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1.
J Microsc ; 294(3): 350-371, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38752662

RESUMEN

Bioimage data are generated in diverse research fields throughout the life and biomedical sciences. Its potential for advancing scientific progress via modern, data-driven discovery approaches reaches beyond disciplinary borders. To fully exploit this potential, it is necessary to make bioimaging data, in general, multidimensional microscopy images and image series, FAIR, that is, findable, accessible, interoperable and reusable. These FAIR principles for research data management are now widely accepted in the scientific community and have been adopted by funding agencies, policymakers and publishers. To remain competitive and at the forefront of research, implementing the FAIR principles into daily routines is an essential but challenging task for researchers and research infrastructures. Imaging core facilities, well-established providers of access to imaging equipment and expertise, are in an excellent position to lead this transformation in bioimaging research data management. They are positioned at the intersection of research groups, IT infrastructure providers, the institution´s administration, and microscope vendors. In the frame of German BioImaging - Society for Microscopy and Image Analysis (GerBI-GMB), cross-institutional working groups and third-party funded projects were initiated in recent years to advance the bioimaging community's capability and capacity for FAIR bioimage data management. Here, we provide an imaging-core-facility-centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community. We highlight which tools and services are ready to be implemented and what the future directions for FAIR bioimage data have to offer.


Asunto(s)
Microscopía , Investigación Biomédica/métodos , Manejo de Datos/métodos , Procesamiento de Imagen Asistido por Computador/métodos , Microscopía/métodos
2.
Biol Chem ; 404(5): 433-439, 2023 04 25.
Artículo en Inglés | MEDLINE | ID: mdl-36853922

RESUMEN

While the FAIR (Findable, Accessible, Interoperable, and Re-usable) principles are well accepted in the scientific community, there are still many challenges in implementing them in the day-to-day scientific process. Data management of microscopy images poses special challenges due to the volume, variety, and many proprietary formats. In particular, appropriate metadata collection, a basic requirement for FAIR data, is a real challenge for scientists due to the technical and content-related aspects. Researchers benefit here from interdisciplinary research network with centralized data management. The typically multimodal structure requires generalized data management and the corresponding acquisition of metadata. Here we report on the establishment of an appropriate infrastructure for the research network by a Core Facility and the development and integration of a software tool MDEmic that allows easy and convenient processing of metadata of microscopy images while providing high flexibility in terms of customization of metadata sets. Since it is also in the interest of the core facility to apply standards regarding the scope and serialization formats to realize successful and sustainable data management for bioimaging, we report on our efforts within the community to define standards in metadata, interfaces, and to reduce the barriers of daily data management.


Asunto(s)
Manejo de Datos , Programas Informáticos , Metadatos
4.
Nat Methods ; 18(12): 1489-1495, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34862503

RESUMEN

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.


Asunto(s)
Metadatos , Microscopía Confocal/instrumentación , Microscopía Confocal/métodos , Microscopía Fluorescente/instrumentación , Microscopía Fluorescente/métodos , Aplicaciones Móviles , Lenguajes de Programación , Programas Informáticos , Animales , Línea Celular , Biología Computacional/métodos , Humanos , Procesamiento de Imagen Asistido por Computador , Ratones , Reconocimiento de Normas Patrones Automatizadas , Control de Calidad , Reproducibilidad de los Resultados , Interfaz Usuario-Computador , Flujo de Trabajo
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