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934 results for “Bovines”
Dataset for Evaluation of a novel microfluidic chip-like device for purifying bovine frozen-thawed semen for in vitro fertilization
<p>VetCount<sup>TM</sup> Harvester (MotilityCount ApS, Copenhagen, Denmark) is a novel sperm<br> purification device. It consists of two chambers separated by a 10 μM microporous<br> membrane. Untreated semen is applied in one chamber, sperm collection medium<br> in the other. Motile sperm cells are selected by actively swimming through the<br> membrane pores into the medium containing chamber. After 30 min incubation,<br> the sperm collection medium can be aspirated and the purified sperm is ready<br> for further use.<br> In a first experiment we assessed sperm quality and recovery of frozen-thawed semen<br> from six different bulls (n = 6) prior to and after purification with the<br> VetCount<sup>TM</sup> Harvester or BoviPure<sup>TM</sup> gradient centrifugation, a commercial available standard technique. In a second approach, a competitive fertilization assay was performed. Ten straws per bull were pooled, split<br> in two subsamples, and simultaneously purified either with the VetCount<sup>TM</sup> Harvester<br> or BoviPure<sup>TM</sup> gradient centrifugation. Following purification, sperm cells<br> from each treatment group were fluorescently labeled with either MitoTracker<sup>TM</sup><br> Red FM or MitoTracker<sup>TM</sup> Green FM. <em>In vitro</em> matured oocytes were inseminated with<br> equal numbers of red and green labeled sperm. Eighteen hours after fertilization,<br> fluorescence microscopy was used to determine the origin of the fertilizing spermatozoon.</p>
X-ray diffraction images of bovine trypsin crystals recorded at the FemtoMAX beamline of Max IV synchrotron facility
<p>The deposition concerns bovine trypsin diffraction images in two wedges. Each image is recorded on a still crystal and separated by 0.1 deg rotation. The x4.tar.gz archive contains summed intensities from individual snapshots at the same orientation, whereas x4_single.tar.gz archive contains single snapshots/orientation. </p>
Number of bovine animals tested by age group, reporting country and target group, 2022
<p>The tables contain the number of bovine animals tested by age group, reporting country and target group, 2020.</p>
A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases
<p>The following data and scripts are part of the manuscript titled 'A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases' which is currently going through the peer-review process and has already been published as a preprint. Please read the README.txt file for information on the files uploaded.</p>
Simulations of bovine rhodopsin
<p>This repository contains the simulations of phosphorylated and unphosphorylated bovine rhodopsin (Uniprot ID: <code>P02699</code>). The simulations and their analysis were published in 'Proteins: Structure, Function, and Bioinformatics'.</p> <p>For any use please cite:</p> <blockquote> <p>Damodaran, K. et al.<br>New simulation insights on the structural transition mechanism of bovine rhodopsin activation.<br>Proteins 91, 771–780 (2023).</p> </blockquote>
Accompanying data for the paper "Non destructive qualification of bovine meat tenderness"
<p>This repository contains the raw data used in the article "Non destructive qualification of bovine meat tenderness",<br>authored by Sarah Iaquinta, Axel Conti, Mathis Coué, Étienne Roquefeuil, Jonathan Barés, Romain Léger, Arnaud Regazzi,<br>Stéphane Corn, Xavier Aleyrangues, Alain Peyron, and Anne-Sophie Caro.</p> <p>The repository is organized in three kind of files, where the raw data from the experiments are stored. <br>- "compression_test.xlsx" : Workbook containing the time-displacement-force measured during the compression tests;<br>- "indentation_relaxation.xlsx" : Workbook containing the time-displacement-force measured during the indentation-relaxation tests;<br>- .csv files containing the laser acquisition of the z_distance of the center of the indented surface during time.</p> <p>* The nomenclature of each sheetname and .csv file starts with the experiment date (April the 04th, 2023), then is the meatcut identifier <br>(FF = "faux filet", the french for "sirloin", and RDG = "rond-de-gîte", the french for "round". <br>Then are numbers to identify the number of the testing. </p>
MALDI-TOF spectra of bovine, caprine and ovine milk and their mixtures
<p>In this dataset we provide MALDI-TOF spectra of bovine milk in caprine and ovine milk. The dataset contains normalized spectra of pure milk samples and their mixtures. <strong>Different level of adulteration (0.5%, 1%, 5%, 10%, 20%, 40%, 60%, 80%)</strong> were analyzed throughout the lactation period of goat and sheep. Two different ranges of peptide-protein spectra <strong>(500–4000 Da; 4–20 kDa)</strong> were used. Exported spectra are in TXT files (<em>m/z</em> and intensity) for processing in other software (ex. mMass). Acquisition methods are included.</p> <p>MALDI-TOF MS analysis was performed using an Autoflex Speed (Bruker Daltonics, Germany) equipped with a SmartBeam<sup>TM</sup> II laser (355 nm) and flexControl software (version 3.4 Build 135, Bruker Daltonics, Germany).</p> <p> </p> <p>The dataset is a part of Supplementary file for the manuscript:</p> <p><em><strong>Evaluation of MALDI‐TOF MS technology in small ruminants’ milk adulteration using raw bovine milk</strong></em> by L. Rysova, P. Cejnar, O. Hanus, V. Legarova, J. Havlik, H. Nejeschlebova, I. Nemeckova, R. Jedelska, M. Bozik, submitted to <em>Journal of Dairy Science</em> (Manuscript ID JDS.2021-21396) on 08-Oct-2021.</p>
Radiofrequency ultrasound signals from bovine cartilage samples degraded with trypsin and collagenase
The folder Repository_RF_data contains the radiofrequency (RF) data acquired with an ArtUS EXT-1H system (Telemed, Italy) equipped with a 192 elements linear probe L15-7H40-A5 working in the frequency range 7.5-15 MHz, in the matlab format ".mat". Data were collected at 15 MHz, with a sampling rate of 40 MHz, adjusting the focus in the middle of the samples. The analysed samples were bovine cartilage samples, divided in three groups: - Control group: cartilage sample without any chemical treatment. - Trypsin group: cartilage samples immersed in a trypsin solution for 4h. - Collagenase group: cartilage samples immersed in a collagenase solution for 24h. The folder Repository_RF_data includes 2 matlab variables: - trypsin.mat = data acquired from 6 samples before and after the trypsin treatment - collagenase.mat = data acquired from 6 samples before and after the collagenase treatment Each variable is a TxN cell, where T is the time point of evaluation and N is the number of samples. The first row of each variable corresponds to the time zero of treatment, that is the control group; while the second row includes measurement at the final time point of treatment (4h for trypsin an 24h for collagenase). In particular, a single RF frame was acquired for all the analyses. Each recorded RF frame resulted in a matrix in which the columns (57) represented the number of RF scanning lines in a specific RF window, while the rows (727) constituted the number of samples in a single scanning line. For the details, see the articles published on Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Sorriento A, Cafarelli A, Valenza G, Ricotti L. Ex-vivo quantitative ultrasound assessment of cartilage degeneration. Annu Int Conf IEEE Eng Med Biol Soc. 2021 Nov;2021:2976-2980. doi: 10.1109/EMBC46164.2021.9630198. PMID: 34891870.
Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria
<p>Supplementary dataset from "<strong><em>Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria</em></strong>"</p> <p> </p> <p><strong>Supplementary Figure legends</strong></p> <p><strong>Figure S1. Illustration of the transposon insertions around the <em>M. bovis </em>genome. </strong>Sequencing of the input library showed that transposon insertions were evenly distributed around the genome and 27,419 of the permissible 66,931 thymine–adenine dinucleotide (TA) sites contained an insertion representing an insertion density of ~41%. The outer ring are the genomic coordinates, the blue lines represent transposon insertions and the gray boxes indicate regions of that did not have any insertions. Plot made with Circlize (Gu et al, 2014).</p> <p> </p> <p><strong>Figure S2. Diversity of the output library isolated from lung and thoracic lymph node lesions compared to the input library. </strong>On average, libraries recovered from lung lesions contained 14,456 unique mutants and those recovered from the lymph nodes contained an average of 16,210 unique mutants. Insertion density is represented as a proportion of the TA sites that contained insertions. The numbers on the x-axis refer to the sequencing file from that sample and come from individual animals (Bioproject ID: PRJNA816175, Submission ID: SUB11067380).</p> <p> </p> <p><strong>Figure S3. Volcano plots showing the distribution of log<sub>2</sub> fold-changes and -log<sub>10</sub> of adjusted p-values for representative lung (A) and lymph node (B) samples. </strong>Adjusted p-values (BH-fdr correction) < 0.000001 cluster at the limits of the plot and precision reflects the number of resampling iterations (10,000).</p> <p> </p> <p><strong>Figure S4. Scatterplot of mean log<sub>2</sub> fold change per gene for all lung samples against all thoracic lymph node samples</strong>. Correlation between mean log<sub>2</sub> fold change among genes between the tissues was calculated with Spearman's ranked correlation, = 0.878, p-value < 2.2e-16.</p> <p> </p> <p><strong>Figure S5. Fold-changes caused by transposon insertions in <em>RD1<sup>BCG</sup></em> and <em>RD1<sup>MIC</sup> </em>in the lungs and lymph nodes of infected cattle. </strong>Boxplot for log<sub>2 </sub>fold-changes in genes of the RD1<sup>BCG</sup> region. Samples with adjusted p-values (BH-fdr corrected) <0.05 are indicated with purple points. Gene names highlighted in magenta have fewer than 5 TA sites located in the gene; too few to determine the statistical significance of changes in insertion levels with this method.</p> <p> </p> <p><strong>Supplementary Tables </strong></p> <p><strong>Table S1. Sequencing statistics of the input and output transposon libraries. </strong>The numbers in the column labelled “filename” refers to the sequencing file from that sample and come from individual animals (Bioproject ID: PRJNA816175, Submission ID: SUB11067380).</p> <p> </p> <p><strong>Table S2. Tissues collected and scored for gross pathology. </strong>Tissues from head and neck lymph nodes (from the right and left sub-mandibular lymph nodes, the right and left medial retropharyngeal lymph nodes), thoracic lymph nodes (the right and left bronchial lymph nodes, the cranial tracheobronchial lymph nodes, the cranial and caudal mediastinal lymph nodes) and from lung lesions, were collected and scored.</p> <p> </p> <p><strong>Table S3. Log<sub>2</sub> fold-changes for insertions across the entire genome of <em>M. bovis</em> AF2122/97. </strong>Cells are coloured according to log<sub>2</sub> fold-change. Refer to the text for the gene groups in individual tabs.</p> <p> </p> <p><strong>Table S4. </strong>Custom transposon sequencing primers and adaptors used in sequencing of the transposon libraries.</p> <p> </p>
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
<p>Pangenomes for minigraph, pggb, and cactus containing assemblies from</p> <ul> <li>Hereford (cattle reference genome)</li> <li>Highland</li> <li>Brown Swiss</li> <li>Angus</li> <li>Simmental</li> <li>Original Braunvieh</li> <li>Piedmontese</li> <li>Nellore</li> <li>Brahman</li> <li>Yak</li> <li>Bison</li> <li>Gaur</li> </ul> <p> </p> <p>Also contains the genomic region classifications for the ARS-UCD1.2 reference genome for</p> <ul> <li>Satellites</li> <li>Tandem repeats</li> <li>Low mappability</li> <li>Repetitive regions</li> <li>Normal (everything else)</li> </ul>
Data for Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
<p><strong>Description of the datasets</strong></p> <p>Data are organized as folders and compressed with tar.gz.</p> <p>There are two compressed data folder: <strong>data </strong>which used for cattle genome graphs experiment and <strong>data_human</strong> which we used for human genome graphs experiment. </p> <p><strong>Cattle genome graphs experiments</strong></p> <p>First you need to unzip the file using command <em>tar -xvzf data.tar.gz</em>. After unzipping, the data folder is organized as follows:</p> <ul> <li>Utilities: contain bovine ARS-UCD 1.2 fasta reference with the accompanying index.</li> <li>Bin: contain the softwares used in the paper (vg, liftover, vcf2diploid)</li> <li>Part1: data for analysis in variant prioritization section, further subdivided into: <ul> <li>vcf_sim: variant files from four animal in each breed used to simulate reads</li> <li>reads_sim: simulated short reads used for read mapping</li> <li>vcf_freq: variants augmented to graphs filtered based on allele frequency</li> </ul> </li> <li>Part2: data used for analysis in the section of graph mapping with breeds-filtered variants, further subdivided into: <ul> <li>vcf_breed: variant files used to graphs construction.</li> </ul> </li> <li>Part3: data used for analysis in the section of consensus genome, further subdivided into: <ul> <li>read_sims: simulated reads as in the part1, but the coordinates are liftovered to the new consensus genomes.</li> <li>reference: contain the original reference and consensus references.</li> <li>vcf_consensus: contain major allele variants to construct consensus genomes.</li> </ul> </li> <li>Part4: data analysis in the section of whole genome graph construction and variant genotyping. <ul> <li>vcf_construct: variants from chromosome 1-29 from 82 Brown Swiss used to construct BSW whole genome graph.</li> <li>BSW_graph: whole genome Brown Swiss graph with the three accompanying indexes (xg,gcsa, and gbwt).</li> </ul> </li> </ul> <p><strong>Human genome graphs experiments</strong></p> <p>First you need to unzip the <em>data_human</em> file using command <em>tar -xvzf data</em><em>_hum.tar.gz</em>. After unzipping, the data folder is organized as follows:</p> <ul> <li>reference: the g1k_v37 reference used as a graph backbone</li> <li>vcf_sim: variant files from four individuals in each population used to simulate reads</li> <li>reads_sim: simulated short reads used for read mapping</li> <li>vcf_freq: variants augmented to graphs filtered based on allele frequency</li> </ul>
FIG. 2 in Protéger et abattre les bovins au pays de la « vache sacrée »: usages symboliques, politiques et économiques des vaches et des buffles dans l'Inde contemporaine
FIG. 2. — Carte de la législation relative à l'abattage des bovins en Inde (2015). Conception et réalisation: M. Bruckert; fond de carte: P. Raffard (UMR ISCC).
Supporting data for Novel functional sequences uncovered through a bovine multi-assembly graph
<p><strong>Description of the datasets</strong></p> <p>Data are organized as a folder and compressed with tar.gz.</p> <p>You need to unzip the folder using the command <em>tar -xz</em><em>v</em><em>f</em> data.tar.gz. Unzipping will output a folder named <em>data_tidy</em>, which is organized as follow:</p> <ul> <li>graph.gfa : Graph in GFA format constructed from 6 cattle assemblies</li> <li>nonref.fa : Non-reference sequences extracted from the graph</li> <li>nonref.fa.masked: Hard masked repetitive regions version of nonref.fa</li> <li>nonref_woflanking.fa: Nonref.fa without flanking sequences</li> <li>nonref_woflanking.fa.masked: Masked version of nonref_woflanking.fa</li> <li>augustus_predict.gtf: Annotated gene models of Augustus from non-ref sequences</li> <li>augustus_prot.fa: Protein fasta of the predicted gene models from Augustus</li> <li>breeds_assembled.gtf: Annotation of the StringTie assembled across-breed transcriptome</li> <li>breeds_expressed.tsv: Expression data of breeds_assembled.gtf</li> <li>de_assembled.gtf: Annotation of the StringTie assembled differentially-expressed transcriptome on non-ref sequences</li> <li>de_expression.tsv: Differential expression results from de_assembled.gtf</li> <li>variant_nonref.tsv: Variants called from non-ref sequences (-1, 0, 1, 2 indicates no call, hom ref, het, and hom alt respectively)</li> </ul>
Data from: Effect of culling on individual badger (Meles meles) behaviour: potential implications for bovine tuberculosis transmission
1. Culling wildlife as a form of disease management can have unexpected and sometimes counterproductive outcomes. In the UK, badgers (Meles meles) are culled in efforts to reduce badger-to-cattle transmission of Mycobacterium bovis, the causative agent of bovine tuberculosis (TB). However, culling has previously been associated with both increased and decreased incidence of M. bovis infection in cattle. 2. The adverse effects of culling have been linked to cull-induced changes in badger ranging, but such changes are not well documented at the individual level. Using GPS-collars, we characterised individual badger behaviour within an area subjected to widespread industry-led culling, comparing it with the same area before culling and with three unculled areas. 3. Culling was associated with a 61% increase (95% CI 27-103%) in monthly home range size, a 39% increase (95% CI 28-51%) in nightly maximum distance from the sett, and a 17% increase (95% CI 11-24%) in displacement between successive GPS-collar locations recorded at 20-minute intervals. Despite travelling further, we found a 91.2 minute (95% CI 67.1-115.3 minute) reduction in the nightly activity time of individual badgers associated with culling. These changes became apparent while culls were ongoing and persisted after culling ended. 4. Expanded ranging in culled areas was associated with individual badgers visiting 45% (95% CI 15-80%) more fields each month, suggesting that surviving individuals had the opportunity to contact more cattle. Moreover, surviving badgers showed a 19.9-fold increase (95% CI 10.8-36.4 increase) in the odds of trespassing into neighbouring group territories, increasing opportunities for intergroup contact. 5. Synthesis and Applications: Badger culling was associated with behavioural changes among surviving badgers which potentially increased opportunities for both badger-to-badger and badger-to-cattle transmission of M. bovis. Furthermore, by reducing the time badgers spent active, culling may have reduced badgers' accessibility to shooters, potentially undermining subsequent population control efforts. Our results specifically illustrate the challenges posed by badger behaviour to cull-based TB control strategies and furthermore, they highlight the negative impacts culling can have on integrated disease control strategies.
Material properties of bovine intervertebral discs across strain rates - dataset
<p>Raw experimental data from axial compression tests of each of the bovine intervertebral disc specimens and the .dat files from each of the subject specific FE models at each strain rate.</p>
X-ray diffraction images for bovine inositol monophosphatase.
<p>X-ray diffraction images for bovine inositol monophosphatase which were collected using the ESRF beamline ID14-4 to a resolution of around 1.4 Å. The data were collected in two passes, the second for measuring intensities that were overloaded in the first. More details are given in the included notes. </p>
Bovine pangenome assemblies
<p>Assemblies used in analysis presented in <a href="https://doi.org/10.1101/2021.11.02.466900">https://doi.org/10.1101/2021.11.02.466900</a>, containing the ARS-UCD1.2 reference genome and 32 assemblies compressed using <a href="https://github.com/refresh-bio/agc">agc</a>.</p> <p>Breed/species included are:</p> <p>N - Nellore</p> <p>B - Brown Swiss</p> <p>G - Gaur</p> <p>P - Piedmontese</p> <p>H - Original Braunvieh (paternal)</p> <p>O - Original Braunvieh (maternal if also an H assembly, otherwise primary assembly)</p> <p>With the following breed/species and assembler combinations.</p> <p>{H,O,N,B,G,P}_hifiasm {H,O,N,B,G,P}_shasta {O,N,B,G,P}_flye {O,N,B,G,P}_raven {O,N,B,G,P}_hicanu {O,N,B,G,P}_peregrine</p>
Supplementary files - Evaluation of MALDI-TOF MS technology in small ruminant milk adulteration using raw bovine milk
<p>The dataset is a part of Supplementary file for the manuscript:</p> <p><strong>Evaluation of MALDI-TOF MS technology in small ruminant milk adulteration using raw bovine milk</strong> by L. Rysova, P. Cejnar, O. Hanus, V. Legarova, J. Havlik, H. Nejeschlebova, I. Nemeckova, R. Jedelska, M. Bozik, submitted to <em>Journal of Dairy Science</em> (Manuscript ID JDS.2021-21396), Received October 8, 2021, Accepted January 31, 2022, Corresponding author: bozik@af.czu.cz, <a href="https://doi.org/10.3168/jds.2021-21396">https://doi.org/10.3168/jds.2021-21396</a></p> <p><strong>File 1:</strong> Detailed MALDI-TOF method description</p> <p><strong>File 2: </strong>Quantification of milk adulteration – calibration of the model Quantification of milk adulteration – calibration of the model</p> <p><strong>Table S1: </strong>Baseline characteristics of pure bovine milk which was used as an adulterant of caprine milk<strong> </strong></p> <p><strong>Table S2: </strong>Baseline characteristics of pure bovine milk which was used as an adulterant of ovine milk</p> <p><strong>Table S3: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using set A as the training set and set B as the test set.</p> <p><strong>Table S4: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using both, set A and set B , as the one training set and set C as the test set.</p> <p><strong>Table S5: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using set AB as the training set and set C as the test set.</p> <p>In this version <strong>SD values in Table S2 were corrected</strong>.</p>
16S Phyloseq R object accompanying the paper: Effects of storage methods on total bacterial count and microbial composition of bovine colostrum
<p>This ready to load <strong>phyloseq</strong> R S4 object contains the ASV table, taxonomy table and sample metadata (16S V3-V4). This data was build using the DaDa2 (version 1.12.1) and phyloseq (version 1.32) R packages using our raw Illumina MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA872909.</p> <p>The accompanying (peer-reviewed) scientific article can be found here: </p> <ul> <li>https://www.todo</li> <li>DOI: todo</li> </ul> <p> </p> <p><strong>Study/draft abstract:</strong></p> <p>Lisa Robbers, Hannes Bijkerk, Lars Ravesloot, Alex Bossers, Mirjam Nielen, Ruurd Jorritsma, Ad Koets, Lindert Benedictus</p> <p>Neonatal calves need to acquire passive immunity through maternal colostrum, as they are immunologically naïve and the structure of the bovine placenta does not allow passage of maternal antibodies during pregnancy. Milked colostrum is not initially sterile and may even contain high bacterial counts. Minimizing total bacterial counts in colostrum is generally advised, however bacterial quality of colostrum comprises more than just bacterial quantities, but also depends on the specific bacteria present. While duration and temperature of colostrum storage are known to affect total plate counts (TPC), less is known about the effects of storage on the actual bacterial composition of the TPC. We speculated that, depending on the storage conditions, colostrum is a substrate in which certain bacterial species can thrive affecting the quality of colostrum.</p> <p>We therefore aimed to characterize the effects of different colostrum storage methods on the composition of the viable, aerobic, microbial community. Colostrum samples were stored at different temperatures and for different durations. Next, bacterial growth was assessed using the aerobe plate count culture method, followed by 16S rRNA gene amplicon sequencing. Differences in the TPC bacterial compositions of the stored colostrum samples, as determined by 16S rRNA gene amplicon sequencing, were mostly explained by the variation in bacterial composition of the colostrum sample directly after milking. In line with earlier studies, the results from our study show that the TPC increased when colostrum was stored for 24 hours at room temperature, but not when stored in a refrigerator for the same duration. Community structure of the TPC of colostrum stored at room temperature for 24 hours and stored in a refrigerator for a week was significantly different from the baseline samples. The 16S rRNA sequencing results indicate this is because of increased numbers of <em>Enterobacteriaceae.</em> <em>Enterobacteriaceae</em> abundance in refrigerated samples seemed to remain stable for the first 24 hours, but increased drastically after one week. The results indicate that microbial composition of stored colostrum is mostly influenced by the composition of the colostrum sample directly after milking, which is most probably the result of contamination or other environmental influences during the milking process. This study provides a deeper insight in the changes in the microbial composition of colostrum TPC during practical storage conditions and provides a primer for more detailed research into the determinants of bacterial composition of colostrum and the linked health effects.</p>
Characterisation and comparison of Mycoplasma bovis strain types from Irish and Scottish bovine isolates in a global context - code and datasets.
<p>The objectives of this paper were to firstly, characterise the strains and genetic diversity within isolates of Mycoplasma bovis collected from clinical samples of bovine respiratory disease in Ireland and Scotland, and secondly, to provide a global phylogenetic context to these isolates. </p> <p>This archive contains associated Jupyter notebooks and metadata used in the analysis for the study.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.