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Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities
<p>Example <strong>Microscopy Metadata </strong>(Microscope.JSON and Settings.JSON)<strong> files </strong>produced using<strong> <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> </strong>to document the <strong>Hardware Specifications</strong> of example Microscopes and the <strong>Image Acquisition Settings</strong> utilized to acquire example images as listed in the table below.</p> <blockquote> <p>For each facility, the dataset contains two JSON files:</p> <ol> <li><strong>Microscope.JSON file</strong> (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)</li> <li><strong>Settings.JSON file</strong> (indicated with the name of the image and with the _AS suffix)</li> </ol> </blockquote> <p><strong>Micro-Meta App was</strong> developed as part of a <strong>global community initiative</strong> including the <a href="http://www.4dnucleome.org/"><strong>4D Nucleome (4DN)</strong> </a>Imaging Working Group, <strong>BioImaging North America (BINA)</strong> <a href="https://www.bioimagingna.org/qc-dm-wg">Quality Control and Data Management Working Group</a>, and <strong>QUAlity and REProducibility for Instrument and Images in Light Microscopy</strong> (<a href="https://quarep.org/"><strong>QUAREP-LiMi</strong></a>), to extend the <strong>Open Microscopy Environment (OME)</strong> <a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html">data model</a>.</p> <blockquote> <p>The works of this <strong>global community effort</strong> resulted in multiple publications featured on a recent <strong>Nature Methods FOCUS ISSUE </strong>dedicated to <a href="https://www.nature.com/collections/djiciihhjh">Reporting and reproducibility in microscopy</a>.</p> </blockquote> <blockquote> <p><strong>Learn More!</strong> For a thorough description of <strong>Micro-Meta App</strong> consult our recent <a href="https://doi.org/10.1038/s41592-021-01315-z">Nature Methods</a> and <a href="https://doi.org/10.1101/2021.05.31.446382">BioRxiv.org</a> publications!</p> </blockquote> <p> </p> <table> <tbody> <tr> <td><strong>Nr.</strong></td> <td><strong>Manufacturer</strong></td> <td><strong>Model</strong></td> <td><strong>Tier</strong></td> <td><strong>Εxperiment Type</strong></td> <td><strong>Facility Name</strong></td> <td><strong>Department and Institution</strong></td> <td><strong>URL</strong></td> <td><strong>References</strong></td> </tr> <tr> <td>1</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1 (with LSM 710 scan head)</strong></td> <td>1</td> <td>3D visualization of superhydrophobic polymer-nanoparticles</td> <td>Centre for Cell Imaging (CCI)</td> <td>University of Liverpool</td> <td>https://cci.liv.ac.uk/equipment_710.html</td> <td>Upton et al., 2020</td> </tr> <tr> <td>2</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer (Axiovert 200M)</strong></td> <td>2</td> <td>Μeasurement of illumination stability on Chinese Hamster Ovary cells expressing Paxillin-EGFP</td> <td>Advanced BioImaging Facility (ABIF).</td> <td>McGill University</td> <td>https://www.mcgill.ca/abif/equipment/axiovert-1</td> <td>Kiepas et al., 2020</td> </tr> <tr> <td>3</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1 (with Spinning Disk)</strong></td> <td>2</td> <td>Immunofluorescence imaging of cryosection of Mouse kidney</td> <td>Imagerie Cellulaire; Quality Control managed by Miacellavie (https://miacellavie.com/)</td> <td>Centre de recherche du Centre Hospitalier Université de Montréal (CR CHUM), University of Montreal</td> <td>https://www.chumontreal.qc.ca/crchum/plateformes-et-services (the web site is for all core facilities, not specifically for the core facility hosting this microscope)</td> <td>Pilliod et al., 2020</td> </tr> <tr> <td>4</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Imager Z2 (with Apotome)</strong></td> <td>2</td> <td>Immunofluorescence imaging of mitotic division in Hela cells using </td> <td>Bioimaging Unit</td> <td>Newcastle University</td> <td>https://www.ncl.ac.uk/bioimaging/</td> <td>Watson et al., 2020</td> </tr> <tr> <td>5</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1</strong></td> <td>2</td> <td>Fluorescence microscopy of human skin fibroblasts from Glycogen Storage Disease patients.</td> <td>Life Imaging Center (LIC)</td> <td>Centre for Integrative Signalling Analysis (CISA), University of Freiburg</td> <td>https://miap.eu/equipments/sd-i-abl/</td> <td>Hannibal et al., 2020</td> </tr> <tr> <td>6</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DMI6000B</strong></td> <td>2</td> <td>3D immunofluorescence imaging rhinovirus infected macrophages </td> <td>IMAG'IC Confocal Microscopy Facility</td> <td>Institut Cochin, CNRS, INSERM, Université de Paris</td> <td>https://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view</td> <td>Jubrail et al., 2020</td> </tr> <tr> <td>7</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DM5500B</strong></td> <td>2</td> <td>Immunofluorescence analysis of the colocalization of PML bodies with DNA double-strand breaks</td> <td>Bioimaging Unit</td> <td>Edwardson Building on the Campus for Ageing and Vitality, Newcastle University</td> <td>https://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview</td> <td>da Silva et al., 2019; Nelson et al., 2012<br> </td> </tr> <tr> <td>8</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DMI8-CS (with TCS SP8 STED 3X)</strong></td> <td>2</td> <td>Live-cell imaging of N. benthamiana leaves cells-derived protoplasts</td> <td>Center for Advanced Imaging (CAi)</td> <td>School of Mathematics/Natural Sciences, Heinrich-Heine-Universität Düsseldorf</td> <td>https://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x</td> <td>Singer et al., 2017; Hänsch et al., 2020</td> </tr> <tr> <td>9</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti</strong></td> <td>2</td> <td>Immunofluorescence analysis of the cytoskeleton structure in COS cells</td> <td>Advanced Imaging Center (AIC)</td> <td>Janelia Research Campus, Howard Hughes Medical Institute</td> <td>https://www.janelia.org/support-team/light-microscopy/equipment</td> <td>Abdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020</td> </tr> <tr> <td>10</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti-E (HCA)</strong></td> <td>2</td> <td>Τime-lapse analysis of the bursting behavior of amine-functionalized vesicular assemblies</td> <td>Light Microscopy Facility (IALS-LIF)</td> <td>Institute for Applied Life Sciences, University of Massachusetts at Amherst</td> <td>https://www.umass.edu/ials/light-microscopy</td> <td>Fernandez et al., 2020</td> </tr> <tr> <td>11</td> <td><strong>Nikon Instruments/Coleman laboratory (customized)</strong></td> <td><strong>TIRF HILO Epifluorescence light Microscope (THEM)/ Eclipse Ti</strong></td> <td>2</td> <td>Single-particle tracking of Halo-tagged PCNA in Lox cells</td> <td>Coleman laboratory</td> <td>Anatomy and Structural Biology Department, The Albert Einstein College of Medicine</td> <td>https://einsteinmed.org/faculty/12252/robert-coleman/</td> <td>Drosopoulos et al., 2020</td> </tr> <tr> <td>12</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti (with Andor Dragon Fly Spinning Disk)</strong></td> <td>2</td> <td>Investigation of the 3D structure of cerebral organoids</td> <td>Montpellier Resources Imagerie</td> <td>Centre de Recherche de Biologie cellulaire de Montpellier (MRI-CRBM), CNRS, Univerity of Montpellier</td> <td>https://www.mri.cnrs.fr/en/optical-imaging/our-facilities/mri-crbm.html</td> <td>Ayala-Nunez et al., 2019</td> </tr> <tr> <td>13</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti2</strong></td> <td>2</td> <td>Ιmmunofluorescence imaging of cryosections of mouse hearth myocardium </td> <td>Neuroscience Center Microscopy Core</td> <td>Neuroscience Center, University of North Carolina</td> <td>https://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/</td> <td>Aghajanian et al., 2021</td> </tr> <tr> <td>14</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti2</strong></td> <td>2</td> <td>Live-cell imaging of bacterial cells expressing GFP-PopZ</td> <td>Microscopy Resources on the North Quad (MicRoN)</td> <td>Harvard Medical School </td> <td>https://micron.hms.harvard.edu/</td> <td>Lim and Bernhardt 2019; Lim et al., 2019</td> </tr> <tr> <td>15</td> <td><strong>Olympus/Biomedical Imaging Group (customized)</strong></td> <td><strong>TIRF Epifluorescence Structured light Microscope (TESM)/IX71</strong></td> <td>3</td> <td>3D distribution of HIV-1 in the nucleus of human cells</td> <td>Biomedical Imaging Group</td> <td>Program in Molecular Medicine, University of Massachusetts Medical School</td> <td>https://trello.com/b/BQ8zCcQC/tirf-epi-fluorescence-structured-light-microscope</td> <td>Navaroli et al., 2012</td> </tr> <tr> <td>16</td> <td><strong>Olympus/Computer Vision Laboratory (customized)</strong></td> <td><strong>3D BrightField Scanner/IX71</strong></td> <td>3</td> <td>Transmitted light brightfield visualization of swimming spermatocytes</td> <td>Laboratorio Nacional de Microscopia Avanzada (LNMA) and Computer Vision Laboratory of the Institute of Biotechnology</td> <td>Universidad Nacional Autonoma de Mexico (UNAM)</td> <td>https://lnma.unam.mx/wp/</td> <td>Pimentel et al., 2012; Silva-Villalobos et al., 2014</td> </tr> </tbody> </table> <p><strong>Getting started</strong></p> <p>Use these videos to get started with using Micro-Meta App after installation into OMERO and downloading the example data files:</p> <ol> <li><a href="https://vimeo.com/562022222">Video 1</a></li> <li><a href="https://vimeo.com/562022281">Video 2</a></li> </ol> <p><strong>More information</strong></p> <blockquote> <p>For full information on how to use Micro-Meta App please utilize the following resources:</p> <ol> <li>Micro-Meta App <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">website</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/index.html">Full documentation</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/intro/installation.html">Installation</a> instructions</li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/tutorials/index.html#step-by-step-instructions">Step-by-Step Instructions</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/tutorials/VideoTutorials.html#micro-meta-app-video-tutorials">Tutorial Videos</a></li> </ol> </blockquote> <p><strong>Background</strong></p> <p>If you want to learn more about the importance of <strong>metadata and quality contro</strong>l to ensure full <strong>reproducibility, quality and scientific value</strong> in light microscopy, please take a look at our recent publications describing the development of community-driven light <strong>4DN-BINA-OME Microscopy Metadata</strong> specifications <a href="https://doi.org/10.1038/s41592-021-01327-9">Nature Methods</a> and <a href="https://doi.org/10.1101/2021.04.25.441198">BioRxiv.org</a> and our <a href="https://arxiv.org/abs/1910.11370">overview manuscript</a> entitled <strong>A perspective on Microscopy Metadata: data provenance and quality control</strong>.</p> <p> </p> <p> </p>
Example Microscopy Metadata JSON files produced using Micro-Meta App to document the acquisition of example images using a custom-built TIRF Epifluorescence Structured Illumination Microscope
<p><strong>Example Microscopy Metadata JSON files produced using the <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> documenting an example raw-image file acquired using the custom-built TIRF Epifluorescence Structured Illumination Microscope.</strong></p> <p>For this use case, which is presented in Figure 5 of <a href="http://doi: https://doi.org/10.1101/2021.05.31.446382">Rigano et al., 2021</a>, Micro-Meta App was utilized to document:</p> <p>1) The <strong>Hardware Specifications</strong> of the custom build TIRF Epifluorescence Structured light Microscope (TESM; <a href="https://www.pnas.org/content/109/8/E471.long">Navaroli et al., 2010</a>) developed, built on the basis of the based on Olympus IX71 microscope stand, and owned by the Biomedical Imaging Group (http://big.umassmed.edu/) at the Program in Molecular Medicine of the University of Massachusetts Medical School. Because TESM was custom-built the most appropriate documentation level is <strong>Tier 3</strong> (<em>Manufacturing/Technical Development/Full Documentation</em>) as specified by the <a href="https://doi.org/10.5281/zenodo.4710731">4DN-BINA-OME</a> Microscopy Metadata model (<a href="https://doi.org/10.1101/2021.04.25.441198">Hammer et al., 2021</a>).</p> <p>The TESM Hardware Specifications are stored in: <strong>Rigano et al._Figure 5_UseCase_Biomedical Imaging Group_TESM.JSON</strong></p> <p>2) The <strong>Image Acquisition Settings</strong> that were applied to the TESM microscope for the acquisition of an example image (FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif) obtained by Nicholas Vecchietti and Caterina Strambio-De-Castillia. For this image, TZM-bl human cells were infected with HIV-1 retroviral three-part vector (FSWT+PAX2+pMD2.G). Six hours post-infection cells were fixed for 10 min with 1% formaldehyde in PBS, and permeabilized. Cells were stained with mouse anti-p24 primary antibody followed by DyLight488-anti-Mouse secondary antibody, to detect HIV-1 viral Capsid. In addition, cells were counterstained using rabbit anti-Lamin B1 primary antibody followed by DyLight649-anti-Rabbit secondary antibody, to visualize the nuclear envelope and with DAPI to visualize the nuclear chromosomal DNA.</p> <p>The Image Acquisition Settings used to acquire the FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif image are stored in: <strong>Rigano et al._Figure 5_UseCase_AS_fswt-6hvirus-10minfix-stk_4-epi.tif.JSON</strong></p> <p><em><strong>Instructional video tutorials on how to use these example data files:</strong></em><br> Use these videos to get started with using Micro-Meta App after downloading the example data files available here.</p> <ul> <li><a href="https://vimeo.com/562022222">Part 1/2</a></li> <li><a href="https://vimeo.com/562022281">Part 2/2</a></li> </ul>
Reference data and documentation for Skills4EOSC Deliverable D6.1 Mapping of existing professional networks
<p>This record presents the data underlying <strong>Skills4EOSC Deliverable D6.1 Mapping of existing professional networks</strong> and relevant documentation of the search string.</p>
Documents first indexed in the SLUB catalog in 2022
<p>The data set is available as a gzip-compressed, line-delimited JSON file and contains the 7,127,497 documents first indexed in the <a href="https://katalog.slub-dresden.de">SLUB catalog</a> in 2022 with the fields id (document identifier) and first_indexed (timestamp). The id consists of a creator id (optional), source id and a record id according to the scheme [{creator_id}-]{source_id}-{record_id}. If the record id contains characters that are unsuitable for URLs, it is base64-encoded without any padding. The first_indexed field, which is part of VuFind's Solr index schema, was determined using a Django application that regularly monitors the Solr cores of the SLUB catalog. The respective document sets from different points in time are compared with each other in order to determine new documents, i.e. document identifiers. If a new document is found, first_indexed is assigned the timestamp from the last_indexed field. The field obtained in this way serves as the basis for creating a list of new titles. However, it should be noted that neither all first indexed documents necessarily represent new titles, nor do the documents contained in this data set still have to be in the catalog. To check whether a document is currently in the SLUB catalog, its detailed view can be retrieved using the following URL scheme: https://katalog.slub-dresden.de/id/{id}. Example: <a href="https://katalog.slub-dresden.de/id/0-173837243X">https://katalog.slub-dresden.de/id/0-173837243X</a>.</p>
Documents first indexed in the SLUB catalog in 2023
<p>The data set is available as a gzip-compressed, line-delimited JSON file and contains the 17,182,153 documents first indexed in the <a href="https://katalog.slub-dresden.de/">SLUB catalog</a> in 2023 with the fields id (document identifier) and first_indexed (timestamp). The id consists of a creator id (optional), source id and a record id according to the scheme [{creator_id}-]{source_id}-{record_id}. If the record id contains characters that are unsuitable for URLs, it is base64-encoded without any padding. The first_indexed field, which is part of VuFind's Solr index schema, was determined using a Django application that regularly monitors the Solr cores of the SLUB catalog. The respective document sets from different points in time are compared with each other in order to determine new documents, i.e. document identifiers. If a new document is found, first_indexed is assigned the timestamp from the last_indexed field. The field obtained in this way serves as the basis for creating a list of new titles. However, it should be noted that neither all first indexed documents necessarily represent new titles, nor do the documents contained in this data set still have to be in the catalog. To check whether a document is currently in the SLUB catalog, its detailed view can be retrieved using the following URL scheme: https://katalog.slub-dresden.de/id/{id}. Example: <a href="https://katalog.slub-dresden.de/id/0-185178604X">https://katalog.slub-dresden.de/id/0-185178604X</a>.</p>
GEOLAB Blind Prediction Contest - Supporting Documentation
<p>As part of the <a href="https://project-geolab.eu/">GEOLAB project</a>, the Institute of Geotechnics of TU Darmstadt called geotechnical engineers from industry and academia to participate in an international Blind Prediction Contest (BPC) on the response of piles under monotonic and cyclic lateral loading. Two separate tests were performed on a hollow open-ended steel pile embedded in dry sand. One test under monotonic loading and the other under quasi-static harmonic loading with more than 10,000 loading cycles.</p> <p>Contestant teams were allowed to submit predictions for both tests or for the monotonic test only. The predictions were objectively marked based on their discrepancy with the experimental values. The teams with the higher score in the prediction of each test were publicly announced. The rest of the submitted predictions will be anonymised and used for assessing the state of the art and the state of practice by the organiser committee.</p> <p>This dataset includes the supporting documentation provided to the participants. </p>
Evidence of a Vulnerable Marine Ecosystem documented via tourist submarine off Cape Well-Met, Vega Island, Eastern Antarctic Peninsula (Subarea 48.1) - Multimedia
<p>Video evidence of a Vulnerable Marine Ecosystem (VME) was collected via submarine deployed by the tourist super-yacht MY Scenic Eclipse flagged with Malta. The dive was conducted on the 29th November 2019 within Subarea 48.1. The video of this resource supplements the dataset "Evidence of a Vulnerable Marine Ecosystem documented via tourist submarine off Cape Well-Met, Vega Island, Eastern Antarctic Peninsula (Subarea 48.1) - data'' available at <a href="https://ipt.biodiversity.aq/resource?r=cape-well-met_2019">https://ipt.biodiversity.aq/resource?r=cape-well-met_2019</a>.</p> <p>Method step description:</p> <ol> <li> <p>Video evidence of a Vulnerable Marine Ecosystem (VME) was collected via submarine deployed by the tourist super-yacht MY Scenic Eclipse flagged with Malta. Recordings begin at the greatest depth and continue as the submarine travels up the wall. Footage was taken with a GoPro Hero 7 Black mounted in the pilot window of a U-Boat Worx Cruise Sub 7-300<a href="https://www.uboatworx.com/model/cruisesub"> (https://www.uboatworx.com/model/cruisesub).</a> Four submarine dives were filmed.</p> </li> <li> <p>Prior to footage clean-up it was decided that the longest resulting video would be the one that would be analysed. Footage of each of these dives were provided in multiple files.</p> </li> <li> <p>Final Cut Pro X was first used to join the files into one video file per dive.</p> </li> <li> <p>The videos were then cropped to remove the edge of the pilot’s window frame and to adjust the colour balance.</p> </li> <li> <p>Clean-up then followed the same methodology as was used for analyzing the submarine footage for the successful nomination of four VMEs in WG-EMM-18/35 to remove unusable sequences. For the Cape Well-Met footage that meant the removal of any sequences where the submarine was too far from the wall, where the visibility was poor and when the submarine was paused.</p> </li> <li> <p>Footage from Dive C was the longest resulting video after the completion of this clean-up procedure, thus it became the footage that was analysed.</p> </li> </ol> <p>This project is funded by The Soap and The Sea, a Swiss organic and ocean-friendly soap enterprise that donates half of its profits to Ocean Conservation initiatives.</p>
LEARN-COVID: Dataset and documentation
<p>The LEARN-COVID pilot study collected data on infants and their parents during the COVID-19 pandemic. Assessments took place between April and July 2021. Predominantly Swiss parents answered a baseline questionnaire on their behaviour related to the pandemic, social support, infant nutrition, and infant regulation. Subsequently, parents answered a 10-day evening diary on daily nutrition, infant regulation, parental mood, and parental soothing behaviour.</p>
Chronological Distribution of the Documents from Yahudu and Its Surroundings
<p>This file presents the chronological distribution of the documents from the village of Yahudu and its surroundings in the Babylonian countryside. It relates to Chapter 4 in Tero Alstola, <em>Judeans in Babylonia: A Study of Deportees in the Sixth and Fifth Centuries BCE</em>. Culture and History of the Ancient Near East. Leiden: Brill. For further information, see the readme file.</p>
Activation market document
<p>CIM ESMP XML document that is used for the flexibility service activation (DSO sends this document to the aggregator).</p> <p>The data set in CIM XML format is for the activation of the flexibility service for DSO, as it gives an example of the activation signal.</p> <div> <p>More about the Slovenian demo in the One Net deliverable 10.4 (<a href="https://www.onenet-project.eu//wp-content/uploads/2023/10/OneNet_D10.4_V1.0.pdf">OneNet_D10.4_V1.0.pdf (onenet-project.eu)</a>)</p> </div> <p>XSD is compliant with ActivationMarket_Document defined by ENTSO-E (<a href="https://eepublicdownloads.entsoe.eu/clean-documents/EDI/Library/cim_based/schema/Activation_document_UML_model_and_schema_v1.2.pdf">Activation document uml model and schema (entsoe.eu)</a>).</p> <p> </p>
American Residential Macrosystems - Complete municipal ordinance documents across six U.S. cities, 2017-2019
These data files are the complete city codes, or municipal ordinances (n=156), across the metropolitan regions of Los Angeles, CA; Phoenix, AZ; Miami, FL; Baltimore, MD; Boston, MA; Minneapolis/St. Paul, MN. The documents were gathered for the specific purposes of a content analysis of how cities regulate residential landscapes; however, the documents include regulations on the books for the municipalities sampled for this project.
Everglades Landscape Model (ELM) Code and Documentation
The Everglades Landscape Model (ELM) is an application instance of the generalized Ecological Landscape Modeling code package. For applications within the Florida Coastal Everglades (FCE) LTER, the ELM is one of the simulation modeling tools used to a) explore hypotheses of ecosystem processes in heterogenous spatial landscapes, b) extrapolate field-scale research findings across space and time, and c) predict the evolution of the Everglades landscape in response to plausible future scenarios. For ELM v.2.8.3-4, the 2 zip-archive packages here contains 1a) all (C) source code and unix (Bourne) shell scripts used to build and run the ELM (& includes Doxygen-generated hyperlinked source code documentation of every file/function/struct/parameter), 1b) all Everglades-specific input data used in historical (1981-2000) simulations; and 2) a complete documentation report with chapters including the Introduction&Goals, Model Data, Model Structure, Model Performance, and Model User's Guide. The ELM is being applied and updated routinely. Such updated information can be found at http://www.ecolandmod.com .
Ferns surveys of individuals of terrestrial ferns in Canopy Trimming Experiment (CTE) plots document changes in species richness and abundance over time in response to canopy opening and/or debris deposition
Whole plot surveys of Canopy Triming Experiment (CTE) plots were done to detect changes in the number of terrestrial fern species and individuals in response to canopy opening and debris deposition. Surveys were conducted annually prior to and after treatments. A count of all terrestrial ferns, identified to species on the CTE plots was recorded for each subplot in January during CTE1 (2002-2010) and in the fall during CTE2 (2014-present). The surveys document losses of individuals of shade tolerant fern species and the appearance of open canopy ferns such as the tree fern Cyathea arborea. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Crowdsourcing Document Similarity Judgements
<p>This is the data obtained from crowdsourcing tasks which ask workers to provide similarity metrics between pairs of documents. Each document, as well as each pair, has a unique ID. We provide crowd workers with the pairs through three different task variations:</p> <ul> <li>Variation 1: We showed workers 5 pairs of documents and, for each, asked them to rate their similarity in a 4-level Likert scale (None, Low, Medium, High), tell us a confidence level of how sure they were (from 0 to 4) and a written reason as to why they chose that similarity level. For quality reasons, two of the 5 pairs were golden-standards, which means we knew their ratings already and checked the workers' responses. They had to give the golden pair with the higher similarity a higher score than the other golden pair, otherwise, their answer would be rejected.</li> <li>Variation 2: We repeated variation 1 but with a slight alteration: instead of a Likert scale for the similarity score, we asked for a Magnitude Estimation, which is any number above 0. It could be 1, 0.0001, 1000, 42, as long as it was coherent, as in a more similar pair had a higher score than a less similar pair and vice-versa;</li> <li>Variation 3: We showed workers 5 rankings. Each ranking had a main document and 3 auxiliary documents to be compared against the main one. They also had to report a confidence score and give a short written reason, just like variation 1. The first ranking is a golden-standard, and we knew the values for the 3 pairs in it (the pairs were the main document paired with each of the 3 auxiliary documents), and they had to give the golden pair with the highest similarity a higher rank than the one with the lower similarity.</li> </ul> <p>The raw results from the tasks are recorded in the JSON file CrowdResults.json. For a description of its contents, please read the file CrowdResults_README.md.</p> <p>These raw annotations from the crowd were then parsed into the three CSVs you see, each corresponding to the aggregated results from one of the task variations.</p> <ul> <li><em>final_scores_likert.csv</em> is the resulting scores for each pair using the variation 1 tasks; <ul> <li><em>pair_id </em>is a unique identifier for each pair;</li> <li><em>similarity_alg </em>is the similarity assigned to the pair of documents from an automated similarity algorithm;</li> <li><em>relation </em>is the type of relationship shown by the pair, where smaller values indicate more similar pairs;</li> <li><em>similarity_crowd_simple_maj </em>stores the simple majority result from the crowd's annotations;</li> <li><em>similarity_crowd_simple_mean </em>stores the mean of the crowd's annotations;</li> <li><em>similarity_crowd_simple_median </em>stores the median of the crowd's annotations;</li> </ul> </li> <li><em>final_scores_magnitude.csv</em> is the resulting scores for each pair using the variation 2 tasks; <ul> <li><em>pair_id </em>is a unique identifier for each pair;</li> <li><em>similarity_alg </em>is the similarity assigned to the pair of documents from an automated similarity algorithm;</li> <li><em>relation </em>is the type of relationship shown by the pair, where smaller values indicate more similar pairs;</li> <li><em>scaled_similarity_worker</em> is the magnitude score scaled based on worker's behaviours</li> <li><em>scaled_similarity_worker_docset </em>is the magnitude score scaled based both on the worker's behaviour and on the pair</li> </ul> </li> <li><em>final_scores_ranking.csv</em> is the resulting scores for each pair using the variation 3 tasks; <ul> <li><em>pair_id </em>is a unique identifier for each pair;</li> <li><em>similarity_alg </em>is the similarity assigned to the pair of documents from an automated similarity algorithm;</li> <li><em>relation </em>is the type of relationship shown by the pair, where smaller values indicate more similar pairs;</li> <li><em>mean_similarity</em> is the mean ranking from that value</li> </ul> </li> </ul> <p>This dataset was built and used as part of the <a href="https://theybuyforyou.eu/">TheyBuyForYou </a>project.</p>
Transkribus - Handwritten Text Recognition for Premodern Documents (SIMS 2020 Lightning Talk)
<p>Transkribus is a platform for text recognition and can be used via the Transkribus Expert Software (available after registration: transkribus.eu). Through Transkribus different tools for document analysis and text recognition can be directly applied. The intro demonstrates very briefly how Transkribus can help with regards to premodern documents especially since a variety of pre-trained models are already available: for Latin (prints and handwriting), for early modern vernaculars in French, Dutch, English, and German. For more information go to transkribus.eu.</p> <p>Presented as a Schoenberg Symposium 2020 Lightning Talk</p>
BAM Generalized National Models Documentation, Version 4.0
<h2>A generalized modeling framework for spatially extensive species abundance prediction and population estimation</h2> <p><span>In the face of rapid environmental change, spatially explicit estimates of species abundance and distribution are needed to inform conservation planning and management decisions across a range of spatial scales. We present a generalized modeling framework bridging the gap between local studies and regional to national management needs by compiling and harmonizing data from many sources to predict avian abundance at a fine resolution and broad extent. We first applied detectability offsets to integrate avian point-count data from a large collection of research and monitoring projects across the entire breadth of subarctic Canada (>250,000 unique sampling locations). We then subsampled the data by two time periods and sixteen geographic regions and developed boosted regression trees to model the density of 143 boreal landbird species as a function of environmental covariates representing climate, local- (250 m) and landscape-level (up to ~1.5 km) vegetation composition, land cover, and topography. Finally, bootstrapped model predictions for each region were combined to generate predictive density maps, habitat- and region-specific density estimates, and Canada-wide population estimates. Our models estimated a total of approximately 3.56 billion breeding males (7.13 billion individuals) across subarctic Canada, with the majority breeding in boreal and hemi-boreal regions. Forest generalist species made up nearly half of this estimate (1.57 billion breeding males), followed by boreal forest specialist species (1.05 billion), habitat generalists (350 million), and species associated with eastern forests (274 million), grasslands (124 million), western forests (74.7 million), wetlands (63.5 million), and Arctic tundra (17.7 million). Introduced species comprised 48.9 million breeding males. An analysis of variable importance showed that, across species, most of the variation in bird abundance was explained by landscape-level vegetation composition, suggesting that the effect of climate on bird abundance is mostly indirect, via vegetation, but that landscape-level variables are needed to capture this variation. Model classification accuracy was highest from a habitat perspective for forest- and grassland-associated species (lowest for mountain- and urban-associated species); and for Regulidae and Phasianidae from a taxonomic perspective (lowest for Bombycillidae and Paridae). In developing these models, we created a standardized, updatable, and reproducible workflow that can be used to update these analytical products and improve their utility for conservation and management planning.</span></p> <p>This data set contains:</p> <ul> <li>Reproducible code for the modeling approach based on <https://github.com/borealbirds/LandbirdModelsV4></li> <li>Source code for the website at <https://borealbirds.github.io/> based on <https://github.com/borealbirds/borealbirds.github.io></li> <li>Data and image assets for the website based on <https://github.com/borealbirds/api></li> </ul> <p>Please note, in late March 2025, we discovered a systematic error in the offsets used in these models, and have since updated the products to correct that error. For more information, please see the <https://github.com/borealbirds/QPAD-offsets-correction> repository for further details or email <bamp@ualberta.ca> for assistance.</p>
Data and documentation from: Microclimate explains little variation in year-round decomposition across an Arctic tundra landscape
<p>The zip file contains data and code to reproduce the analysis in the submitted manuscript entitled <i>Microclimate explains little variation in year-round decomposition across an Arctic tundra landscape</i>. Please see the manuscript for further details on background, methodology, results and discussion.</p>
zbMATHOpenRec: A Gold Standard Dataset for Recommending Scientific Documents with Mathematical Content
<p> </p> <p>Here we include the first gold standard dataset for recommending scientific documents with mathematical content. </p> <p><strong>Contents: </strong></p> <p>As of Feb-2023, there are 421 recommendation pairs with 80 seed documents.</p> <ol> <li>All recommendation pairs are available: recommendationPairs.csv</li> <li>Each document's contents, such as title, abstract/review/summary, authors, MSC codes, Full-text link, references, etc. are available in: documentContents.csv</li> </ol> <p><strong>Dataset construction process</strong>:</p> <p>This is the first gold standard content-based RS dataset, consisting of 421 scientific research entry recommendation pairs with mathematical content. The purpose is to enable math in scientific documents for document recommendations, meaning if two documents have similar math content, one could be recommended to the other. </p> <p>To create this dataset, we analyzed 4.5 million research entires from zbMATH Open (https://zbmath.org/) and performed the following steps to obtain the final dataset:</p> <ol> <li>We selected 80 seeds that capture the most word and math tokens in zbMATH Open using statistical measures.</li> <li>Three experts, one with several years of experience reviewing research entries in mathematics, curated the recommendations for 80 seeds.</li> </ol> <p>Using this dataset, researchers can accelerate the development and testing of recommendation approaches for scientific literature with mathematical content, improving recommendations for the STEM fields where mathematical content is currently being ignored</p> <p>## License </p> <p>Legal restrictions and copyright: The zbMATH Open data is subject to the Terms and Conditions for the zbMATH Open API Service of FIZ Karlsruhe – Leibniz-Institut für Informationsinfrastruktur GmbH. Content generated by zbMATH Open, such as reviews, classifications, software, or author disambiguation data, are distributed under CC-BY-SA 4.0. This defines the license for the whole dataset, which also contains non-copyrighted bibliographic metadata and reference data derived from I4OSC (CC0).</p>
Fatiando a Terra data v1.0.0: A curated collection of open geophysics data for tutorials and documentation
<p>This repository holds curated sample datasets that can be used in the documentation and tutorials of the <a href="https://www.fatiando.org/">Fatiando a Terra</a> project. All datasets are cleaned and formatted versions of openly available data under permissive licenses or in the public domain.</p> <p>More information about datasets and the code for cleaning, formatting, and preprocessing the data can be found at: <a href="https://github.com/fatiando/data">https://github.com/fatiando/data</a></p> <p>See the README.md file for information on data sources and their original licenses.</p> <p><strong>NOTE:</strong> This collection uses <a href="https://semver.org/">semantic versioning</a> (i.e., MAJOR.MINOR.BUGFIX). Major releases mean that backwards incompatible changes were made to the data. Minor releases add new data without changing existing files. Bug fix releases fix errors in a previous release that makes the data unusable. Changes to the current data files will always be published as a major release unless the file(s) in the previous release was unusable/corrupted.</p>
Students' perceived obstacles with Forced Online Distance Learning during the CoVID-19 outbreak and their preferences to continue with the introduced teaching methods after the reopening of the University of Maribor [Project documentation]
<p>The outbreak of COVID -19 forced most universities into distance education. Three didacticians and researchers from the University of Maribor, Slovenia: Kosta Dolenc, Mateja Ploj Virtič and Andrej Šorgo formed a self-initiated initiative project group during the COVID -19 epidemic and started the first project with the working title: The Side Effects of Forced Online Distance Education (FODE).</p> <p>The aim of the second study, conducted during the first wave of the epidemic in March 2020, was to investigate the response of university students to the new situation. The project documentation provided for the Forced Online Distance Learning (FODL) consists of:</p> <ul> <li>abstract,</li> <li>instrument,</li> <li>copy of the descriptive statistics,</li> <li>and SPSS dataset.</li> </ul>
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.