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Application of Open-Source Digital Resources for 3D Visualization of Clustered Transcriptomic Data.

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Bibliographic Details
Title: Application of Open-Source Digital Resources for 3D Visualization of Clustered Transcriptomic Data.
Authors: Strickland HF; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, USA.; Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA., Shen A; Department of Digital Arts and Sciences, University of Florida, Gainesville, Florida, USA., Paul AL; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, USA.; Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA.; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA., Ferl R; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, USA.; Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA.; Office of Research, University of Florida, Gainesville, Florida, USA.
Source: Physiologia plantarum [Physiol Plant] 2025 Sep-Oct; Vol. 177 (5), pp. e70500.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Scandinavian Society For Plant Physiology Country of Publication: Denmark NLM ID: 1256322 Publication Model: Print Cited Medium: Internet ISSN: 1399-3054 (Electronic) Linking ISSN: 00319317 NLM ISO Abbreviation: Physiol Plant Subsets: MEDLINE
Imprint Name(s): Publication: Copenhagen : Scandinavian Society For Plant Physiology
Original Publication: Lund, Sweden [etc.]
MeSH Terms: Transcriptome*/genetics , Imaging, Three-Dimensional*/methods , Gene Expression Profiling*/methods , Data Visualization*, Software ; Cluster Analysis
Abstract: As datasets grow in size with the increased accessibility of high-throughput transcriptome sequencing, methods of dimensionality reduction have become invaluable for data analysis. The methods of dimensionality reduction, including t-distributed stochastic neighbor embedding or Uniform Manifold Approximation and Projection, are utilized to create figures and projections of the high-dimensional data into a set of lower dimensions, 2D or 3D, which are more well-suited for human comprehension. These methods of dimensionality reduction have continually grown in popularity and widespread use. Despite this popularity, creating engaging and visually attractive features remains an issue for many users without significant coding experience. To remediate this issue, an HTML-based digital resource was created that utilizes publicly available scripts from JsDelivr and GitHub, and Blender, an open-source modeling software. We have generated two open-source digital data visualization resources that can be applied to the transcriptomic data processed using the aforementioned methods of dimensionality reduction. The first, HTMLview, utilizes a provided HTML file template to create an interactive and engaging 3D model in digital space. The second method, Blenderview, utilizes the open-source modeling software, Blender, to create and animate high-quality models and videos of processed datapoints. The two methods were tested with transcriptomic data processed via dimensionality reduction algorithms. The methods provided create two distinct paths for researchers to better visualize, examine, and share their data, while also utilizing open-source technologies that are readily available to most potential users.
(© 2025 The Author(s). Physiologia Plantarum published by John Wiley & Sons Ltd on behalf of Scandinavian Plant Physiology Society.)
References: Physiol Plant. 2023 Nov-Dec;175(6):e14068. (PMID: 38148248)
Cell Rep. 2019 May 14;27(7):2241-2247.e4. (PMID: 31091459)
Nat Biotechnol. 2018 Dec 03;:. (PMID: 30531897)
NPJ Microgravity. 2023 Dec 20;9(1):95. (PMID: 38123588)
Nat Commun. 2019 Nov 28;10(1):5416. (PMID: 31780648)
Physiol Plant. 2025 Sep-Oct;177(5):e70500. (PMID: 40958711)
iScience. 2021 Oct 27;24(11):103251. (PMID: 34849461)
Grant Information: 80NSSC18K1294 United States NASA NASA
Entry Date(s): Date Created: 20250917 Date Completed: 20250917 Latest Revision: 20250919
Update Code: 20250919
PubMed Central ID: PMC12441758
DOI: 10.1111/ppl.70500
PMID: 40958711
Database: MEDLINE
Description
Abstract:As datasets grow in size with the increased accessibility of high-throughput transcriptome sequencing, methods of dimensionality reduction have become invaluable for data analysis. The methods of dimensionality reduction, including t-distributed stochastic neighbor embedding or Uniform Manifold Approximation and Projection, are utilized to create figures and projections of the high-dimensional data into a set of lower dimensions, 2D or 3D, which are more well-suited for human comprehension. These methods of dimensionality reduction have continually grown in popularity and widespread use. Despite this popularity, creating engaging and visually attractive features remains an issue for many users without significant coding experience. To remediate this issue, an HTML-based digital resource was created that utilizes publicly available scripts from JsDelivr and GitHub, and Blender, an open-source modeling software. We have generated two open-source digital data visualization resources that can be applied to the transcriptomic data processed using the aforementioned methods of dimensionality reduction. The first, HTMLview, utilizes a provided HTML file template to create an interactive and engaging 3D model in digital space. The second method, Blenderview, utilizes the open-source modeling software, Blender, to create and animate high-quality models and videos of processed datapoints. The two methods were tested with transcriptomic data processed via dimensionality reduction algorithms. The methods provided create two distinct paths for researchers to better visualize, examine, and share their data, while also utilizing open-source technologies that are readily available to most potential users.<br /> (© 2025 The Author(s). Physiologia Plantarum published by John Wiley & Sons Ltd on behalf of Scandinavian Plant Physiology Society.)
ISSN:1399-3054
DOI:10.1111/ppl.70500