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Spatial landmark detection and tissue registration with deep learning
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.ORCID iD: 0000-0001-6942-0458
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-5108-4481
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-4773-9975
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.ORCID iD: 0000-0001-8150-4021
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2024 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 21, no 4, p. 673-679Article in journal (Refereed) Published
Abstract [en]

Spatial landmarks are crucial in describing histological features between samples or sites, tracking regions of interest in microscopy, and registering tissue samples within a common coordinate framework. Although other studies have explored unsupervised landmark detection, existing methods are not well-suited for histological image data as they often require a large number of images to converge, are unable to handle nonlinear deformations between tissue sections and are ineffective for z-stack alignment, other modalities beyond image data or multimodal data. We address these challenges by introducing effortless landmark detection, a new unsupervised landmark detection and registration method using neural-network-guided thin-plate splines. Our proposed method is evaluated on a diverse range of datasets including histology and spatially resolved transcriptomics, demonstrating superior performance in both accuracy and stability compared to existing approaches.

Place, publisher, year, edition, pages
Springer Nature , 2024. Vol. 21, no 4, p. 673-679
National Category
Computer graphics and computer vision Medical Imaging Radiology and Medical Imaging
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URN: urn:nbn:se:kth:diva-367072DOI: 10.1038/s41592-024-02199-5ISI: 001178071600001PubMedID: 38438615Scopus ID: 2-s2.0-85186550191OAI: oai:DiVA.org:kth-367072DiVA, id: diva2:1984170
Note

QC 20250715

Available from: 2025-07-15 Created: 2025-07-15 Last updated: 2025-07-15Bibliographically approved

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Ekvall, MarkusBergenstråhle, LudvigAndersson, AlmaCzarnewski, PauloKäll, LukasLundeberg, Joakim

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Ekvall, MarkusBergenstråhle, LudvigAndersson, AlmaCzarnewski, PauloKäll, LukasLundeberg, Joakim
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Nature Methods
Computer graphics and computer visionMedical ImagingRadiology and Medical Imaging

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