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bioRxiv · 10.1101/2024.12.10.627814

Depositing biological segmentation datasets FAIRly

Ho, E. M. L.·Ladakis, D.·Basham, M.·Darrow, M. C.
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Abstract

Segmentation of biological images identifies regions of an image which correspond to specific features of interest, which can be analysed quantitatively to answer biological questions. This task has long been a barrier to conducting large-scale biological imaging studies as it is time- and labour-intensive. Modern artificial intelligence segmentation tools can automate this process, but require high quality segmentation data for training, which is challenging to acquire. Biological segmentation data has been produced for many years, but this data is not often reused to develop new tools as it is hard to find, access, and use. Recent disparate efforts (Iudin, et al., 2023; Xu, et al., 2021; Vogelstein, et al., 2018; Ermel, et al., 2024) have been made to facilitate deposition and re-use of these valuable datasets, but more work is needed to increase re-usability. In this work, we review the current state of publicly available annotation and segmentation datasets and make specific recommendations to increase re-usability following FAIR (findable, accessible, interoperable, re-usable) principles (Wilkinson, et al., 2016) for the future.

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Ho, E. M. L., Ladakis, D., Basham, M., Darrow, M. C.. 2024-12-12. Depositing biological segmentation datasets FAIRly. https://doi.org/10.1101/2024.12.10.627814

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