starmapVR: immersive visualisation of single cell spatial omic data Article Swipe
Andrian Yang
,
Yao Yu
,
Xiunan Fang
,
Jianfu Li
,
Yongyan Xia
,
Crystal S. M. Kwok
,
Michelle C. K. Lo
,
Dickson M. D. Siu
,
Kevin K. Tsia
,
Joshua W. K. Ho
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1101/2020.09.01.277079
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1101/2020.09.01.277079
Motivation Advances in high throughput single-cell and spatial omic technologies have enabled the profiling of molecular expression and phenotypic properties of hundreds of thousands of individual cells in the context of their two dimensional (2D) or three dimensional (3D) spatial endogenous arrangement. However, current visualisation techniques do not allow for effective display and exploration of the single cell data in their spatial context. With the widespread availability of low-cost virtual reality (VR) gadgets, such as Google Cardboard, we propose that an immersive visualisation strategy is useful. Results We present starmapVR, a light-weight, cross-platform, web-based tool for visualising single-cell and spatial omic data. starmapVR supports a number of interaction methods, such as keyboard, mouse, wireless controller and voice control. The tool visualises single cells in a 3D space and each cell can be represented by a star plot (for molecular expression, phenotypic properties) or image (for single cell imaging). For spatial transcriptomic data, the 2D single cell expression data can be visualised alongside the histological image in a 2.5D format. The application of starmapVR is demonstrated through a series of case studies. Its scalability has been carefully evaluated across different platforms. Availability and implementation starmapVR is freely accessible at https://holab-hku.github.io/starmapVR , with the corresponding source code available at https://github.com/holab-hku/starmapVR under the open source MIT license. Supplementary Information Supplementary data are available at Bioinformatics online.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2020.09.01.277079
- https://www.biorxiv.org/content/biorxiv/early/2020/09/04/2020.09.01.277079.full.pdf
- OA Status
- green
- Cited By
- 3
- References
- 18
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3083227876
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https://openalex.org/W3083227876Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2020.09.01.277079Digital Object Identifier
- Title
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starmapVR: immersive visualisation of single cell spatial omic dataWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2020Year of publication
- Publication date
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2020-09-04Full publication date if available
- Authors
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Andrian Yang, Yao Yu, Xiunan Fang, Jianfu Li, Yongyan Xia, Crystal S. M. Kwok, Michelle C. K. Lo, Dickson M. D. Siu, Kevin K. Tsia, Joshua W. K. HoList of authors in order
- Landing page
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https://doi.org/10.1101/2020.09.01.277079Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2020/09/04/2020.09.01.277079.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2020/09/04/2020.09.01.277079.full.pdfDirect OA link when available
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Computer science, Visualization, Scalability, Context (archaeology), Virtual reality, Computer graphics (images), Data mining, Artificial intelligence, Biology, Database, PaleontologyTop concepts (fields/topics) attached by OpenAlex
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3Total citation count in OpenAlex
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2025: 1, 2023: 1, 2022: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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