Fibroglandular Tissue Segmentation in Breast MRI using Vision Transformers -- A multi-institutional evaluation

Accurate and automatic segmentation of fibroglandular tissue in breast MRI screening is essential for the quantification of breast density and background parenchymal enhancement. In this retrospective study, we developed and evaluated a transformer-based neural network for breast segmentation (TraBS) in multi-institutional MRI data, and compared its performance to the well established convolutional neural network nnUNet. TraBS and nnUNet were trained and tested on 200 internal and 40 external breast MRI examinations using manual segmentations generated by experienced human readers. Segmentation performance was assessed in terms of the Dice score and the average symmetric surface distance. The Dice score for nnUNet was lower than for TraBS on the internal testset (0.909$\pm$0.069 versus 0.916$\pm$0.067, P<0.001) and on the external testset (0.824$\pm$0.144 versus 0.864$\pm$0.081, P=0.004). Moreover, the average symmetric surface distance was higher (=worse) for nnUNet than for TraBS on the internal (0.657$\pm$2.856 versus 0.548$\pm$2.195, P=0.001) and on the external testset (0.727$\pm$0.620 versus 0.584$\pm$0.413, P=0.03). Our study demonstrates that transformer-based networks improve the quality of fibroglandular tissue segmentation in breast MRI compared to convolutional-based models like nnUNet. These findings might help to enhance the accuracy of breast density and parenchymal enhancement quantification in breast MRI screening

Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness

International audienceThe Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness research. It brings together 17 research infrastructures (RIs) and networks to provide a broad range of services to infectious disease researchers. An efficient and structured treatment of data is central to ISIDORe’s aim to furnish seamless access to its multidisciplinary catalogue of services, and to ensure that users’ results are treated FAIRly. ISIDORe therefore requires a data management plan (DMP) covering both access management and research outputs, applicable over a broad range of disciplines, and compatible with the constraints and existing practices of its diverse partners. Here, we describe how, to achieve that aim, we undertook an iterative, step-by-step, process to build a community-approved living document, identifying good practices and processes, on the basis of use cases, presented as proof of concepts. International fora such as the RDA and EOSC, and primarily the BY-COVID project, furnished registries, tools and online data platforms, as well as standards, and the support of data scientists. Together, these elements provide a path for building an umbrella, FAIR-compliant DMP, aligned as fully as possible with FAIR principles, which could also be applied as a framework for data management harmonisation in other large-scale, challenge-driven projects. Finally, we discuss how data management and reuse can be further improved through the use of knowledge models when writing DMPs and, how, in the future, an inter-RI network of data stewards could contribute to the establishment of a community of practice, to be integrated subsequently into planned trans-RI competence centres

Umbrella Data Management Plans to integrate FAIR data:Lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness

The Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness research. It brings together 17 Research Infrastructures (RIs) and networks to provide a broad range of services to infectious disease researchers. An efficient and structured treatment of data is central to ISIDORe’s aim to furnish seamless access to its multidisciplinary catalogue of services, and to ensure that users’ results are treated FAIRly. ISIDORe therefore requires a data management plan (DMP) covering both access management and research outputs, applicable over a broad range of disciplines, and compatible with the constraints and existing practices of its diverse partners. We undertook an iterative, step-by-step, process to build a community-approved living document, identifying good practices and processes, on the basis of use cases, presented as proof of concepts. International fora such as the RDA and EOSC, and primarily the BY-COVID project, furnished registries, tools and online data platforms, as well as standards, and the support of data scientists. Together, these elements provide a path for building an umbrella, FAIR-compliant DMP, aligned as fully as possible with FAIR principles, which could also be applied as a framework for data management harmonisation in other large-scale, challenge-driven projects. Finally, we discuss how data management and reuse can be further improved through the writing of realistic DMPs using 'DMP profiles' and, in the future, the contribution of an inter RIs data steward network, to produce a Community of Practice that could be integrated into planned trans-RI competence centres.Preprint added on zenodo with the autorisation of DSJ Edito