Broad‐scale applications of the Raspberry Pi: A review and guide for biologists

Methods in Ecology and Evolution, Год журнала: 2021, Номер 12(9), С. 1562 - 1579

Опубликована: Июнь 23, 2021

Abstract The field of biology has seen tremendous technological progress in recent years, fuelled by the exponential growth processing power and high‐level computing, rise global information sharing. Low‐cost single‐board computers are predicted to be one key advancements further revolutionise this field. So far, an overview current uptake these devices a general guide help researchers integrate them their work been missing. In paper I focus on most widely used computer, Raspberry Pi, review its broad applications uses across biological domain. Since release 2012, Pi increasingly taken up biologists, laboratory, classroom, wide range disciplines. A hugely diverse exists that ranges from simple solutions dedicated custom‐build devices, including nest‐box monitoring, wildlife camera trapping, high‐throughput behavioural recording, large‐scale plant phenotyping, underwater video surveillance, closed‐loop operant learning experiments autonomous ecosystem monitoring. Despite breadth implementations, depth scientific community is still limited. capabilities combined with low cost, ease use large user make it great research tool for almost any project. To accelerate community, provide detailed guidelines, recommendations considerations, 30+ step‐by‐step guides accompanying website ( http://raspberrypi‐guide.github.io ). hope will generate more awareness about among scientists thereby both fuel democratisation science ultimately advance our understanding biology, micro‐ macro‐scale.

Язык: Английский

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Open Hardware in Science: The Benefits of Open Electronics

Integrative and Comparative Biology, Год журнала: 2022, Номер 62(4), С. 1061 - 1075

Опубликована: Май 20, 2022

Freely and openly shared low-cost electronic applications, known as open electronics, have sparked a new open-source movement, with much un-tapped potential to advance scientific research. Initially designed appeal hobbyists, electronics formed global community of "makers" inventors are increasingly used in science industry. Here, we review the current benefits for research guide academics enter this emerging field. We discuss how from experimental theoretical sciences, can help (I) individual researchers by increasing customization, efficiency, scalability experiments, while improving data quantity quality; (II) institutions access maintenance high-end technologies, visibility interdisciplinary collaboration potential; (III) transparency reproducibility, helping decouple capacity funding, innovation, among public. Open powerful tools increase creativity, democratization, reproducibility thus offer practical solutions overcome significant barriers science.

Язык: Английский

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Selective integration of diverse taste inputs within a single taste modality

eLife, Год журнала: 2023, Номер 12

Опубликована: Янв. 24, 2023

A fundamental question in sensory processing is how different channels of input are processed to regulate behavior. Different may converge onto common downstream pathways drive the same behaviors, or they activate separate distinct behaviors. We investigated this Drosophila bitter taste system, which contains diverse bitter-sensing cells residing organs. First, we optogenetically activated subsets neurons within each organ. These elicited broad and highly overlapping behavioral effects, suggesting that pathways, but also observed differences argue for biased convergence. Consistent with these results, transsynaptic tracing revealed organs connect connectivity. one type neuron projects higher brain. integrate from multiple specific taste-related then traced circuits, providing first glimpse into Together, results reveal inputs selectively integrated early circuit, enabling pooling information, while circuit diverges have roles.

Язык: Английский

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

Frontiers in Molecular Neuroscience, Год журнала: 2024, Номер 17

Опубликована: Март 12, 2024

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 larvae allow microscopic imaging of the developing brain. also share a degree genetic similarity with humans, amenable manipulation techniques, such as gene knockdown, knockout, or knock-in, which allows researchers study role specific genes relevant human brain development, function, disease. can serve model behavioral studies, including locomotion, learning, social interactions. In this review, we present state-of-the-art methods function zebrafish, tools labeling single neurons neuronal circuits, live neural activity, synaptic dynamics protein interactions brain, optogenetic manipulation, use virtual reality technology testing. We highlight potential research, especially regarding genetic-based disorders discuss its certain limitations model.

Язык: Английский

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Sensation of electric fields in the Drosophila melanogaster larva

Current Biology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Electrosensation has emerged as a crucial sensory modality for social communication, foraging, and predation across the animal kingdom. However, its presence functional role well neural basis of electric field perception in Drosophila other invertebrates remain unclear. In environments with controlled fields, we identified electrosensation new sense melanogaster larva. We found that larva performs robust electrotaxis: when exposed to uniform field, larvae migrate toward cathode (negatively charged elecrode) quickly respond changes orientation maintain cathodal movement. Through behavioral screen, subset neurons located at tip larval head are necessary electrotaxis. Calcium imaging revealed pair Gr66a-positive (one on each side head) encodes strength field. Our results indicate fields elicit responses larva, providing evidence significance invertebrates.

Язык: Английский

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PiVR: An affordable and versatile closed-loop platform to study unrestrained sensorimotor behavior

PLoS Biology, Год журнала: 2020, Номер 18(7), С. e3000712 - e3000712

Опубликована: Июль 14, 2020

Tools enabling closed-loop experiments are crucial to delineate causal relationships between the activity of genetically labeled neurons and specific behaviors. We developed Raspberry Pi Virtual Reality (PiVR) system conduct optogenetic stimulation neural functions in unrestrained animals. PiVR is an experimental platform that operates at high temporal resolution (70 Hz) with low latencies (<30 milliseconds), while being affordable (

Язык: Английский

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Depolarization block in olfactory sensory neurons expands the dimensionality of odor encoding

Science Advances, Год журнала: 2022, Номер 8(50)

Опубликована: Дек. 16, 2022

Upon strong and prolonged excitation, neurons can undergo a silent state called depolarization block that is often associated with disorders such as epileptic seizures. Here, we show in the peripheral olfactory system part of their normal physiological function. Typically, sensory enter at odor concentrations three orders magnitude above detection threshold, thereby defining receptive fields over concentration bands. The silencing high-affinity produces sparser representations high-odor concentrations, which might facilitate perceptual discrimination. Using conductance-based model transduction cascade paired spike generation, provide numerical experimental evidence arises from slow inactivation sodium channels—a process could affect variety neurons. existence ethologically relevant creates an additional dimension expands encoding odors.

Язык: Английский

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High-resolution analysis of individual Drosophila melanogaster larvae uncovers individual variability in locomotion and its neurogenetic modulation

Open Biology, Год журнала: 2023, Номер 13(4)

Опубликована: Апрель 1, 2023

Neuronally orchestrated muscular movement and locomotion are defining faculties of multicellular animals. Due to its simple brain genetic accessibility, the larva fruit fly Drosophila melanogaster allows one study these processes at tractable levels complexity. However, although faculty clearly pertains individual, most studies in larvae use measurements aggregated across animals, or animals tested by one, an extravagance for larger-scale analyses. This prevents grasping inter- intra-individual variability neurogenetic determinants. Here, we present IMBA (individual maggot behaviour analyser) analysing individual within groups, reliably resolving identity collisions. We systematically describe wild-type how is reduced associative learning. then report a novel phenotype adhesion GPCR mutant. further investigated modulation repeated activations dopamine neurons transient backward induced brief optogenetic activation brain-descending 'mooncrawler' neurons. In summary, easy-to-use toolbox allowing unprecedentedly rich view larvae, with utility multiple biomedical research contexts.

Язык: Английский

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Broad-scale Applications of the Raspberry Pi: A Review and Guide for Biologists

Опубликована: Апрель 12, 2021

The field of biology has seen tremendous technological progress in recent years, fuelled by the exponential growth processing power and high-level computing, rise global information sharing.Low-cost single-board computers are predicted to be one key advancements further revolutionise this field.2. So far, an overview current uptake these devices a general guide help researchers integrate them their work been missing.In paper I focus on most widely used computer, Raspberry Pi, review its broad applications uses across biological domain.3. Since release 2012, Pi increasingly taken up biologists, laboratory, classroom, wide range disciplines.A hugely diverse exists that ranges from simple solutions dedicated custom-build devices, including nest-box monitoring, wildlife camera trapping, high-throughput behavioural recording, large-scale plant phenotyping, underwater video surveillance, closed-loop operant learning experiments autonomous ecosystem monitoring.Despite breadth implementations, depth scientific community is still limited.4. capabilities combined with low cost, ease use large user make it great research tool for almost any project.To accelerate community, provide detailed guidelines, recommendations considerations, 30+ step-by-step guides accompanying website (http://raspb erryp i-guide.github.io).I hope will generate more awareness about among scientists thereby both fuel democratisation science ultimately advance our understanding biology, micro-to macro-scale.

Язык: Английский

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Marigold: a machine learning-based web app for zebrafish pose tracking

BMC Bioinformatics, Год журнала: 2025, Номер 26(1)

Опубликована: Янв. 28, 2025

Abstract Background High-throughput behavioral analysis is important for drug discovery, toxicological studies, and the modeling of neurological disorders such as autism epilepsy. Zebrafish embryos larvae are ideal applications because they spawned in large clutches, develop rapidly, feature a relatively simple nervous system, have orthologs to many human disease genes. However, existing software video-based can be incompatible with recordings that contain dynamic backgrounds or foreign objects, lack support multiwell formats, require expensive hardware, and/or demand considerable programming expertise. Here, we introduce Marigold, free open source web app high-throughput embryonic larval zebrafish. Results Marigold features an intuitive graphical user interface, tracks up 10 user-defined keypoints, supports both single- exports range kinematic parameters addition publication-quality data visualizations. By leveraging highly efficient, custom-designed neural network architecture, achieves reasonable training inference speeds even on modestly powered computers lacking discrete graphics processing unit. Notably, app, does not any installation runs within popular browsers ChromeOS, Linux, macOS, Windows. To demonstrate Marigold’s utility, used two sets biological experiments. First, examined novel aspects touch-evoked escape response techno trousers ( tnt ) mutant embryos, which previously described loss-of-function mutation gene encoding Eaat2b, glial glutamate transporter. We identified differences interactions between touch location (head vs. tail) genotype. Second, investigated effects feeding visuomotor behavior at 5 7 days post-fertilization (dpf). found number vigor swimming bouts fed unfed fish time points, well developmental stage regimen. Conclusions In experiments presented here, use facilitated findings. ease use, robust pose tracking, amenability diverse experimental paradigms, flexibility regarding hardware requirements make it powerful tool analyzing zebrafish behavior, especially low-resource settings course-based undergraduate research experiences. available at: https://downeslab.github.io/marigold/ .

Язык: Английский

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