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8,537 results for “Openness”
Volker Mahnert opening the 13 in Volker Mahnert 3 December 1943 – 23 November 2018
Volker Mahnert opening the 13th International Congress of Arachnology, which he organized in the MHNG, on 3 september 1995 (photo C. Ratton, MHNG).
CaImAn: An open source tool for scalable Calcium Imaging data Analysis
<p>Advances in fluorescence microscopy enable monitoring larger brain areas <em>in-vivo</em> with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to preprocessing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data.</p> <p>To benchmark the performance of CaImAn we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets, that are contained in this open access repository. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.</p> <p>In order to reproduce the results of the paper or download the annotations and the raw movies, please refer to the readme.md at:</p> <p>https://github.com/flatironinstitute/CaImAn/blob/master/use_cases/eLife_scripts/README.md</p> <p> </p>
Object-based image analysis for monitoring plant invasions, can we use an open-source solution?
<p><strong>Introduction</strong></p> <p>This is a practical exercise testing possibilities of open-source solutions (FOSS) for object-based image analysis (OBIA) to monitor plant invasion using unoccupied aerial system (UAS, drone).</p> <p>The material is accompanying a chapter <strong><em>Müllerová, J. et al. (2023). Vegetation mapping and monitoring by unoccupied aerial systems – current state and perspectives. In: Manfreda, S. et Eyal B.D. (eds). Unmanned Aerial Systems for Monitoring Soil, Vegetation, and Riverine Environments. Elsevier.</em></strong></p> <p>The material is meant for readers to run the workflow and detect invasion of giant hogweed on the UAS data themselves testing different FOSS solutions.</p> <p> </p> <p><strong>Data</strong></p> <p>• a subset of UAS-borne data (consumer camera) collected in Czech Republic during the flowering of a noxious invasive plant species giant hogweed (<em>Heracleum mantegazzianum</em>)</p> <p>• training dataset</p> <p>• eCognition rulebase (proprietary OBIA software)</p> <p>• a script for SegOptim package implemented in R</p> <p> </p> <p><strong>Description</strong></p> <p>The use case represents a simple application of OBIA approach based on the SegOptim package implemented in R.</p> <p>Four bands (RGBN) UAS image subset are available, capturing the central area of a heavily invaded location (CZ) by giant hogweed (Heracleum mantegazzianum). Thanks to the proper image timing, the invasive species is clearly observable as white objects (in RGB) representing the various stage of the blossom. Considering the complex shape of the flower heads, detection based on image segmentation outperforms pixel-based classification (Müllerová et al., 2017). Simple segmentation of input imagery is performed (for simplicity only the spectral bands are considered both for segmentation and feature space definition, however additional features such as vegetation indices or textural measures may be included), followed by supervised classification using training data. Finally, a visual comparison of result detection both from proprietary (eCognition) and open-source (SegOptim) implementation is provided, confirming comparable results.</p> <p>Based on #github("joaofgoncalves/SegOptim")</p> <p> </p> <p><strong>References</strong></p> <p>Gonçalves, J., Pôças, I., Marcos, B., Mücher, C. A., & Honrado, J. P. (2019). SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data. <em>International Journal of Applied Earth Observation and Geoinformation</em>, <em>76</em>, 218-230.</p> <p>Müllerová, J., Brůna, J., Bartaloš, T., Dvořák, P., Vítková, M. & Pyšek, P. (2017b). Timing Is Important: Unmanned Aircraft vs. Satellite Imagery in Plant Invasion Monitoring. Frontiers in Plant Science 8:1–13.</p> <p>Accompanying material for</p> <p>Müllerová, J. et al. (2023). Vegetation mapping and monitoring by unoccupied aerial systems – current state and perspectives. In: Manfreda, S. et Eyal B.D. (eds). Unmanned Aerial Systems for Monitoring Soil, Vegetation, and Riverine Environments. Elsevier</p>
Open Dataset for publication: Resonant laser ionization and mass separation of Ac-225
<p>The dataset for publication in preparation:</p> <p>Resonant laser ionization and mass separation of Ac-225.</p> <p> </p> <p>Includes all data analysed for results given in the publication.</p>
Open Chat Series: How-to-Advocacy "Why advocate for open scholarly communication in the social sciences and humanities?"
<p>On the 21.10.2022 Alíz Horváth, researcher, expert in East Asian studies, creator of “Humanista” podcast - and member of OPERAS's Special Interest Group "Advocacy" moderated an Open Chat with our guest speaker Per Pippin Aspaas, Head of Library Research and Publishing Support at the UiT in Tromsø, discussing the question "Why advocate for scholarly communication in the social sciences and humanities?"</p>
Dataset for "Open access books through open data sources: Assessing prevalence, providers, and preservation"
<p>This dataset contains the raw collected data reported on in the manuscript titled "Open access books through open data sources: Assessing prevalence, providers, and preservation" which is available here: https://doi.org/10.5281/zenodo.7305490</p> <p>One file contains the results of the digital object identifier queries, and the other data on which publication records were found to be included in which of the studied bibliometric data sources, and preservation services.</p> <p>The author is grateful to Alicia Wise and Ronald Snijder for assisting in the identification of available datasets and valuable feedback throughout the study.</p> <p>This research was commissioned by CLOCKSS, DOAB, and OAPEN.</p>
DATASET SPARC Europe Open Education in European Libraries of Higher Education Survey 2022
<p>This is the anonymised dataset for the 2022 edition of the SPARC Europe Open Education Survey amongst Higher Education libraries in Europe.</p>
FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking
<p>This is the software described in our article 'FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking' and the used datasets for image analysis. It is intended as a easy to use software for tracking of cytoskeletal fibers offering both source code and GUI-based executable. Datasets are sorted according to figures in the article with folders containing raw images, analysis results and resulting figure files. The source folder also includes a tutorial and installation notes.</p> <p>For a system running Ubuntu 21.04 there is a slightly modified command line needed: java --module-path /usr/share/openjfx/lib –add-modules=javafx.base,javafx.controls,javafx.fxml,javafx.graphics,javafx.media,javafx.swing,javafx.web -jar GUIFocalAdhesionOnly.jar</p>
Open Chat Series: How-to-Advocacy "How to Advocate for Innovation in Scholarly Communication?"
<p>On 25. November 2022 Magdalena Wnuk moderated the Open Chat with Maciej Maryl from IBL PAN and talked about how to advocate for innovation in scholarly communication. Together with our guest speaker and the audience we discussed the advocacy goals and challenges for the SSH community while advocating for innovation in open science. </p>
Zenodo Open Metadata snapshot - Training dataset for records and communities classifier building
<p>This dataset contains Zenodo's published open access records and communities metadata, including entries marked by the Zenodo staff as spam and deleted.</p> <p>The datasets are gzipped compressed JSON-lines files, where each line is a JSON object representation of a Zenodo record or community.</p> <p><strong>Records dataset</strong></p> <p>Filename:<strong> </strong>zenodo_open_metadata_{ date of export }.jsonl.gz</p> <p>Each object contains the terms: <em>part_of, thesis, description, doi, meeting, imprint, references, recid, alternate_identifiers, resource_type, journal, related_identifiers, title, subjects, notes, creators, communities, access_right, keywords, contributors, publication_date</em></p> <p>which correspond to the fields with the same name available in Zenodo's record JSON Schema at <a href="https://zenodo.org/schemas/records/record-v1.0.0.json">https://zenodo.org/schemas/records/record-v1.0.0.json</a>.</p> <p>In addition, some terms have been altered:</p> <ul> <li>The term <strong>files</strong> contains a list of dictionaries containing <strong>filetype</strong>, <strong>size,</strong> and <strong>filename </strong>only.</li> <li>The term <strong>license</strong> contains a short Zenodo ID of the license (e.g. "cc-by").</li> </ul> <p><strong>Communities dataset</strong></p> <p>Filename:<strong> </strong>zenodo_community_metadata_{ date of export }.jsonl.gz</p> <p>Each object contains the terms: <em>id, title, description, curation_policy, page </em></p> <p>which correspond to the fields with the same name available in Zenodo's community creation form.</p> <p><strong>Notes for all datasets</strong></p> <p>For each object the term <strong>spam</strong> contains a boolean value, determining whether a given record/community was marked as spam content by Zenodo staff.</p> <p>Some values for the top-level terms, which were missing in the metadata may contain a <strong>null</strong> value.</p> <p>A smaller uncompressed random sample of 200 JSON lines is also included for each dataset to test and get familiar with the format without having to download the entire dataset.</p>
Dataset from: Leveraging open tools to realize the potential of self-archiving: A cohort study in clinical trials
<p>This record includes the data associated with the study "Leveraging open tools to increase the potential of self-archiving to increase discoverability: A cohort study in clinical trials". The code used to generate these data is available under an open license in GitHub (<a href="https://github.com/delwen/oa-archiving-permissions">https://github.com/delwen/oa-archiving-permissions</a>). The deposit includes:</p> <p>- `intovalue.csv`: download of the IntoValue dataset (IntoValue 1 and IntoValue 2), which is actively maintained in GitHub (<a href="https://github.com/maia-sh/intovalue-data">https://github.com/maia-sh/intovalue-data</a>). The data was downloaded on 17 December 2022. More information on the generation of this dataset can be found at: <a href="https://doi.org/10.5281/zenodo.5141343">https://doi.org/10.5281/zenodo.5141343</a>. This data corresponds to the start of the trial screening flow diagram in the manuscript (n = 3,788).</p> <p>- `oa-unpaywall.csv`: dataset containing the results of the Unpaywall API query (query date: 17 December 2022). The dataset queried includes the following adaptations from `intovalue.csv`:</p> <ul> <li>As updated registry data had been downloaded on 1 November 2022, the IntoValue inclusion criteria were re-applied: <ul> <li>Interventional</li> <li>Study completion date between 2009 and 2017</li> <li>Complete based on study status</li> <li>Conducted by a German university medical center.</li> </ul> </li> <li>The dataset was further limited to: <ul> <li>Unique trials (trials from IntoValue 2 were preserved)</li> <li>Unique publications with a DOI</li> </ul> </li> </ul> <p>- `oa-syp-permissions.csv`: dataset containing the results of the Shareyourpaper API query (query date: 17 December 2022). The dataset queried is the same as in `oa-unpaywall.csv`.</p> <p>- `oa-merged-data.csv`: dataset containing the merged Unpaywall and Shareyourpaper data for all clinical trial results publications considered in this study. The dataset was further limited to journal articles that resolved in Unpaywall and were published between 2010 - 2020 (based on the publication date in Unpaywall). This is the main dataset underlying the analyses in the manuscript.</p>
Data and Code for "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility"
<p>This snapshot contains code and data for the preprint "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility".</p> <p>Instructions on re-using the data and running the code can be found in the README.md.</p> <p>Changes:</p> <ul> <li>Added survey instrument and informed consent.</li> </ul>
Dataset: Harmonized and Open Energy Dataset for Modeling a Highly Renewable Brazilian Power System
<p>The dataset provided here is intended for publication - Harmonized and Open Energy Dataset for Modeling a Highly Renewable Brazilian Power System.</p> <p>Direct use of our provided datasets is available from Zenodo, and the source code to generate the datasets is published in <a href="https://gitlab.com/dlr-ve/esy/open-brazilian-energy-data">Gitlab</a>. We describe the data collection process in detail and open source the code for data processing and analysis in our publication.</p> <p><br> The assembled dataset includes the following subcategories, as detailed in the methods section of our publication: i) geospatial data for Brazil, ii) aggregated grid network topology, iii) vRES potentials --- profile and installable generation capacity, iv) geographically installable capacity of biomass thermal plants, v) hydropower plants inflow, vi) existing and planned power generators with their capacity, vii) electricity load profile, viii) scenarios of sectoral energy demand and ix) cross-border electricity exchanges. This dataset is resolved geographically by Brazilian federal states, and time series data are resolved by hours, spanning 2012-2020.</p> <p>The dataset can be used as input to popular open energy system models such as PyPSA and any other modelling framework.</p> <p>We encourage you to contribute to improving the datasets.</p>
Data and Code Supplement to: "Processes of change in a randomized clinical trial of Radically Open Dialectical Behavior Therapy (RO DBT) for adults with treatment refractory depression"
<p>Dataset to support secondary analyses reported in "Processes of change in a randomized clinical trial of Radically Open Dialectical Behavior Therapy (RO DBT) for adults with treatment refractory depression" in the Journal of Consulting and Clinical Psychology</p>
Mapping the Swiss Landscape of Diamond Open Access Journals. The PLATO Study on Scholar-Led Publishing. Dataset
<p><strong>Context</strong><br> From March to September 2022, the <a href="https://www.openscience.uzh.ch/en/openaccess/plato.html">«Platinum Open Access Funding» Project (PLATO)</a>, in collaboration with the Institute for Applied Data Science & Finance at the Bern University of Applied Sciences, undertook a bibliometric and empirical study of the Platinum/Diamond open access journal landscape in Switzerland. The PLATO project is an initiative of six Swiss universities – the University of Zurich, the University of Bern, the University of Geneva, the University of Neuchâtel, the Zurich University of the Arts and ETH Zurich –, dedicated to furthering community-led scholarly publishing in Switzerland. Diamond open access stands for a concept of equitable open access to and participation in scholarly publishing that is free for both authors and readers.</p> <p><strong>Presentation</strong><br> The main objective of the PLATO Study was to gain insight into the Platinum/Diamond open access publishing ecosystem in Switzerland through a mixed-method approach. The study consisted of three parts: First, bibliometric data were combined with inputs from Swiss open access publishers, institutional open access experts as well as information on journal websites to identify Swiss Diamond OA journals and their main characteristics. Second, seven semi-structured interviews with editors of select Diamond OA journals were conducted to generate a thorough understanding of their workflows, infrastructures, business models, challenges and opportunities. Third, based on the inputs from the interviews, three surveys were designed and sent to authors/reviewers, editors, and representatives of hosting and funding institutions of Swiss Diamond OA journals.</p> <p>The results of the study are published in the form of the following outputs:</p> <ul> <li>DOI Report: 10.5281/zenodo.7461728</li> <li>DOI Bibliometric List: <a href="https://zenodo.org/record/6992615#.YzK3ElJBw-Q">10.34914/olos:l2tys6tie5f63h35lqpqzzlx24</a></li> <li>DOI Data Set: 10.5281/zenodo.7461754</li> </ul> <p>The Data Set comprises the following files:</p> <ul> <li>Survey questionnaires</li> </ul> <p> SurveyQuestionnaire_Author.pdf<br> SurveyQuestionnaire_Editor.pdf<br> SurveyQuestionnaire_Publisher.pdf</p> <ul> <li>Data collected in three survey studies addressing journal editors, authors/reviewers as well as representatives of hosting and funding institutions:</li> </ul> <p> StudyData_Author.csv<br> StudyData_Editor.csv<br> StudyData_Publisher.csv</p> <ul> <li>Codebooks explaining the coding of the survey data files:</li> </ul> <p> StudyCodebook_Author.pdf<br> StudyCodebook_Editor.pdf<br> StudyCodebook_Publisher.pdf</p>
Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h).
Text-fig. 45. Scanning electron microscope (SEM) images of "Staminate structure"; Catefica locality, Portugal. a–c) Staminate structure in oblique apical (a), oblique basal (b) and lateral (c) views showing distinct stalk and head with a cluster of about 20 stamens; note bracts at the base of the structure (asterisks) and probable secretory openings in the anther tissues (arrows). Specimen, Catefica 358-S135451 (a–c). Scale bars = 600 Μm (a–c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 45. Scanning electron microscope (SEM) images of "Staminate structure"; Catefica locality, Portugal. a–c) Staminate structure in oblique apical (a), oblique basal (b) and lateral (c) views showing distinct stalk and head with a cluster of about 20 stamens; note bracts at the base of the structure (asterisks) and probable secretory openings in the anther tissues (arrows). Specimen, Catefica 358-S135451 (a–c). Scale bars = 600 Μm (a–c).
U.S. Science Journalists' Knowledge and Opinion of Open Access Articles as Sources
<p>Survey data of U.S. science journalists and their knowledge and opinions of OA research as news sources.</p>
The LOTUS Initiative for Open Natural Products Research: wikidata query results
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p> <p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p> <p>This dataset is constituted of 4 tables.</p> <ol> <li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li> <li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li> <li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li> <li>compound_reference_taxon.tsv - the documented structure-organism pairs</li> </ol> <p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p> <p> </p> <p><br> </p>
The LOTUS Initiative for Open Natural Products Research: frozen dataset
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></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.