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datasets available to search
ShareScore release 0.9.0
Dataset results
49 results for “File formats”
Example of GenX ORSO file format export
<p>An example file produced by GenX when exporting a dataset including model, parameters and statistical analysis.</p> <p>(Data header has been modified as original data did not have metadata.)</p>
Bundles for tractography file format testing and example
<p>Bundle files and their reference anatomy for testing and examples IO in Dipy</p>
Data and Analysis Files Repository: Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics
<p>Data and Analysis Files from "Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics"</p> <p>ArraySeq_Method.zip contains the following folder and contents:</p> <ul> <li>STARSolo: All code and count matrix output from fastq spatial barcode demultiplexing. </li> <li>Images: All resolution-downsampled H&E image scans from analyzed tissues</li> <li>Space_Ranger: All 10x Space Ranger output from Visium datasets generated in the paper. </li> <li>Analysis: All scripts for analyzing and plotting Array-seq and Visium datasets generated in this paper. Also contains output h5ad files. </li> </ul> <p>ArraySeq_Barcode_generation_n12.rmd: The script used to generate the Array-seq probes with 12-mer spatial barcodes. </p>
Waxholm Space atlas of the Sprague Dawley Rat Brain V4.2 ASR - BigDataViewer Xml/Hdf5 File Format
<p>This dataset is the <a href="https://www.nitrc.org/projects/whs-sd-atlas/">Waxholm Space atlas of the Sprague Dawley Rat Brain V4 atlas</a> converted to a Fiji BigDataViewer compatible file format.</p> <p>To cite this dataset, please follow the <a href="https://www.nitrc.org/citation/?group_id=1081">citation policy of the authors of this atlas.</a></p> <p>Channels:</p> <ul> <li>T2star_v1.01 masked by the label image</li> <li>T2star_v1.01 full data</li> <li>LABELS BORDER, a channel generated by delineating the original labels</li> <li>LABELS, the label image of the atlas</li> </ul> <p>ilf file : ontology structure</p> <p>Compared to the previous version, the first channel is the result of the second channel masked by the presence of labels (last channel). This allows to use more easily automated registration methods.</p> <p>The version 4.1 had an issue with the left/right definition (but not the 4.0)</p> <p>https://forum.image.sc/t/help-for-abba-in-fiji-rat-atlas-tags-atlas-regions-on-both-hemispheres-as-belonging-to-the-right-hemisphere/83020</p> <p>The only modification between this version and the previous one is to use an ASR convention for the positioning in 3D. It will match exactly the BrainGlobe atlases.</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>
Simulation input files: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or Pore Formation
<p>Simulation input files, and code for modification to simulation software for article:</p> <p>Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or PoreFormation</p> <p>Lukáš Sukeník,†,‡</p> <p>Liya Mukhamedova,†</p> <p>Michaela Procházková,†</p> <p>Karel Škubník,†</p> <p>Pavel Plevka,†</p> <p>and Robert Vácha∗,†,‡,¶</p> <p>†CEITEC – Central European Institute of Technology, Masaryk University, Kamenice753/5, 625 00 Brno, Czech Republic</p> <p>‡Department of Condensed Matter Physics, Faculty of Science, Masaryk University,Kotl ́aˇrsk ́a 267/2, 611 37 Brno, Czech Republic</p> <p>¶National Centre for Biomolecular Research, Faculty of Science, Masaryk University,Kamenice 5, 625 00 Brno, Czech Republic</p> <p>E-mail: robert.vacha@mail.muni.cz</p>
Example dataset for Bioformats issue with Nikon ND2 file format
<p>This is an example dataset to help troubleshoot issues with opening ND2 files in the current version of Fiji (latest Bioformats installed). The dataset opens fine in NIS Elements including the free Viewer version. There should be 4 separate images/channels. Three of the images are fluorescence (DAPI, GFP, Texas Red) and the last is DIC (transmitted light). They were taken with a Nikon DS-Ri2 colour camera. However, the data set opens as a 4 channel set where the first image is not recognisable and the subsequent 3 have vertical stripes (missing information?) but look a bit like the DIC image.</p>
PHYLIP format text files for BioGeoBEARS analysis. MSc thesis, University of Edinburgh.
<p>PHYLIP format text files for BioGeoBEARS analysis for each dataset. MSc thesis, University of Edinburgh.</p>
Model input files and output data for Pluto clathrate formation modeling
<p>Geochemical and thermal modeling input files and data for "Timing and abundance of clathrate formation controls ocean evolution in outer solar system bodies"</p>
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
Open the record for dataset details and reuse information.
Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Data, analysis scripts, and simulations files for "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"
<p>Measured data and analysis script, as well as, simulated data, and input scripts for our publication "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"</p>
Nexus-formatted text file of ISSR band presence/absence for 75 loci in Corallorhiza bentleyi
<p class="MsoNoSpacing">Mycoheterotrophic plants derive most or all carbon and nutrients from fungal partners and represent poorly understood components of forest biodiversity. Many are rare or endangered yet can be ecological indicators of forest ecosystem function due to their often highly specific fungal host requirements. One such species is the IUCN red-listed ('vulnerable'), fully mycoheterotrophic orchid, <i>Corallorhiza bentleyi</i>. This recently described species is among the rarest plants in Appalachia, known from five counties in Virginia and West Virginia, USA. The species has a restricted range, small population size, and is self-pollinating. Here, an integrative approach was taken in conservation genetic assessment of <i>C. bentleyi</i> using floral morphometrics, simple-sequence repeats, and fungal host DNA to characterize variation within and among sampling localities. Morphology reveals some differentiation among individuals from six sampling localities. Surprisingly, most genetic variation is found within localities, contrary to the expectation for a selfing species. Fungal host DNA reveals extreme specificity upon a few genotypes of a single ectomycorrhizal host species, <i>Tomentella fuscocinerea,</i> across all localities. The conservation implications of morphological, genetic, and symbiotic diversity in this vulnerable species are discussed, and additional assessment of conservation status is recommended based on: an obligate reproductive mode of selfing, preventing benefits of outcrossing among genetically non-identical individuals; extreme host specificity, severely restricting niche space; and highly fragmented habitat under threat from anthropogenic disturbance. This study underscores the importance of integrative conservation assessment, analyzing multiple data sources, and reveals patterns not readily apparent from census-based assessments alone.</p>
Metop-B level 1B file granules, EPS format
<p>Two short Metop-B scenes from the 2014-12-02, covering Western Canada+Groenland and Antarctica+South Africa.<br /> </p>
GNSS TEC Files CMN format
<p>Total electron content for 4 stations in Africa in .cmn format (text) 30 second sampling for 7 days.</p>
Figure files and simulation code for The formation of a nuclear-spin dark state in silicon
<p>This repository contains MATLAB figure files and simulation code for The formation of a nuclear-spin dark state in silicon. It includes a Readme file that provides a brief description of each file's contents.</p>
Data set (stata format) + do file for : Risk misperceptions of structured financial products with worst-of payout characteristics revisited
<p>This file contains the data set (in stata format) and do file associated with the paper entitled "Risk misperceptions of structured financial products with worst-of payout characteristics revisited"</p>
NYU -Machine Learning Data (coronal_pd_fs directory converted to BART file format)
<p>This is part of the training and test data that was used for the 2017 MRM manuscript on learning a variational network to reconstruct accelerated MR data (If you work with this data, please cite this paper):</p> <p>Hammernik K, Klatzer T, Kobler E, Recht M, Sodickson D, Pock T, Knoll F. Learning a Variational Network for Reconstruction of Accelerated MRI Data. Magnetic Resonance in Medicine 79: 3055–3071 (2018)</p> <p>The data has been converted to the BART cfl format. The same data is available in the MATLAB format on GLOBUS (https://app.globus.org/file-manager?origin_id=15c7de28-a76b-11e9-821c-02b7a92d8e58&origin_path=%2F). k-Space data is partly available in the ismrmrd file format at mridata.org.</p>
test files: video formats
For testing of harvesting code<p></p>with format=video/ogg or video/x-flv
Nexus-formatted text file of ISSR band presence/absence for 75 loci in Corallorhiza bentleyi
Open the record for dataset details and reuse information.
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.