Effectively Communicating Bioimage Analysis
About
Bioimage analysis is a critically needed discipline, especially as the number of new tools is exploding as part of the “deep learning revolution” and as larger data sizes and automated screening systems make manual data handling of microscopy data increasingly impractical. While there are more educational and training materials than ever, a few major challenges still exist:
- Bioimage analysis is still often seen as an “add-on” – not required activity, meaning researchers need to learn it on their own rather than having it included as part of general graduate education and/or microscopy education.
- A large number of bioimage analysis resources now exist including open source software software, training materials and workshops, but without community standards and recommendations many of these are of uncertain quality. Complicating existing efforts to track these comprehensively, bioimage analysis tools are constantly evolving – some become unmaintained and unusable, while others add new functionalities and/or update interfaces for interaction. This gives many materials a short “shelf life” and makes it difficult to determine what is still useful, even for experts but especially for non-experts.
- The community of users covers a wide range of experience levels and computational comfort levels, meaning some materials must have multiple versions created to reach the entire community.
- Map our “landscape” – catalogue globally what efforts are already underway, where do current efforts overlap and so could lead to collaboration or de-duplication, where funding may come from, and who can we can tap for more community involvement and/or promotion.
- Bring together both users and creators of training materials and courses, to share lessons of what has worked and what has not in terms of training effectiveness and material dissemination.
- Curate the resources that currently exist, and brainstorm how these can be shared more effectively or used in novel ways, such as in the creation of flipped classroom curricula.
- Create a draft set of standards to recommend to stakeholders, such as funding agencies, organizations with influence on graduate training, or others.
Website: https://www.biologists.com/workshops/february-2024/
Organisers & Speakers
Beth Cimini Broad Institute, USA
Kevin Eliceiri University of Wisconsin-Madison, USA
Peter Bankhead University of Edinburgh, UK
Rocco D’Antuono The Francis Crick Institute, UK
Julia Fernandez-Rodriguez University of Gothenburg, Sweden
Robert Haase Technische Universität Dresden, Germany
Helena Jambor Technische Universität Dresden, Germany
Martin Jones The Francis Crick Institute, UK
Florian Jug Human Technopole, Germany
Anna Klemm Uppsala University, Sweden
Anna Kreshuk European Molecular Biology Laboratory, Germany
Gaby Martins Instituto Gulbenkian de Ciência, Portugal
Kota Miura Network of European Union Bioimage Analysts, Germany
Laura Murphy The University of Edinburgh, UK
Simon Nørrelykke Harvard Medical School, USA
Thomas Pengo University of Minnesota, USA
Annika Reinke German Cancer Research Center, Germany
Caterina Strambio De Castillia University of Massachusetts Chan Medical School, USA
Virginie Uhlmann EMBL European Bioinformatics Institute, UK
Jason Williams Cold Spring Harbor Laboratory, USA
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