Challenges and opportunities for bioimage analysis core‐facilities

Modern life science research is a collaborative effort. Few research groups can single‐handedly support the necessary equipment, expertise and personnel needed for the ever‐expanding portfolio of technologies that are required across multiple disciplines in today's life science endeavours. Thus, research institutes are increasingly setting up scientific core facilities to provide access and specialised support for cutting‐edge technologies. Maintaining the momentum needed to carry out leading research while ensuring high‐quality daily operations is an ongoing challenge, regardless of the resources allocated to establish such facilities. Here, we outline and discuss the range of activities required to keep things running once a scientific imaging core facility has been established. These include managing a wide range of equipment and users, handling repairs and service contracts, planning for equipment upgrades, renewals, or decommissioning, and continuously upskilling while balancing innovation and consolidation.

Section: Keeping Trackmentioning

confidence: 99%

Staying on track – Keeping things running in a high‐end scientific imaging core facility

Renaud,

Aulner,

Salles

et al. 2024

“…As computer power and tailored analysis solutions became available, state-of-the art microscopy experiments need to be coupled to substantial know-how about image analysis. 4 Altogether, it makes financial and practical sense to co-locate microscopy equipment and microscopy experts in centralised core facilities, which is why this approach is gaining popularity.…”

Section: The Adaptation Of Core Facilities In Response To Evolving Us...mentioning

confidence: 99%

“…Now it is increasingly common to find professionals with backgrounds in bioinformatics, computer science or mathematics to specifically address the growing demand for advanced image analysis capabilities in microscopy cores or closely affiliated image analysis cores. 4 Additionally, backgrounds in chemistry and engineering are also essential to address the growing complexity of sample preparation and instrument operation/maintenance, respectively.…”

Section: The Core Facility Team Pillarmentioning

confidence: 99%

Future proofing core facilities with a seven‐pillar model

Tranfield,

Lippens

2024

Centralised core facilities have evolved into vital components of life science research, transitioning from a primary focus on centralising equipment to ensuring access to technology experts across all facets of an experimental workflow. Herein, we put forward a seven‐pillar model to define what a core facility needs to meet its overarching goal of facilitating research. The seven equally weighted pillars are Technology, Core Facility Team, Training, Career Tracks, Technical Support, Community and Transparency. These seven pillars stand on a solid foundation of cultural, operational and framework policies including the elements of transparent and stable funding strategies, modern human resources support, progressive facility leadership and management as well as clear institute strategies and policies. This foundation, among other things, ensures a tight alignment of the core facilities to the vision and mission of the institute. To future‐proof core facilities, it is crucial to foster all seven of these pillars, particularly focusing on newly identified pillars such as career tracks, thus enabling core facilities to continue supporting research and catalysing scientific advancement.Lay abstract: In research, there is a growing trend to bring advanced, high‐performance equipment together into a centralised location. This is done to streamline how the equipment purchase is financed, how the equipment is maintained, and to enable an easier approach for research scientists to access these tools in a location that is supported by a team of technology experts who can help scientists use the equipment. These centralised equipment centres are called Core Facilities.The core facility model is relatively new in science and it requires an adapted approach to how core facilities are built and managed. In this paper, we put forward a seven‐pillar model of the important supporting elements of core facilities. These supporting elements are: Technology (the instruments themselves), Core Facility Team (the technology experts who operate the instruments), Training (of the staff and research community), Career Tracks (for the core facility staff), Technical Support (the process of providing help to apply the technology to a scientific question), Community (of research scientist, technology experts and developers) and Transparency (of how the core facility works and the costs associated with using the service). These pillars stand on the bigger foundation of clear policies, guidelines, and leadership approaches at the institutional level. With a focus on these elements, the authors feel core facilities will be well positioned to support scientific discovery in the future.

“…[85][86][87][88] Image analysis is a science in itself, and aspects to consider are outlined elsewhere. [89][90][91][92][93][94] Notably, data management is crucial in image analysis: accessing large data sets, sharing copies of data or results, maintaining records of processed data and their provenance and associating results with the corresponding raw data for later exploration. 95 This becomes even more pivotal in the context of automated analysis pipelines, where the code heavily relies on well-structured data sources.…”

Section: Image Analysismentioning

confidence: 99%

“…While some institutions build on independent bioimage analysis facilities, 92 core facilities may provide support and training with image analysis. Existing pipelines and software should be considered for reuse to lower the overall cost of software development and maintenance.…”

Section: Role Of a Core Facility In Rdm For Image Analysismentioning

confidence: 99%

A practical guide to bioimaging research data management in core facilities

Schmidt,

Boissonnet,

Dohle

et al. 2024

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.