Defining Keypoints to Align H&E Images and Xenium DAPI-Stained Images Automatically Article Swipe
Yu Lin
,
Yan Wang
,
Juexin Wang
,
Mauminah Raina
,
Ricardo Melo Ferreira
,
Michael T. Eadon
,
Yanchun Liang
,
Dong Xu
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3390/cells14131000
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3390/cells14131000
10X Xenium is an in situ spatial transcriptomics platform that enables single-cell and subcellular-level gene expression analysis. In Xenium data analysis, defining matched keypoints to align H&E and spatial transcriptomic images is critical for cross-referencing sequencing and histology. Currently, it is labor-intensive for domain experts to manually place keypoints to perform image registration in the Xenium Explorer software. We present Xenium-Align, a keypoint identification method that automatically generates keypoint files for image registration in Xenium Explorer. We validated our proposed method on 14 human kidney samples and one human skin Xenium sample representing healthy and diseased states, with expert manually marked results. These results show that Xenium-Align could generate accurate keypoints for automatically implementing image alignment in the Xenium Explorer software for spatial transcriptomics studies. Our future research aims to optimize the method’s runtime efficiency and usability for image alignment applications.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/cells14131000
- https://www.mdpi.com/2073-4409/14/13/1000/pdf?version=1751294824
- OA Status
- gold
- References
- 53
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4411802940
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4411802940Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/cells14131000Digital Object Identifier
- Title
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Defining Keypoints to Align H&E Images and Xenium DAPI-Stained Images AutomaticallyWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-06-30Full publication date if available
- Authors
-
Yu Lin, Yan Wang, Juexin Wang, Mauminah Raina, Ricardo Melo Ferreira, Michael T. Eadon, Yanchun Liang, Dong XuList of authors in order
- Landing page
-
https://doi.org/10.3390/cells14131000Publisher landing page
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https://www.mdpi.com/2073-4409/14/13/1000/pdf?version=1751294824Direct link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.mdpi.com/2073-4409/14/13/1000/pdf?version=1751294824Direct OA link when available
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Computer science, Software, Usability, Artificial intelligence, Computer vision, Image registration, Image (mathematics), Pattern recognition (psychology), Human–computer interaction, Programming languageTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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