Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network DOI Creative Commons

Aniket Ravan,

Ruopei Feng, Martin Gruebele

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 8, 2023

Abstract Quantitative ethology requires an accurate estimation of organism’s postural dynamics in three dimensions plus time. Technological progress over the last decade has made animal pose challenging scenarios possible with unprecedented detail. Here, we present (i) a fast automated method to record and track individual larval zebrafish 3-D environment, applicable when human labeling is not possible; (ii) rich annotated dataset poses for ethologists general machine learning community; (iii) technique generate realistic, images novel behavioral contexts. Using three-camera system calibrated refraction correction, diverse swims under free swimming conditions response acoustic optical stimuli. We then employ convolutional neural network estimate from video images. The trained against set synthetic rendered using physical model larvae. This samples distribution realistic that priori template-based small number swim bouts. Our model, without any annotation, performs much higher speed comparable accuracy approach, capturing detailed kinematics swims. Author Summary Larval been studied extensively 2-D environments, which are restrictive compared natural habitats. To enable rapid capture poses, collect orthogonal projections behaviors several settings fit model. use auto-annotated stream train network. highly predictions on 600 real bouts faster than fit. results show larvae frequently exhibit motions inaccessible setup. could be used by studying dynamics, community interested multi-dimensional time series reconstruction. ability render multiple our can extended collective behavior.

Language: Английский

If a fish can pass the mark test, what are the implications for consciousness and self-awareness testing in animals? DOI Creative Commons
Masanori Kohda, Takashi Hotta, Tomohiro Takeyama

et al.

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(2), P. e3000021 - e3000021

Published: Feb. 7, 2019

The ability to perceive and recognise a reflected mirror image as self (mirror self-recognition, MSR) is considered hallmark of cognition across species. Although MSR has been reported in mammals birds, it not known occur any other major taxon. Potentially limiting our test for taxa that the established assay, mark test, requires animals display contingency testing self-directed behaviour. These behaviours may be difficult humans interpret taxonomically divergent animals, especially those lack dexterity (or limbs) required touch mark. Here, we show fish, cleaner wrasse Labroides dimidiatus, shows behaviour reasonably interpreted passing through all phases test: (i) social reactions towards reflection, (ii) repeated idiosyncratic mirror, (iii) frequent observation their reflection. When subsequently provided with coloured tag modified fish attempt remove by scraping body presence but no response transparent marks or absence mirror. This remarkable finding presents challenge interpretation test—do accept these behavioural responses, which are taken evidence self-recognition species during lead conclusion self-aware? Or do rather decide patterns have basis cognitive process than pass test? If former, what does this mean understanding animal intelligence? latter, application metric abilities?This Short Report received both positive negative reviews experts. Academic Editor written an accompanying Primer publishing alongside article (https://doi.org/10.1371/journal.pbio.3000112). linked complementary expert perspective; discusses how current study should context against self-awareness wide range animals.

Language: Английский

Citations

175

Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments DOI Creative Commons
Vilim Štih, Luigi Petrucco, Andreas M. Kist

et al.

PLoS Computational Biology, Journal Year: 2019, Volume and Issue: 15(4), P. e1006699 - e1006699

Published: April 8, 2019

We present Stytra, a flexible, open-source software package, written in Python and designed to cover all the general requirements involved larval zebrafish behavioral experiments. It provides timed stimulus presentation, interfacing with external devices simultaneous real-time tracking of parameters such as position, orientation, tail eye motion both freely-swimming head-restrained preparations. Stytra logs recorded quantities, metadata, code version standardized formats allow full provenance tracking, from data acquisition through analysis publication. The package is modular expandable for different experimental protocols setups. Current releases can be found at https://github.com/portugueslab/stytra. also provide complete documentation examples extending new stimuli hardware, well schema parts list showcase by reproducing previously published larvae. demonstrate use context calcium imaging experiment, where it interfaces other devices. Our aims are enable more laboratories easily implement experiments, platform sharing that permits easy reproduction experiments straightforward validation. Finally, we how serve design involving or visual stimulation animals an example integration DeepLabCut neural network-based method.

Language: Английский

Citations

84

Azole-Induced Color Vision Deficiency Associated with Thyroid Hormone Signaling: An Integrated In Vivo, In Vitro, and In Silico Study DOI
Zhifeng Chen,

Zhicheng Lin,

Siqi Lu

et al.

Environmental Science & Technology, Journal Year: 2022, Volume and Issue: 56(18), P. 13264 - 13273

Published: Sept. 9, 2022

Azoles that are used in pesticides, pharmaceuticals, and personal care products can have toxic effects on fish. However, there is no information regarding azole-induced visual disorder associated with thyroid disruption. We evaluated changes retinal morphology, optokinetic response, transcript abundance of the genes involved color perception hypothalamic–pituitary–thyroid (HPT) axis, hormone (TH) levels zebrafish larvae exposed to common azoles, such as climbazole (CBZ, 0.1 10 μg/L) triadimefon (TDF, 50 500 μg/L), at environmentally relevant predicted worst-case environmental concentrations. Subsequently, effect azoles TH-dependent GH3 cell proliferation receptor (TR)-regulated transcriptional activity, well silico binding affinity between TR isoforms, was investigated. Azole exposure decreased densities ganglion layer, inner nuclear photoreceptor layer. Zebrafish concentrations CBZ TDF showed a decrease response green–white red–white stripes but not blue–white stripes, consistent disturbance corresponding opsin gene expression. also reduced triiodothyronine concomitantly increased HPT-related Molecular docking analysis combined vitro TR-mediated transactivation dual-luciferase reporter assays demonstrated exhibited antagonism. These results comparable those obtained from known antagonist, namely, antagonist 1, positive control. Therefore, damage specific by appears result lowered TH signaling, indicating potential threat disruptors function

Language: Английский

Citations

34

Efficacy of Tricaine (MS-222) and Hypothermia as Anesthetic Agents for Blocking Sensorimotor Responses in Larval Zebrafish DOI Creative Commons

Claire Leyden,

Timo Brüggemann,

Florentyna Debinski

et al.

Frontiers in Veterinary Science, Journal Year: 2022, Volume and Issue: 9

Published: March 28, 2022

Tricaine, or MS-222, is the most commonly used chemical anesthetic in zebrafish research. It thought to act via blocking voltage-gated sodium channels, though its mechanism of action, particularly at neuronal level, not yet fully understood. Here, we first characterized effects tricaine on both body balance and touch responses freely swimming animals, before determining effect neural activity underlying optokinetic response level motion perception, sensorimotor signaling generation behavior immobilized animals. We found that standard dose for larvae (168 mg/L) induced loss righting reflex within 30 seconds, which then recovered 3 minutes. Optokinetic 15 Calcium imaging showed interferes with by interruption signals between pretectum hindbrain. The sensitivity indices identified sensory neurons were unchanged exposed tricaine, fewer such detected, leaving a small population active neurons. compared gradual cooling, potential non-chemical alternative method anesthesia. While tuning appeared be affected similar manner during cooling surge calcium levels This surge, alongside drop heartrate, potentially associated harmful changes physiology suggests better agent than laboratory

Language: Английский

Citations

21

BDE-99 Disrupts the Photoreceptor Patterning of Zebrafish Larvae via Transcription Factor six7 DOI
Sheng Wei, Fu Chen, Ting Xu

et al.

Environmental Science & Technology, Journal Year: 2022, Volume and Issue: 56(9), P. 5673 - 5683

Published: April 12, 2022

Proper visual function is essential for collecting environmental information and supporting the decision-making in central nervous system therefore tightly associated with wildlife survival human health. Polybrominated diphenyl ethers (PBDEs) were reported to impair zebrafish vision development, thyroid hormone (TH) signaling was suspected as main contributor. In this study, a pentabrominated PBDE, BDE-99, chosen further explore action mechanism of PBDEs on disruption color vision. The results showed that BDE-99 could multiple photoreceptors retina disturb behavior guided by larvae at 120 h post-fertilization. Although resulting alteration photoreceptor patterning highly resembled effects 3,3′,5-triiodo-l-thyroine, introducing antagonist TH receptors unable fully recover alteration, which suggested involvement other potential regulatory factors. By modulating expression six7, key inducer middle-wavelength opsins, we demonstrated not THs, dominated BDE-99. Our work promoted understanding role six7 process proposed novel toxicity PBDEs.

Language: Английский

Citations

20

Effects of air pollution exposure on social behavior: a synthesis and call for research DOI Creative Commons
Chelsea A. Weitekamp, Hans A. Hofmann

Environmental Health, Journal Year: 2021, Volume and Issue: 20(1)

Published: June 25, 2021

Abstract Background There is a growing literature from both epidemiologic and experimental animal studies suggesting that exposure to air pollution can lead neurodevelopmental neuropsychiatric disorders. Here, we suggest effects of pollutant on the brain may be even broader, with potential affect social decision-making in general. Methods We discuss how neurobiological substrates behavior are vulnerable pollution, then briefly present examine behavior-related outcomes. Results Few have investigated those focus standard laboratory tests rodent model systems. Nonetheless, there sufficient evidence support critical need for more research. Conclusion For future research, comparative approach utilizes diverse systems probe wider range behaviors, regions, neurochemical pathways.

Language: Английский

Citations

26

Trait sensitivity to stress and cognitive bias processes in fish: A brief overview DOI Creative Commons
Jhon Buenhombre, Erika Alexandra Daza-Cardona, Daniel Mota‐Rojas

et al.

Personality Neuroscience, Journal Year: 2024, Volume and Issue: 7

Published: Jan. 1, 2024

Abstract Like other animals, fish have unique personalities that can affect their cognition and responses to environmental stressors. These individual personality differences are often referred as “behavioural syndromes” or “stress coping styles” include traits such boldness, shyness, aggression, exploration, locomotor activity, sociability. For example, bolder proactive may be more likely take risks present lower hypothalamo–pituitary–adrenal/interrenal axis reactivity compared shy reactive individuals. Likewise, learning memory differ between personalities. Reactive individuals tend faster better association recall with aversive stimuli, while bold learn quickly when presented appetitive incentives. However, the influence of on cognitive processes than achievement in has been scarcely explored. Cognitive bias tests employed investigate interplay emotion both humans animals. Fish (CBP) which fish’s interpretation stimuli could influenced by its current emotional state open modulation. no study explored whether CBP, like species, interpreted long-lasting characteristics explain variation. We hold perspective CBP serve a vulnerability factor for onset, persistence, recurrence stress-related disorders. Therefore, studying trait interactions variations valuable future efforts enhance our understanding anxiety stress neurobiology animal models humans.

Language: Английский

Citations

3

Spherical arena reveals optokinetic response tuning to stimulus location, size, and frequency across entire visual field of larval zebrafish DOI Creative Commons
Florian A. Dehmelt,

Rebecca Meier,

Julian Hinz

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: June 8, 2021

Many animals have large visual fields, and sensory circuits may sample those regions of space most relevant to behaviours such as gaze stabilisation hunting. Despite this, relatively small displays are often used in vision neuroscience. To stimulus locations across the field, we built a spherical arena with 14,848 independently controllable LEDs. We measured optokinetic response gain immobilised zebrafish larvae stimuli different steradian size field locations. find that two eyes less yoked than previously thought spatial frequency tuning is similar positions. However, react strongly lateral, nearly equatorial stimuli, consistent reported densities red, green, blue photoreceptors. Upside-down experiments suggest further extra-retinal processing. Our results demonstrate motion anisotropic, preferentially monitor areas putative behavioural relevance.

Language: Английский

Citations

20

Functional architecture underlying binocular coordination of eye position and velocity in the larval zebrafish hindbrain DOI Creative Commons

Christian Brysch,

Claire Leyden,

Aristides B. Arrenberg

et al.

BMC Biology, Journal Year: 2019, Volume and Issue: 17(1)

Published: Dec. 1, 2019

The oculomotor integrator (OI) in the vertebrate hindbrain transforms eye velocity input into persistent position coding output, which plays a crucial role retinal image stability. For mechanistic understanding of function and control, knowledge about tuning OI other nuclei is needed. Zebrafish are increasingly used to study sensorimotor circuits, yet precise neuronal motor variables remains uncharacterized.Here, we recorded cellular calcium signals while evoking monocular binocular optokinetic movements at different slow-phase velocities. Our analysis reveals anatomical distributions motoneurons internuclear neurons nucleus abducens as well those caudally adjacent volumes. Each neuron tuned and/or variable extents only activated after surpassing particular thresholds. While (rhombomeres 5/6) mainly codes for position, rhombomeres 7/8, velocity-to-position gradient exists along rostro-caudal axis, likely corresponds structures storing agreement with feedforward mechanism activity generation. Position encoding recruited thresholds distributed across behaviourally relevant dynamic range, velocity-encoding have more centred firing velocity. In abducens, exclusively one intermingle both eyes. Many these preferentially active during conjugate less movements. This differential recruitment versus tasks represents functional diversification final common pathway.We localized functionally characterized repertoire zebrafish hindbrain. findings provide evidence mixed but task-specific code suggest that generation organized axis

Language: Английский

Citations

19

Toxic effects of triclocarban on larval zebrafish: A focus on visual dysfunction DOI
Xiaofan Chen, Zhifeng Chen,

Zhicheng Lin

et al.

Aquatic Toxicology, Journal Year: 2021, Volume and Issue: 241, P. 106013 - 106013

Published: Oct. 29, 2021

Language: Английский

Citations

16