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- Andersson, AxelUppsala universitet,Science for Life Laboratory, SciLifeLab,Bildanalys och människa-datorinteraktion,Avdelningen Vi3 (author)
Points2Regions : Fast, interactive clustering of imaging-based spatial transcriptomics data
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- LIBRIS-ID:oai:DiVA.org:uu-523994
- https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-523994URI
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- Language:English
- Summary in:English
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- Imaging-based spatial transcriptomics techniques generate image data that, once processed, results in a set of spatial points with categorical labels for different mRNA species. A crucial part of analyzing downstream data involves the analysis of these point patterns. Here, biologically interesting patterns can be explored at different spatial scales. Molecular patterns on a cellular level would correspond to cell types, whereas patterns on a millimeter scale would correspond to tissue-level structures. Often, clustering methods are employed to identify and segment regions with distinct point-patterns. Traditional clustering techniques for such data are constrained by reliance on complementary data or extensive machine learning, limiting their applicability to tasks on a particular scale. This paper introduces 'Points2Regions', a practical tool for clustering spatial points with categorical labels. Its flexible and computationally efficient clustering approach enables pattern discovery across multiple scales, making it a powerful tool for exploratory analysis. Points2Regions has demonstrated efficient performance in various datasets, adeptly defining biologically relevant regions similar to those found by scale-specific methods. As a Python package integrated into TissUUmaps and a Napari plugin, it offers interactive clustering and visualization, significantly enhancing user experience in data exploration. In essence, Points2Regions presents a user-friendly and simple tool for exploratory analysis of spatial points with categorical labels.
Subject headings and genre
- NATURVETENSKAP Data- och informationsvetenskap Bioinformatik hsv//swe
- NATURAL SCIENCES Computer and Information Sciences Bioinformatics hsv//eng
- Bioinformatics
- Bioinformatik
- Immunologi
- Immunology
- Computerized Image Processing
- Datoriserad bildbehandling
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- Behanova, AndreaUppsala universitet,Science for Life Laboratory, SciLifeLab,Bildanalys och människa-datorinteraktion,Avdelningen Vi3(Swepub:uu)andbe848 (author)
- Avenel, ChristopheUppsala universitet,Bildanalys och människa-datorinteraktion,Avdelningen Vi3,Science for Life Laboratory, SciLifeLab(Swepub:uu)chrav452 (author)
- Windhager, JonasUppsala universitet,Science for Life Laboratory, SciLifeLab,Bildanalys och människa-datorinteraktion,Avdelningen Vi3(Swepub:uu)jonwi709 (author)
- Malmberg, Filip,1980-Uppsala universitet,Bildanalys och människa-datorinteraktion,Avdelningen Vi3,Science for Life Laboratory, SciLifeLab(Swepub:uu)filma606 (author)
- Wählby, Carolina,professor,1974-Uppsala universitet,Bildanalys och människa-datorinteraktion,Science for Life Laboratory, SciLifeLab,Avdelningen Vi3(Swepub:uu)cli05194 (author)
- Uppsala universitetScience for Life Laboratory, SciLifeLab (creator_code:org_t)
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