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Schoppe, O. ; Pan, C. ; Coronel, J.* ; Mai, H. ; Rong, Z. ; Todorov, M.I. ; Müskes, A.* ; Navarro, F.* ; Li, H.* ; Ertürk, A. ; Menze, B.H.*

Deep learning-enabled multi-organ segmentation in whole-body mouse scans.

Nat. Commun. 11:5626 (2020)
Publ. Version/Full Text DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Whole-body imaging of mice is a key source of information for research. Organ segmentation is a prerequisite for quantitative analysis but is a tedious and error-prone task if done manually. Here, we present a deep learning solution called AIMOS that automatically segments major organs (brain, lungs, heart, liver, kidneys, spleen, bladder, stomach, intestine) and the skeleton in less than a second, orders of magnitude faster than prior algorithms. AIMOS matches or exceeds the segmentation quality of state-of-the-art approaches and of human experts. We exemplify direct applicability for biomedical research for localizing cancer metastases. Furthermore, we show that expert annotations are subject to human error and bias. As a consequence, we show that at least two independently created annotations are needed to assess model performance. Importantly, AIMOS addresses the issue of human bias by identifying the regions where humans are most likely to disagree, and thereby localizes and quantifies this uncertainty for improved downstream analysis. In summary, AIMOS is a powerful open-source tool to increase scalability, reduce bias, and foster reproducibility in many areas of biomedical research.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords In-vivo; Biodistribution; Tomography; Tissue; Organs
ISSN (print) / ISBN 2041-1723
e-ISSN 2041-1723
Journal Nature Communications
Quellenangaben Volume: 11, Issue: 1, Pages: , Article Number: 5626 Supplement: ,
Publisher Nature Publishing Group
Publishing Place London
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute for Tissue Engineering and Regenerative Medicine (ITERM)
Grants NVIDIA
DFG
Fritz Thyssen Stiftung
Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy within the framework of the Munich Cluster for Systems Neurology
Vascular Dementia Research Foundation
German Federal Ministry of Education and Research via the Software Campus initiative