PatternExtract: A facile, scalable pipeline for point pattern generation from spatial imaging data Article Swipe
Shruti Sridhar
,
Gayatri Kumar
,
Siddham Jasoria
,
Ziwei Meng
,
Patrick Jaynes
,
Vaibhav Rajan
,
David W. Scott
,
Claudio Tripodo
,
Kasthuri Kannan
,
Anand D. Jeyasekharan
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.06.25.661424
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.06.25.661424
We present PatternExtract, an open-source pipeline that generates accurate spatial point patterns from RGB pathology images and cell coordinate data without relying on composite channels or proprietary software. Using a novel two-kernel tissue segmentation method combined with automated pixel classification in QuPath, PatternExtract precisely excludes tissue artifacts such as necrosis and blood vessels to define spatial windows. Optimized on 568 diffuse large B-cell lymphoma images and validated on an independent cohort, the pipeline enables robust spatial analyses.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.06.25.661424
- https://www.biorxiv.org/content/biorxiv/early/2025/06/28/2025.06.25.661424.full.pdf
- OA Status
- green
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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- DOI
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https://doi.org/10.1101/2025.06.25.661424Digital Object Identifier
- Title
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PatternExtract: A facile, scalable pipeline for point pattern generation from spatial imaging dataWork title
- Type
-
preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-06-28Full publication date if available
- Authors
-
Shruti Sridhar, Gayatri Kumar, Siddham Jasoria, Ziwei Meng, Patrick Jaynes, Vaibhav Rajan, David W. Scott, Claudio Tripodo, Kasthuri Kannan, Anand D. JeyasekharanList of authors in order
- Landing page
-
https://doi.org/10.1101/2025.06.25.661424Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2025/06/28/2025.06.25.661424.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2025/06/28/2025.06.25.661424.full.pdfDirect OA link when available
- Concepts
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Scalability, Pipeline (software), Computer science, Point (geometry), Database, Geometry, Operating system, MathematicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- Related works (count)
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10Other works algorithmically related by OpenAlex
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