A biologist’s guide to planning and performing quantitative bioimaging experiments

Senft, Rebecca A.; Diaz-Rohrer, Barbara; Colarusso, Pina; Swift, Lucy; Jamali, Nasim; Jambor, Helena; Pengo, Thomas; Brideau, Craig; Llopis, Paula Montero; Uhlmann, Virginie; Kirk, Jason M; Gonzales, Kevin Andrew Uy; Bankhead, Peter; Evans, Edward L.; Eliceiri, Kevin W.; Cimini, Beth A.

doi:10.1371/journal.pbio.3002167

Cited by 12 publications

(5 citation statements)

References 72 publications

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“…An overview of resources can be found in David et al 104 and in a 2023 biologist's guide to planning quantitative imaging. 105 These, however, do not substitute for data management support provided by core facilities.…”

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

Journal of Microscopy

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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.

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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

Journal of Microscopy

View full text Add to dashboard Cite

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“…To fully take advantage of optical microscopy as an experimental tool, its inherently quantitative nature should be exploited, as quantitative analysis of microscopy images can lead to unprecedented biological insights (Myers, 2012;Senft et al, 2023). All the considerations with respect to sample preparation and choosing the most suitable imaging modalities are, therefore, crucial when planning future analysis of the acquired imaging data, as all these major steps of an imaging experiment are tightly interconnected (Culley et al, 2023;Senft et al, 2023). Different analysis avenues for F-actin image analysis have been explored, covering cytoskeletal dynamics, architecture and mechanics.…”

Section: Approaches To Actin Image Analysismentioning

confidence: 99%

Imaging actin organisation and dynamics in 3D

Phillips,

Marcotti,

Cox

et al. 2024

Journal of Cell Science

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The actin cytoskeleton plays a critical role in cell architecture and the control of fundamental processes including cell division, migration and survival. The dynamics and organisation of F-actin have been widely studied in a breadth of cell types on classical two-dimensional (2D) surfaces. Recent advances in optical microscopy have enabled interrogation of these cytoskeletal networks in cells within three-dimensional (3D) scaffolds, tissues and in vivo. Emerging studies indicate that the dimensionality experienced by cells has a profound impact on the structure and function of the cytoskeleton, with cells in 3D environments exhibiting cytoskeletal arrangements that differ to cells in 2D environments. However, the addition of a third (and fourth, with time) dimension leads to challenges in sample preparation, imaging and analysis, necessitating additional considerations to achieve the required signal-to-noise ratio and spatial and temporal resolution. Here, we summarise the current tools for imaging actin in a 3D context and highlight examples of the importance of this in understanding cytoskeletal biology and the challenges and opportunities in this domain.

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“…Microscopy is an essential tool in cell biology. The use of microscopes to observe cells and organisms has changed from a qualitative, descriptive approach, into a quantitative method [4][5][6][7]. The development of digital cameras and image analysis software has catalyzed this transition [8].…”

Section: Introductionmentioning

confidence: 99%

Studentsourcing—Aggregating and reusing data from a practical cell biology course

Goedhart

2024

PLoS Comput Biol

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Practical courses mimic experimental research and may generate valuable data. Yet, data that is generated by students during a course is often lost as there is no centrally organized collection and storage of the data. The loss of data prevents its reuse. To provide access to these data, I present an approach that I call studentsourcing. It collects, aggregates, and reuses data that is generated by students in a practical course on cell biology. The course runs annually, and I have recorded the data that was generated by >100 students over 3 years. Two use cases illustrate how the data can be aggregated and reused either for the scientific record or for teaching. As the data is obtained by different students, in different groups, over different years, it is an excellent opportunity to discuss experimental design and modern data visualization methods such as the superplot. The first use case demonstrates how the data can be presented as an online, interactive dashboard, providing real-time data of the measurements. The second use case shows how central data storage provides a unique opportunity to get precise quantitative data due to the large sample size. Both use cases illustrate how data can be effectively aggregated and reused.

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A biologist’s guide to planning and performing quantitative bioimaging experiments

Cited by 12 publications

References 72 publications

A practical guide to bioimaging research data management in core facilities

A practical guide to bioimaging research data management in core facilities

Imaging actin organisation and dynamics in 3D

Studentsourcing—Aggregating and reusing data from a practical cell biology course

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