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

Published on May 4, 2021in Nature Methods28.547
· DOI :10.1038/S41592-021-01113-7
Jason R. Swedlow59
Estimated H-index: 59
(Dund.: University of Dundee),
Pasi Kankaanpää20
Estimated H-index: 20
(Åbo Akademi University)
+ 14 AuthorsSilvio Aime94
Estimated H-index: 94
(UNITO: University of Turin)
Sources
Abstract
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.
References32
Newest
#1Srinivas Niranj Chandrasekaran (Broad Institute)H-Index: 8
#2Hugo Ceulemans (Janssen Pharmaceutica)H-Index: 28
Last. Anne E. Carpenter (Broad Institute)H-Index: 64
view all 4 authors...
Image-based profiling is a maturing strategy by which the rich information present in biological images is reduced to a multidimensional profile, a collection of extracted image-based features. These profiles can be mined for relevant patterns, revealing unexpected biological activity that is useful for many steps in the drug discovery process. Such applications include identifying disease-associated screenable phenotypes, understanding disease mechanisms and predicting a drug's activity, toxici...
Source
#1Glyn Nelson (Newcastle University)H-Index: 27
#2Ulrike Boehm (HHMI: Howard Hughes Medical Institute)H-Index: 4
Last. Orestis Faklaris (CNRS: Centre national de la recherche scientifique)H-Index: 20
view all 100 authors...
In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata mo...
Source
#1Bartha Maria Knoppers (McGill University)H-Index: 70
#2Henry T. Greely (Stanford University)H-Index: 42
Source
#3Michael SnyderH-Index: 186
#4Shin LinH-Index: 18
Last. Leslie GaffneyH-Index: 4
view all 134 authors...
Author(s): Snyder, Michael P; Lin, Shin; Posgai, Amanda; Atkinson, Mark; Regev, Aviv; Rood, Jennifer; Rozenblatt-Rosen, Orit; Gaffney, Leslie; Hupalowska, Anna; Satija, Rahul; Gehlenborg, Nils; Shendure, Jay; Laskin, Julia; Harbury, Pehr; Nystrom, Nicholas A; Silverstein, Jonathan C; Bar-Joseph, Ziv; Zhang, Kun; Borner, Katy; Lin, Yiing; Conroy, Richard; Procaccini, Dena; Roy, Ananda L; Pillai, Ajay; Brown, Marishka; Galis, Zorina S; Cai, Long; Shendure, Jay; Trapnell, Cole; Lin, Shin; Jackson, ...
Source
#1Richard Colling (John Radcliffe Hospital)H-Index: 12
#2Helen Pitman (National Cancer Research Institute)H-Index: 3
Last. Clare VerrillH-Index: 24
view all 8 authors...
The use of artificial intelligence will likely transform clinical practice over the next decade and the early impact of this will likely be the integration of image analysis and machine learning into routine histopathology. In the UK and around the world, a digital revolution is transforming the reporting practice of diagnostic histopathology and this has sparked a proliferation of image analysis software tools. While this is an exciting development that could discover novel predictive clinical ...
Source
#2Andrew L. Janke (UQ: University of Queensland)H-Index: 26
Last. Andrew TreloarH-Index: 15
view all 10 authors...
The National Imaging Facility (NIF) provides Australian researchers with state-of-the-art instrumentation—including magnetic resonance imaging (MRI), positron emission tomography (PET), X-ray computed tomography (CT) and multispectral imaging – and expertise for the characterisation of animals, plants and materials. To maximise research outcomes, as well as to facilitate collaboration and sharing, it is essential not only that the data acquired using these instruments be managed, curated and arc...
Source
#1Pilar Cacheiro (QMUL: Queen Mary University of London)H-Index: 7
#2Melissa A. Haendel (Linus Pauling Institute)H-Index: 54
Last. Damian Smedley (QMUL: Queen Mary University of London)H-Index: 53
view all 3 authors...
The International Mouse Phenotyping Consortium (IMPC) continues to expand the catalogue of mammalian gene function by conducting genome and phenome-wide phenotyping on knockout mouse lines. The extensive and standardized phenotype screens allow the identification of new potential models for human disease through cross-species comparison by computing the similarity between the phenotypes observed in the mutant mice and the human phenotypes associated to their orthologous loci in Mendelian disease...
Source
#1Susanna-Assunta Sansone (University of Oxford)H-Index: 58
#2Peter McQuilton (University of Oxford)H-Index: 16
Last. FAIRsharing CommunityH-Index: 1
view all 8 authors...
Source
#1Michael SnyderH-Index: 186
#2Shin LinH-Index: 18
Last. James A. AndersonH-Index: 68
view all 25 authors...
Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding a...
Source
#1Kathryn Maxson Jones (Princeton University)H-Index: 3
#2Rachel A. Ankeny (University of Adelaide)H-Index: 22
Last. Robert Cook-Deegan (ASU: Arizona State University)H-Index: 31
view all 3 authors...
The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans research...
Source
Cited By9
Newest
#1Akira Sasaki (AIST: National Institute of Advanced Industrial Science and Technology)H-Index: 38
Fluorescence microscopy is a broadly used technique within a variety of different fields, including life sciences and medical research, and its quantitative aspects are becoming emphasized. The challenge now lies in improving the accuracy and precision of the measurements obtained from fluorescence microscopy. Improving these will facilitate the comparison of results between different instruments/institutions and therefore ensure the reproducibility of results. In this review, recent standardiza...
Source
#1Susanne KunisH-Index: 1
#2Sebastian HänschH-Index: 8
Last. Stefanie Weidtkamp-PetersH-Index: 18
view all 6 authors...
Source
#1Andrey Andreev (California Institute of Technology)H-Index: 5
#2Thomas E. MorrellH-Index: 5
Last. Uri Manor
view all 5 authors...
Modern tools for biological research, especially microscopy, have rapidly advanced in recent years, which has led to the generation of increasingly large amounts of data on a regular basis. The result is that scientists desperately need state-of-the-art technical infrastructure for raw data storage, transfer, and processing. These scientists currently rely on outdated ways to move and store data, costing valuable time and risking loss of valuable data. While the community is aware of modern appr...
Abstract null null Purpose null Micron-scale computed tomography (micro-CT) imaging is a ubiquitous, cost-effective, and non-invasive three-dimensional imaging modality. We review recent developments and applications of micro-CT for preclinical research. null null null Methods null Based on a comprehensive review of recent micro-CT literature, we summarize features of state-of-the-art hardware and ongoing challenges and promising research directions in the field. null null null Results null Repr...
Source
#1Orestis Faklaris (CNRS: Centre national de la recherche scientifique)H-Index: 20
#2Bancel-Vallee L (French Institute of Health and Medical Research)H-Index: 1
Last. Damien Schapman (French Institute of Health and Medical Research)H-Index: 10
view all 13 authors...
Reliable, reproducible and comparable results are what biology requires from microscopy. To achieve that level of confidence, monitoring the stability of the microscope performance over time with standardized quality testing routines is essential for mining quantitative data. Three levels of microscope quality control procedures should be considered: i) usage of accessible and affordable tools and samples, ii) execution of easy and fast, preferably automatized, acquisition protocols, iii) analys...
Source
#1Alessandro Rigano (UMMS: University of Massachusetts Medical School)H-Index: 3
#2Shannon Ehmsen (Harvard University)H-Index: 1
Last. Claire M. Brown (McGill University)H-Index: 29
view all 33 authors...
For the information content of microscopy images to be appropriately interpreted, reproduced, and meet FAIR (Findable Accessible Interoperable and Reusable) principles, they should be accompanied by detailed descriptions of microscope hardware, image acquisition settings, image pixel, and dimensional structure, and instrument performance. Nonetheless, the thorough documentation of imaging experiments is significantly impaired by the lack of community-sanctioned easy-to-use software tools to faci...
Source
#1Ugis Sarkans (EMBL-EBI: European Bioinformatics Institute)H-Index: 27
#2Wah Chiu (Stanford University)H-Index: 101
Last. Alvis Brazma (EMBL-EBI: European Bioinformatics Institute)H-Index: 74
view all 46 authors...
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.
Source
Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments' images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reu...
This website uses cookies.
We use cookies to improve your online experience. By continuing to use our website we assume you agree to the placement of these cookies.
To learn more, you can find in our Privacy Policy.