Challenges of building medical image datasets for development of deep learning software in stroke

Alessandro Fontanella; Wenwen Li; Grant Mair; Antreas Antoniou; Eleanor Platt; Chloe Martin; Paul Armitage; Emanuele Trucco; Joanna Wardlaw; Amos Storkey

arXiv · 2309.15081

Challenges of building medical image datasets for development of deep learning software in stroke

Alessandro Fontanella·Wenwen Li·Grant Mair·Antreas Antoniou·Eleanor Platt·Chloe Martin·Paul Armitage·Emanuele Trucco·Joanna Wardlaw·Amos Storkey

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Abstract

Despite the large amount of brain CT data generated in clinical practice, the availability of CT datasets for deep learning (DL) research is currently limited. Furthermore, the data can be insufficiently or improperly prepared for machine learning and thus lead to spurious and irreproducible analyses. This lack of access to comprehensive and diverse datasets poses a significant challenge for the development of DL algorithms. In this work, we propose a complete semi-automatic pipeline to address the challenges of preparing a clinical brain CT dataset for DL analysis and describe the process of standardising this heterogeneous dataset. Challenges include handling image sets with different orientations (axial, sagittal, coronal), different image types (to view soft tissues or bones) and dimensions, and removing redundant background. The final pipeline was able to process 5,868/10,659 (45%) CT image datasets. Reasons for rejection include non-axial data (n=1,920), bone reformats (n=687), separated skull base/vault images (n=1,226), and registration failures (n=465). Further format adjustments, including image cropping, resizing and scaling are also needed for DL processing. Of the axial scans that were not localisers, bone reformats or split brains, 5,868/6,333 (93%) were accepted, while the remaining 465 failed the registration process. Appropriate preparation of medical imaging datasets for DL is a costly and time-intensive process.

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Alessandro Fontanella, Wenwen Li, Grant Mair, Antreas Antoniou, Eleanor Platt, Chloe Martin, Paul Armitage, Emanuele Trucco, Joanna Wardlaw, Amos Storkey. 2023-09-26. Challenges of building medical image datasets for development of deep learning software in stroke. https://arxiv.org/abs/2309.15081

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