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1,676 results for “C elegans”
Cryo soft X-ray tomography of 5 microns thick slab extracted from C. elegans anterior region
<p>Samples of C. elegans <span>larvae of strain DM8005 </span>were high pressure frozen using the waffle method. Multiple <span>roughly </span>5 micron thick slabs spanning <span>an L2 larva</span> were extracted using <span>the Serial Lift-Out</span> technique, and placed on rectangular <span>mesh </span>grids. Soft X-ray tomography was performed on individual slabs using the SXT-100 soft x-ray microscope at SiriusXT. The data reveals label free internal structure of fully hydrated C. elegans tissue, annotating the worm volume and adding context to cryo electron tomography data. </p> <p>SXT data was acquired from -50° to +53° in 1° steps and reconstructed using Weighted Back Projection. A 32 nm objective zone plate was used. Data pixel size is 29 nm. </p>
3D nuclei instance segmentation dataset of fluorescence microscopy volumes of C. elegans
<p>The dataset consists of 28 confocal microscopy volumes of C. elegans worms at the L1 stage and corresponding stacks of densely annotated nuclei instance segmentation masks.</p> <p>* 28 raw images and corresponding masks of average dimension (xyz) 1050 x 140 x 140<br> * Pixelsize (xyz): 0.116 x 0.116 x 0.122μm<br> * Microscope: Leica confocal microscopy, 63x oil objective</p> <p><br> The original raw data and preliminary annotations were part of the following publication (please cite if you use the dataset):<br> <br> <em>Long, F., Peng, H., Liu, X., Kim, S. K., & Myers, E. (2009). A 3D digital atlas of C. elegans and its application to single-cell analyses. Nature methods, 6(9), 667-672.</em></p> <p>The nuclei annotation masks were further manually curated by Dagmar Kainmueller (MDC Berlin) for the following publication:</p> <p><em>Hirsch, P., & Kainmueller, D. (2020). An auxiliary task for learning nuclei segmentation in 3d microscopy images. In Medical Imaging with Deep Learning (pp. 304-321). PMLR.</em></p> <p>We provide the dataset already structured into the train/validation/test split as used by the above as well as the following publications: </p> <p><em>Weigert, M., Schmidt, U., Haase, R., Sugawara, K., & Myers, G. (2020). Star-convex polyhedra for 3d object detection and segmentation in microscopy. In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (pp. 3666-3673).</em><br> </p> <p> </p>
Data set for the article 'Temporal scaling in C. elegans larval development'
<p>This directory contains all analyzed data and data analysis scripts to create all figures for the article<br> Filina et al., Temporal scaling in C. elegans larval development, PNAS 2022 119:e2123110119</p>
A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva
<p>Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis<sup>1</sup> when environmental conditions are unfavorable. This state-transition requires the execution of complex genetic and biochemical programs<sup>1</sup><sup>,</sup><sup>2</sup><sup>,</sup><sup>3</sup>, that enables the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera <em>Panagrolaimus</em> and <em>Plectus</em><sup>4</sup>. Here, we present precise radiocarbon dating indicating that the <em>Panagrolaimus</em> individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named <em>Panagrolaimus n. sp</em>. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in <em>Panagrolaimus n. sp. </em>and in <em>C. elegans</em> is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that <em>C. elegans</em> dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.</p>
Data from: Neuropeptide signalling shapes feeding and reproductive behaviours in male C. elegans
<p><span><span>Sexual dimorphism occurs where different sexes of the same species display differences in characteristics not limited to reproduction. For the nematode <em><span>Caenorhabditis elegans</span></em>, in which the complete neuroanatomy has been solved for both hermaphrodites and males, sexually dimorphic features have been observed both in terms of the number of neurons and in synaptic connectivity. In addition, male behaviours, such as food-leaving to prioritise searching for mates, have been attributed to neuropeptides released from sex-shared or sex-specific neurons.</span></span></p> <p><span> </span></p> <p>This dataset compiles the results obtained in our investigation of how LURY-1 neuropeptides regulate feeding and mating behaviours in <em>C. elegans</em>. These contain confocal micrographs and z-stacks of fluorescence reporter imaging used to demonstrate the expression pattern of<em> lury-1</em> and <em>npr-22</em>, including micrographs used for cell identification of <em>lury-1</em> expressing neurons in the male worm. Other behavioural data from mating efficiency assays, pharyngeal pumping assays and food leaving assays are also shown. These include male turning behaviour examined through video recordings of male mating; the videos are also included as part of this dataset.</p> <p>In this study ("Neuropeptide signalling shapes feeding and reproductive behaviours in male <em>C. elegans</em>"), our findings indicate sex-specific roles of this peptide in feeding and reproduction in <em>C. elegans</em>. This provides further insight into neuromodulatory control of sexually dimorphic behaviours.</p>
3D+time nuclei tracking dataset of confocal fluorescence microscopy time series of C. elegans embryos
<p>The dataset consists of 3 confocal microscopy time series of <em>C. elegans</em> embryos, fully tracked with StarryNite followed by manual curation</p> <ul> <li>3 raw time-series and the corresponding tracks/lineage trees</li> <li>temporal resolution; 75s</li> <li>temporal extent: 400 frames, tracked for at least 370 frames</li> <li>spatial resolution (zyx): 0.75 x 0.15 x 0.15 μm</li> <li>spatial extent (zyx):/ 41 x 512 x 512px</li> <li>Microscope: Zeiss Axio Observer.Z1</li> </ul> <p>The annotations were created using the method described in:</p> <p><em> Santella, A., Du, Z. & Bao, Z. A semi-local neighborhood-based framework for probabilistic cell lineage tracing. BMC Bioinformatics 15, 217 (2014). <a href="https://doi.org/10.1186/1471-2105-15-217">https://doi.org/10.1186/1471-2105-15-217</a></em></p> <p>Additionally the data was extended and used for the development of a new tracking method in the following publication:</p> <p><em> Hirsch, P., Malin-Mayor C., Santella, A., Preibisch, S., Kainmueller, D., Funke, J. Tracking by weakly-supervised learning and graph optimization for whole-embryo C. elegans lineages. MICCAI 2022.</em></p> <p>For questions please contact Peter Hirsch (<a href="mailto:peter.hirsch@mdc-berlin.de">peterhirsch@posteo.de</a>).</p>
Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools - C. elegans unc-16 and N2 motion behavior dataset
<p>Dataset contains <em>Caenorhabditis</em> <em>elegans </em>motor behaviors originally used in this publication <a href="https://www.nature.com/articles/nmeth.2560">10.1038/nmeth.2560</a> and downloaded from the available <a href="http://wormbehavior.mrc-lmb.cam.ac.uk/">DB</a> which points to Zenodo. The dataset consists in two worm strains, 20 individuals from a mutant unc-16 strain with reduced mobility and 40 individuals from a control N2 strain. The behavioral measures derived from each individual worm trajectory were available in a HDF5-formatted file (Hierarchical Data Format Version 5) that has been included in this dataset.</p> <p>The data set consist in:</p> <p>- a "mappings" folder containing all the mappings used by the pergola in the pipeline to convert data.</p> <p>- a "N2" folder containing the 40 HDF5 files with the measures derived from the N2 worms.</p> <p>- a "N2" folder containing the 20 HDF5 files with the measures derived from the unc-16 worms.</p>
Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence
Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.
Systematic creation and phenotyping of Mendelian disease models in C. elegans: towards large-scale drug repurposing
<p>Data collected for the eLife OpenAccess paper: Systematic creation and phenotyping of Mendelian disease models in <em>C. elegans</em>: towards large-scale drug repurposing. (doi: 10.7554/eLife.92491.1)</p> <p>Contains: extracted features, calculated stats, normalised z-scores and timerseries data of all the disease model mutants generated. In addition, there is a static .html file that allows for mousing over the clustermaps to easily view differences in strains compared to the N2 wild-type. Dataset also contains, metadata and feature summary/file name information of FDA-library drug screen and the confirmation screen of the hit from this (i.e., all data collected in published in the associated paper). </p>
High-throughput behavioural phenotyping of 25 C. elegans disease models including patient-specific mutations
<p>This repository contains: all code, phenomic data, extracted features, calculated stats, normalised z-scores and timerseries data for all of the disease mutant phenologs and data in our paper: High-throughput behavioural phenotyping of 25 C. elegans disease models including patient-specific mutations.</p>
A high-precision method of segmenting complex postures in C. elegans and deep phenotyping to analyze lifespan
<p>The data for our paper, "A high-precision method of segmenting complex postures in <em>C. elegans</em> and deep phenotyping to analyze lifespan", includes the following three components:</p> <ol> <li>Synthetic image dataset, CSB-1 dataset, and MD dataset, which originate from the paper <em>"WormSwin: Instance segmentation of C. elegans using Vision Transformer"</em>.</li> <li>BBC010 dataset, sourced from the paper <em>"Annotated high-throughput microscopy image sets for validation".</em></li> <li>Training weights for the Synthetic image dataset, CSB-1 dataset, MD dataset, and BBC010 dataset, as well as the pretrained weights used for worm tracking. The training weights from the synthetic image dataset can serve as pretrained weights for training on other datasets.</li> </ol> <p>Our experimental results are based on the average of multiple training runs; here, we have only uploaded one set of weights per dataset to facilitate reproducibility for readers. For more detailed information on the datasets, please refer to the relevant papers.</p> <p> </p>
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
<p>The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using <i>C. elegans</i> germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of <i>eggd-1</i> and <i>eggd-2</i> results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.</p>
Visualizing the organization and differentiation of the male-specific nervous system of C. elegans
<p>Image volumes and annotations for male NeuroPAL, flp-3, flp-27, and nlp-51 expression.</p> <p>The following image volumes were annotated by Tessa Tekieli, Chen Wang, and Robert Fernandez for:<br> "Visualizing the organization and differentiation of the male-specific nervous system of C. elegans".</p> <p>The publication is available here:<br> https://journals.biologists.com/dev/article-abstract/doi/10.1242/dev.199687/271902/Visualizing-the-organization-and-differentiation</p> <p>These image files can be viewed with the NeuroPAL ID software, available at:<br> https://www.hobertlab.org/neuropal/<br> OR<br> https://github.com/amin-nejat/CELL_ID</p> <p>This software was provided for the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. <em>elegans</em>".<br> The publication is available here:<br> https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2</p> <p>Please cite the NeuroPAL publication when using the software.</p>
Probiotic Bacillus subtilis Protects against a-Synuclein Aggregation in C. elegans (fluorescence microscopy data)
<p>This project has been submitted by the Maria Doitsidou Lab.<br> <br> Project contents:<br> This project contains datasets of z-stack images of <em>C. elegans</em> strains used to study how the gut microbiome affects Parkinson’s disease. Each strain contains a chromosomal insertion containing YFP fused to α-synuclein (pkIs2386[Punc-54::α-synuclein::YFP + unc-119(+)]). The following<em> C. elegans</em> strains were used and/or created for this project:<br> NL5901 pkIs2386[Punc-54::α-synuclein::YFP + unc-119(+)]<br> MDH586 daf-2(e1370) III; pkIs2386<br> MDH585 daf-16(mu86) I; pkIs2386<br> MDH587 hsf-1(sy441) I; pkIs2386<br> MDH657 daf-2(e1370) III; daf-16(mu86) I; pkIs2386<br> MDH614 daf-2(gk390525) III; pkIs2386<br> MDH611 eat-2(ad465) II; pkIs2386<br> MDH711 lagr-1(gk331) I, pkIs2386<br> MDH725 sptl-3(ok1927) II; pkIs2386<br> MDH724 asm-3(ok1744) IV; pkIs2386.<br> <br> High magnification (40x objective) z stack images of the head region were obtained by using a Zeiss Axio imager 2 microscope.<br> <br> <br> Aim:<br> Study how a probiotic<em> B. subtilis</em> strain affects alpha-synuclein protein aggregation.<br> <br> Main results:<br> The authors showed that the probiotic<em> B. subtilis</em> strain PXN21 inhibits and clears a-synuclein aggregation in a <em>C. elegans </em>model. The bacterium acts via metabolites and biofilm formation to activate protective pathways in the host, including DAF-16/FOXO and sphingolipid metabolism.<br> <br> Contributors:<br> Maria Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andres Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley-Wall and Maria Doitsidou<br> <br> These datasets were used in the following publication:<br> <br> Probiotic Bacillus subtilis Protects against a-Synuclein Aggregation in <em>C. elegans</em><br> <br> Maria Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andres Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley-Wall and Maria Doitsidou<br> <br> Cell Reports January 14, 2020 30 367-380; first published January 14, 2020 <a href="https://doi.org/10.1016/j.celrep.2019.12.078">https://doi.org/10.1016/j.celrep.2019.12.078</a></p>
Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans
<p>To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in <em>Caenorhabditis elegans,</em> neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal <em>hsf-1</em> is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.</p>
JU394 C. elegans Wild Isolate (Hermanville, France) | 2011-06-14T15:11:35+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=Jsj3MvSbNes</li> <li><b>strain</b> : JU394</li> <li><b>timestamp</b> : 2011-06-14T15:11:35+01:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : C. elegans Wild Isolate (Hermanville, France)</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : 655 JU394 on food R_2011_06_14__15_11_35___1___11</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.33597</li> <li><b>number of segmented skeletons</b> : 26820</li> </ul>
JU394 C. elegans Wild Isolate (Hermanville, France) | 2011-06-14T12:50:02+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=ebum6dhZ7A8</li> <li><b>strain</b> : JU394</li> <li><b>timestamp</b> : 2011-06-14T12:50:02+01:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : C. elegans Wild Isolate (Hermanville, France)</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : 655 JU394 on food L_2011_06_14__12_50_02___1___7</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.33597</li> <li><b>number of segmented skeletons</b> : 26843</li> </ul>
ED3017 C. elegans Wild Isolate (Ediburgh, Scotland) | 2011-06-30T10:07:35+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=RUJDhCtJ4G4</li> <li><b>strain</b> : ED3017</li> <li><b>timestamp</b> : 2011-06-30T10:07:35+01:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : C. elegans Wild Isolate (Ediburgh, Scotland)</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : 422 ED3017 on food L_2011_06_30__10_07_35___1___1</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.40989</li> <li><b>number of segmented skeletons</b> : 26205</li> </ul>
ED3017 C. elegans Wild Isolate (Ediburgh, Scotland) | 2011-06-14T15:16:24+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=JJ3i4Qaiaec</li> <li><b>strain</b> : ED3017</li> <li><b>timestamp</b> : 2011-06-14T15:16:24+01:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : C. elegans Wild Isolate (Ediburgh, Scotland)</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : 422 ED3017 on food R_2011_06_14__15_16_24___8___11</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.52754</li> <li><b>number of segmented skeletons</b> : 26669</li> </ul>
ED3017 C. elegans Wild Isolate (Ediburgh, Scotland) | 2011-06-14T12:54:51+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=uLuqJULcUMU</li> <li><b>strain</b> : ED3017</li> <li><b>timestamp</b> : 2011-06-14T12:54:51+01:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : C. elegans Wild Isolate (Ediburgh, Scotland)</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : 422 ED3017 on food L_2011_06_14__12_54_51___8___7</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.52754</li> <li><b>number of segmented skeletons</b> : 26495</li> </ul>
ScienceDex guides
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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.