fluorescence microscopy techniques. With the development of sensitive genetically encoded calcium indicators, this has extended to the whole-brain imaging of neural activity with cellular resolution. This technique has been used to study brain-wide population dynamics accompanying sensory processing and sensorimotor transformations, and has spurred the development of innovative closed-loop behavioral paradigms in which stimulus-response relationships can be studied. More recently, microscopes have been developed that allow whole-brain calcium imaging in freely swimming and behaving larvae. In this review, we highlight the technologies underlying whole-brain functional imaging in zebrafish, provide examples of the sensory and motor processes that have been studied with this technique, and discuss the need to merge data from whole-brain functional imaging studies with neurochemical and anatomical information to develop holistic models of functional neural circuits.

A microfluidic device for partial immobilization, chemical exposure and behavioural screening of zebrafish larvae

The zebrafish larva is an important vertebrate model for sensory-motor integration studies, genetic screening, and drug discovery because of its excellent characteristics such as optical transparency, genetic manipulability, and genetic similarity to humans. Operations such as precise manipulation of zebrafish larvae, controlled exposure to chemicals, and behavioural monitoring are of utmost importance to the abovementioned studies. In this work, a novel microfluidic device is presented to easily stabilize an individual larva's head using a microfluidic trap while leaving the majority of the body and the tail unhindered to move freely in a downstream chamber. The device is equipped with a microvalve to prevent the larva's escape from the trap and a microchannel beside the larva's head to expose it to chemicals at desired concentrations and times, while investigating multiple behaviours such as the tail, eye, and mouth movement frequencies. An in situ air bubble removal module was also incorporated to increase the yield of experiments. The functionality of our device in comparison to a conventional droplet-based technique was tested using l-arginine exposure and viability assays. We found that the larvae in the device and the droplet exhibit similar tail and eye response trends to nM-mM concentrations of l-arginine, and that the survival of the larvae is not affected by the device. However, the tail responses in the device were numerically higher than the droplet-tested larvae at nM-mM l-arginine concentrations. In the future, our device has the potential to be used for conducting simultaneous whole-brain functional imaging, upon optimized immobilization of the brain, and behavioural analysis to uncover differences between diseased and healthy states in zebrafish.