Find research datasets worth reusing

opencc-by-4.0Apr 2013View details →

Figure 1 in Effects of a Spirulina platensis-based diet on zebrafish female reproductive performance and larval survival rate

Figure 1. - Percentage of spawn according to the size of the clutch. Error bars represents standard error mean (SEM). **: p-value ≤ 0.01; FG: Flakes Group; SG: Spirulina platensis Group.

opencc-by-4.0Apr 2013View details →

Figure 3 in Effects of a Spirulina platensis-based diet on zebrafish female reproductive performance and larval survival rate

Figure 3. - Larvae survival rate (mean +/- SEM) when larvae are fed with 3 different diets, starting from 7 days post fertilization (0 hour).

opencc-by-4.0Apr 2013View details →

Figure 2 in Effects of a Spirulina platensis-based diet on zebrafish female reproductive performance and larval survival rate

Figure 2. - HT50 represents the time required to observe 50% hatched embryos in the two diet groups spawned one (Day 1), five (Day 5) and ten (Day 10) days after diet change. **: p-value ≤ 0.01; ***: p-value ≤ 0.001. Standard errors are represented. FG: Flakes Group; SG: Spirulina platensis Group.

opencc-by-4.0Nov 2022View details →

Data for "An optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish"

This dataset contains the free arena data and imaging data for the following research paper. Sy, S.K.H., Chan, D.C.W., Chan, R.C.H. et al. An optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish. Nat Commun 14, 227 (2023). https://doi.org/10.1038/s41467-023-35836-2

opencc-by-4.0May 2020View details →

Fluorescent microscopy images of larval zebrafish of either TraNac, Nacre or WT background

The images show larval zebrafish at 5 days post-fertilization using fluorescent microscopy. The fish are either of Nacre, TraNac, or WT background. The fluorescent channels are either GFP, YFP or mCherry.

opencc-zeroJan 2021View details →

Larval zebrafish H2B bulk spectral sensitivity

The encoding of light increments and decrements by separate On- and Off- systems is a fundamental ingredient of vision, which supports edge detection and makes efficient use of the limited dynamic range of visual neurons. Theory predicts that the neural representation of On- and Off-signals should be balanced, including across an animals' visible spectrum. Here we find that larval zebrafish violate this textbook expectation: in the zebrafish brain, UV-stimulation near exclusively gives On-responses, blue/green stimulation mostly Off-responses, and red-light alone elicits approximately balanced On- and Off-responses. We link these findings to zebrafish visual ecology, and suggest that the observed spectral tuning boosts the encoding of object "colourfulness", which correlates with object proximity in their underwater world.

opencc-by-nc-4.0Jul 2016View details →

Dense skeleton reconstructions of neurons in the larval zebrafish olfactory bulb

Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25 × 9.25 × 25 nm3 (Wanner et al., 2016). Skeletons of 1,022 neurons, ~98% of all neurons in the OB, were reconstructed by manual tracing and efficient error correction procedures. An ergonomic software package, PyKNOSSOS, was created in Python for data browsing, neuron tracing, synapse annotation, and visualization. PyKNOSSOS is available for free download (https://github.com/adwanner/PyKNOSSOS). The reconstructions as provided for download here allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The high density of reconstructions enables geometrical and topological analyses of the OB circuitry. Image data can be accessed and viewed through the neurodata web services (http://www.neurodata.io/wanner16). Raw data and reconstructions can be visualized in PyKNOSSOS.   PyKNOSSOS: https://github.com/adwanner/PyKNOSSOS Wanner AA, Genoud C, Masudi T, Siksou L, Friedrich RW (2016) Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb. Nat Neurosci 19:816-825. http://www.nature.com/neuro/journal/v19/n6/full/nn.4290.html

opencc-zeroJan 2024View details →

PFOS negatively impacts prey capture in larval zebrafish

Per- and polyfluoroalkyl substances (PFAS) are widely used in many industrial and domestic applications. The wide range use of PFAS has resulted in unintentional human exposures and bioaccumulation in blood and other organs. Perfluorooctanesulfonate (PFOS) is among the most prevalent PFAS in the environment and has been postulated to affect brain functions in exposed organisms. However, the impacts of PFOS on early neural development have not been well-described. Here, we used zebrafish larvae to assess the effects of PFOS on two fundamental complex behaviors, prey capture and learning. Zebrafish exposed to PFOS concentrations ranging from 2 – 20 µM for differing 48-hour periods were viable through early larval stages. In addition, PFOS uptake was unaffected by the presence of a chorion. We employed two different experimental paradigms; we first assessed the impacts of increasing organismal PFOS bioaccumulation on prey capture and learning, and second, we probed stage-specific sensitivity to PFOS by exposing zebrafish at different developmental stages (0-2 vs 3-5 days post fertilization). Following both assays we measured the amount of PFOS present in each larva. PFOS levels varied in larvae from different groups within each experimental paradigm. Significant negative correlations were observed between larval PFOS accumulation and the percentage of captured prey, while non-significant negative correlations were observed between PFOS accumulation and experienced-induced prey capture learning. These findings suggest that PFOS accumulation negatively affects larval zebrafish's ability to perform complicated multisensory behaviors and highlight potential risks of PFOS exposure to animals in the wild, with implications for human health.

opencc-by-4.0Dec 2021View details →

Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish

Supplementary material for paper entitled "Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish". Raw data, scripts, models and results are made available along with supplementary figures.

opencc-by-4.0Oct 2017View details →

Blind Sparse Deconvolution for Spike Inference from Fluorescence: Larval Zebrafish fluorescence recordings

This repository contains the two fluorescence imaging datasets used in the publication "Blind Sparse Deconvolution for Spike Inference from Fluorescence Recordings". Each dataset is a T X N DF/F matrix, where T is the number of fluorescence measurement and N is the number of neurons. They were obtained from light-sheet fluorescence microscopy. Both recordings correspond to spontaneous activity. The first file "DFF_20Hz_GCaMP3.mat" was obtained by a 2D recording acquired at 20 frame/second for 20 minutes of a 5dpf-old zebrafish larva expressing the genetically encoded indicator GCaMP3 (elavl3:GCaMP3). The images were parsed into 8082 neural traces. The second file "DFF_1Hz_GCaMP5.mat" was obtained by a 3D, whole-brain recording acquired at 20 frame/second and 20 stacks, (1 measurement/voxel/s) of a 5dpf-old zebrafish larva expressing the genetically encoded indicator GCaMP5. After segmentation, 255463 fluorescence traces encompassing the brain volume are computed independently.

opencc-by-4.0May 2024View details →

Dataset for Uncovering multiscale structure in the variability of larval zebrafish navigation

Datasets needed for recreating the figures from the paper "Uncovering multiscale structure in the variability of larval zebrafish navigation"

opencc-zeroJan 2023View details →

Data for: Inhibition drives habituation of a larval zebrafish visual response

Habituation allows animals to learn to ignore persistent but inconsequential stimuli. Despite being the most basic form of learning, a consensus model on the underlying mechanisms has yet to emerge. To probe relevant mechanisms we took advantage of a visual habituation paradigm in larval zebrafish, where larvae reduce their reactions to abrupt global dimming (a dark flash). Using Ca2+ imaging during repeated dark flashes, we identified 12 functional classes of neurons that differ based on their rate of adaptation, stimulus response shape, and anatomical location. While most classes of neurons depressed their responses to repeated stimuli, we identified populations that did not adapt, or that potentiated their response. To identify molecular players, we used a small molecule-screening approach to search for compounds that alter habituation learning. Among the pathways we identified were Melatonin and Estrogen signaling, as well as GABAergic inhibition. By analyzing which functional classes of neurons are GABAergic, and the result of pharmacological manipulations of the circuit, we propose that GABAergic inhibitory motifs drive habituation, perhaps through the potentiation of GABAergic synapses. Our results have identified multiple molecular pathways and cell types underlying a form of long-term plasticity in a vertebrate brain, and allow us to propose the first iteration of a model for how and where this learning process occurs.

opencc-zeroMar 2023View details →

Behavior and brain size of larval zebrafish exposed to environmentally relevant concentrations of betamethylamino- L-alanine (BMAA)

Harmful algal blooms (HABs) release toxic compounds in water and are increasing in frequency worldwide. The neurotoxin β-methylamino-L-alanine (BMAA) is released by HABs and has garnered much attention over the past twenty years due to its association with human neurodegenerative disorders, but its effects on wildlife are still largely unknown. This study characterized the effects of chronic exposure to environmentally relevant concentrations of BMAA on the behavior and brain size of developing zebrafish (Danio rerio). Zebrafish were continuously exposed to 0, 1, 10, or 100 μg/L waterborne BMAA between 0- and 5-days post-fertilization (dpf) before the onset of exogenous feeding. At 5 dpf, locomotion and responses to vibrational and visual stimuli were assessed. Following behavioral testing, larvae body and brain size were measured. Survival between 0 and 5 dpf did not differ between treatments. Moreover, BMAA exposure did not affect thigmotaxis, startle response magnitude, habituation to repeated presentation of vibrational startling stimuli, or relative brain size. A moderate increase in overall activity was observed in larvae exposed to 10 ug/L BMAA under light, but this effect was not seen in dark conditions, indicating that visual processing may have been affected by chronic BMAA exposure. Thus, our results show that passive continuous exposure to environmentally relevant concentrations of BMAA prior to first feeding in zebrafish does not affect overall brain development, locomotion, anxiety, and motor neuron-mediated reflexes, but suggest targeted neurotoxicity within the visual system.

opencc-by-4.0Sep 2023View details →

Predictive neural computations in cerebellar circuits contribute to motor planning and faster behavioral responses in larval zebrafish

This dataset contains raw and processed data along with jupyter notebooks to generate figures in Narayanan et al., 2023. Instructions for navigating through the dataset and for running the analysis codes are in README.pdf.