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Todorov, M.I. ; Paetzold, J.C.* ; Schoppe, O.* ; Tetteh, G.* ; Shit, S.* ; Efremov, V.* ; Todorov-Völgyi, K.* ; Düring, M.* ; Dichgans, M.* ; Piraud, M.* ; Menze, B.* ; Ertürk, A.

Machine learning analysis of whole mouse brain vasculature.

Nat. Methods 17, 442-449 (2020)
Postprint DOI PMC
Open Access Green
Tissue clearing methods enable the imaging of biological specimens without sectioning. However, reliable and scalable analysis of large imaging datasets in three dimensions remains a challenge. Here we developed a deep learning-based framework to quantify and analyze brain vasculature, named Vessel Segmentation & Analysis Pipeline (VesSAP). Our pipeline uses a convolutional neural network (CNN) with a transfer learning approach for segmentation and achieves human-level accuracy. By using VesSAP, we analyzed the vascular features of whole C57BL/6J, CD1 and BALB/c mouse brains at the micrometer scale after registering them to the Allen mouse brain atlas. We report evidence of secondary intracranial collateral vascularization in CD1 mice and find reduced vascularization of the brainstem in comparison to the cerebrum. Thus, VesSAP enables unbiased and scalable quantifications of the angioarchitecture of cleared mouse brains and yields biological insights into the vascular function of the brain.VesSAP is a tissue clearing- and deep learning-based pipeline for comprehensively analyzing mouse vasculature, from large vessels to small capillaries.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Expression; Networks; Disease; Organs
Sprache englisch
Veröffentlichungsjahr 2020
HGF-Berichtsjahr 2020
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Zeitschrift Nature Methods
Quellenangaben Band: 17, Heft: 4, Seiten: 442-449 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort New York, NY
Begutachtungsstatus Peer reviewed
Institut(e) Institute for Tissue Engineering and Regenerative Medicine (ITERM)
POF Topic(s) 30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
PSP-Element(e) G-505800-001
DOI 10.1038/s41592-020-0792-1
WOS ID WOS:000519157100001
Scopus ID 85081910282
PubMed ID 32161395
Erfassungsdatum 2020-03-24
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