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Record W3094520390 · doi:10.1038/s41592-021-01113-7

A global view of standards for open image data formats and repositories

2021· preprint· en· W3094520390 on OpenAlexafffund
Jason R. Swedlow, Pasi Kankaanpää, Uğis Sarkans, Wojtek Goscinski, Graham J. Galloway, Ryan P. Sullivan, Claire M. Brown, Antje Keppler, Ben Loos, Sara Zullino, Dario Livio Longo, Silvio Aime, Shuichi Onami

Bibliographic record

VenueNature Methods · 2021
Typepreprint
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicCell Image Analysis Techniques
Canadian institutionsMcGill University
FundersRIKEN Center for Biosystems Dynamics ResearchNational Cancer InstituteRIKENNational Institute of Standards and TechnologyNational Institutes of HealthUniversidad de la República UruguayUniversidad de ChileHorizon 2020 Framework ProgrammeTurun YliopistoUniversiteit StellenboschEuropean Molecular Biology LaboratoryÅbo AkademiMonash UniversityChan Zuckerberg InitiativeUniversidad Nacional Autónoma de MéxicoBiotechnology and Biological Sciences Research CouncilUniversity of SydneyNederlandse Organisatie voor Wetenschappelijk OnderzoekAgence Nationale de la RechercheSilicon Valley Community FoundationEuropean CommissionNational Imaging FacilityEuropean Bioinformatics InstituteMcGill UniversityDeutsche ForschungsgemeinschaftInfrastructures en Biologie Santé et AgronomieUniversity of QueenslandUniversity of DundeeNational Science Foundation
KeywordsData scienceComputer scienceInformaticsHealth informaticsMedicinePolitical sciencePathologyPublic health

Abstract

fetched live from OpenAlex

Imaging technologies are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine. We present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.064
metaresearch head score (Gemma)0.070
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesOpen science
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Review · Consensus signal: none
Teacher disagreement score0.992
Threshold uncertainty score0.338

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0640.070
Meta-epidemiology (narrow)0.0030.003
Meta-epidemiology (broad)0.0020.003
Bibliometrics0.0110.010
Science and technology studies0.0040.005
Scholarly communication0.0220.022
Open science0.0080.015
Research integrity0.0110.014
Insufficient payload (model declined to judge)0.0170.027

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.025
GPT teacher head0.472
Teacher spread0.446 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designNot applicable
Domainnot available
GenreReview

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations10
Published2021
Admission routes2
Has abstractyes

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