Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive ima...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Cambridge University Press
2023-01-01
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| Series: | Biological Imaging |
| Subjects: | |
| Online Access: | https://www.cambridge.org/core/product/identifier/S2633903X2300017X/type/journal_article |
| _version_ | 1797687294212177920 |
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| author | Chaichontat Sriworarat Annie Nguyen Nicholas J. Eagles Leonardo Collado-Torres Keri Martinowich Kristen R. Maynard Stephanie C. Hicks |
| author_facet | Chaichontat Sriworarat Annie Nguyen Nicholas J. Eagles Leonardo Collado-Torres Keri Martinowich Kristen R. Maynard Stephanie C. Hicks |
| author_sort | Chaichontat Sriworarat |
| collection | DOAJ |
| description | High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive image visualization tool that runs completely in the web browser. Samui is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Samui with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Samui along with example datasets is available at https://samuibrowser.com. |
| first_indexed | 2024-03-12T01:16:09Z |
| format | Article |
| id | doaj.art-eae8bdc7fb7b49d9b405ab84a0327b5c |
| institution | Directory Open Access Journal |
| issn | 2633-903X |
| language | English |
| last_indexed | 2024-03-12T01:16:09Z |
| publishDate | 2023-01-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | Biological Imaging |
| spelling | doaj.art-eae8bdc7fb7b49d9b405ab84a0327b5c2023-09-13T12:00:43ZengCambridge University PressBiological Imaging2633-903X2023-01-01310.1017/S2633903X2300017XPerformant web-based interactive visualization tool for spatially-resolved transcriptomics experimentsChaichontat Sriworarat0https://orcid.org/0000-0002-1917-3409Annie Nguyen1https://orcid.org/0000-0003-3842-6923Nicholas J. Eagles2https://orcid.org/0000-0002-9808-5254Leonardo Collado-Torres3https://orcid.org/0000-0003-2140-308XKeri Martinowich4https://orcid.org/0000-0002-5237-0789Kristen R. Maynard5https://orcid.org/0000-0003-0031-8468Stephanie C. Hicks6https://orcid.org/0000-0002-7858-0231Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USALieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USALieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USALieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USADepartment of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA The Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USADepartment of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USADepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USAHigh-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive image visualization tool that runs completely in the web browser. Samui is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Samui with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Samui along with example datasets is available at https://samuibrowser.com.https://www.cambridge.org/core/product/identifier/S2633903X2300017X/type/journal_articlegeoreferencinginteractive image viewermulti-dimensional imagesingle-cell transcriptomicsspatially resolved transcriptomicsweb-based browser |
| spellingShingle | Chaichontat Sriworarat Annie Nguyen Nicholas J. Eagles Leonardo Collado-Torres Keri Martinowich Kristen R. Maynard Stephanie C. Hicks Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments Biological Imaging georeferencing interactive image viewer multi-dimensional image single-cell transcriptomics spatially resolved transcriptomics web-based browser |
| title | Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments |
| title_full | Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments |
| title_fullStr | Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments |
| title_full_unstemmed | Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments |
| title_short | Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments |
| title_sort | performant web based interactive visualization tool for spatially resolved transcriptomics experiments |
| topic | georeferencing interactive image viewer multi-dimensional image single-cell transcriptomics spatially resolved transcriptomics web-based browser |
| url | https://www.cambridge.org/core/product/identifier/S2633903X2300017X/type/journal_article |
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