|
View: |
Part 1: Document Description
|
|
Citation |
|
|---|---|
|
Title: |
Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics (Software and Data) |
|
Identification Number: |
doi:10.18419/darus-4254 |
|
Distributor: |
DaRUS |
|
Date of Distribution: |
2024-06-21 |
|
Version: |
1 |
|
Bibliographic Citation: |
Bienroth, Denis; Charitakis, Natalie; Jaeger-Honz, Sabrina; Garkov, Dimitar; Elliott, David; Porrello, Enzo R.; Klein, Karsten; Nim, Hieu T.; Schreiber, Falk; Ramialison, Mirana, 2024, "Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics (Software and Data)", https://doi.org/10.18419/darus-4254, DaRUS, V1 |
|
Citation |
|
|
Title: |
Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics (Software and Data) |
|
Identification Number: |
doi:10.18419/darus-4254 |
|
Identification Number: |
swh:1:rev:a0c0f78607f4b6e1ad2e496689a37a170143e929;origin=https://github.com/Ramialison-Lab/VR-Omics;visit=swh:1:snp:a0496c0f1f17ab324ca6b3561f8cd7d1c85aca0b |
|
Authoring Entity: |
Bienroth, Denis (reNEW Novo Nordisk Foundation Center for Stem Cell Medicine & Stem Cell Biology, Murdoch Children’s Research Institute Melbourne) |
|
Charitakis, Natalie (reNEW Novo Nordisk Foundation Center for Stem Cell Medicine & Stem Cell Biology, Murdoch Children’s Research Institute Melbourne, Department of Paediatrics University of Melbourne) |
|
|
Jaeger-Honz, Sabrina (Universität Konstanz) |
|
|
Garkov, Dimitar (Universität Konstanz) |
|
|
Elliott, David (reNEW Novo Nordisk Foundation Center for Stem Cell Medicine & Stem Cell Biology, Murdoch Children’s Research Institute Melbourne, Department of Paediatrics University of Melbourne, Australian Regenerative Medicine Institute Monash University) |
|
|
Porrello, Enzo R. (reNEW Novo Nordisk Foundation Center for Stem Cell Medicine & Stem Cell Biology, Murdoch Children’s Research Institute Melbourne, Department of Paediatrics University of Melbourne, Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Department of Anatomy and Physiology, School of Biomedical Sciences University of Melbourne) |
|
|
Klein, Karsten (Universität Konstanz) |
|
|
Nim, Hieu T. (reNEW Novo Nordisk Foundation Center for Stem Cell Medicine & Stem Cell Biology, Murdoch Children’s Research Institute Melbourne, Department of Paediatrics University of Melbourne, Australian Regenerative Medicine Institute Monash University, System Biology Institute Clayton) |
|
|
Schreiber, Falk (Universität Konstanz, Faculty of Information Technologies Monash University) |
|
|
Ramialison, Mirana (reNEW Novo Nordisk Foundation Center for Stem Cell Medicine & Stem Cell Biology, Murdoch Children’s Research Institute Melbourne, Department of Paediatrics University of Melbourne, Australian Regenerative Medicine Institute Monash University, System Biology Institute Clayton) |
|
|
Grant Number: |
251654672 |
|
Distributor: |
DaRUS |
|
Access Authority: |
Ramialison, Mirana |
|
Access Authority: |
Bienroth, Denis |
|
Depositor: |
Jaeger-Honz, Sabrina |
|
Date of Deposit: |
2024-06-10 |
|
Holdings Information: |
https://doi.org/10.18419/darus-4254 |
|
Study Scope |
|
|
Keywords: |
Computer and Information Science, Medicine, Health and Life Sciences, Spatial Transcriptomics, Virtual Reality, Information Visualization |
|
Topic Classification: |
Computer Science |
|
Abstract: |
Here, we summarise available data and source code regarding the publication "Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics". <br> <b> Abstract </b> <br> Spatially resolved transcriptomics (SRT) technologies produce complex, multi-dimensional data sets of gene expression information that can be obtained at subcellular spatial resolution. While several computational tools are available to process and analyse SRT data, no platforms facilitate the visualisation and interaction with SRT data in an immersive manner. Here we present VR-Omics, a computational platform that supports the analysis, visualisation, exploration, and interpretation SRT data compatible with any SRT technology. VR-Omics is the first tool capable of analysing and visualising data generated by multiple SRT platforms in both 2D desktop and virtual reality environments. It incorporates an in-built workflow to automatically pre-process and spatially mine the data within a user-friendly graphical user interface. Benchmarking VR-Omics against other comparable software demonstrates its seamless end-to-end analysis of SRT data, hence making SRT data processing and mining universally accessible. <br> VR-Omics is an open-source software freely available at: <a href="https://ramialison-lab.github.io/pages/vromics.html">https://ramialison-lab.github.io/pages/vromics.html</a> or below.<br> |
|
Notes: |
For development of VR-Omics publicly available data was used. <br> The Visium data from 10XGenomics is available at the 10X Genomics website: <a href="https://www.10xgenomics.com/resources/datasets">https://www.10xgenomics.com/resources/datasets</a>. <br> The 10X Genomics Xenium dataset is available under: <a href="https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast">https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast</a>. <br> The STOmics database is available at: <a href="https://db.cngb.org/stomics">https://db.cngb.org/stomics</a>. <br> The Vizgen MERFISH data release program can be accessed via: <a href="https://vizgen.com/data-release-program/">https://vizgen.com/data-release-program/</a>.<br> The Tomo-seq data is available via their publication <a href="https://doi.org/10.1016/j.cell.2014.09.038">https://doi.org/10.1016/j.cell.2014.09.038</a> which also contains the MATLAB code for the 3D data reconstruction. <br> <br> The Visium demo was adapted from Asp et al. and can be accessed via the related publication <a href="https://doi.org/10.1016/j.cell.2019.11.025">https://doi.org/10.1016/j.cell.2019.11.025</a> or at <a href="https://data.mendeley.com/datasets/zkzvyprd5z/1">https://data.mendeley.com/datasets/zkzvyprd5z/1</a>.<br> <br> The demo datasets generated for VR-Omics can be found at: <a href="https://doi.org/10.26180/22207579.v1">https://doi.org/10.26180/22207579.v1</a> or below for download. <br> <br> The 3D Visium data set of the human developing heart adapted from Asp et al. can be found within the application and can be accessed from the main menu following the Visium, Demo context menu.<br> <br> The complete standalone version of VR-Omics (containing Python AW and Visualiser) can be downloaded at <a href="https://ramialison-lab.github.io/pages/vromics.html">https://ramialison-lab.github.io/pages/vromics.html</a> or at <a href="https://doi.org/10.26180/20220312.v1">https://doi.org/10.26180/20220312.v1</a> or below for download. <br> <br> Alternatively, the code is available at GitHub (<a href="https://github.com/Ramialison-Lab/VR-Omics">https://github.com/Ramialison-Lab/VR-Omics</a>). To use the GitHub version an installation of Unity Gaming Engine (version 2021.3.11f1) is required. This version does not include the Python AW. <br> <br> The Python AW can be accessed at: <a href="https://doi.org/10.26180/22207903.v1">https://doi.org/10.26180/22207903.v1</a>. More information of run VR-Omics via Unity can be found in the full documentation accessible at <a href="https://ramialison-lab.github.io/pages/vromics.html">https://ramialison-lab.github.io/pages/vromics.html</a>.<br> |
|
Methodology and Processing |
|
|
Sources Statement |
|
|
Data Access |
|
|
Other Study Description Materials |
|
|
Related Publications |
|
|
Citation |
|
|
Title: |
Denis Bienroth, Natalie Charitakis, Sabrina Jaeger-Honz, Dimitar Garkov, David A. Elliott, Enzo R. Porrello, Karsten Klein, Hieu T. Nim, Falk Schreiber, Mirana Ramialison: Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics, bioRxiv 2023.03.31.535025 |
|
Identification Number: |
10.1101/2023.03.31.535025 |
|
Bibliographic Citation: |
Denis Bienroth, Natalie Charitakis, Sabrina Jaeger-Honz, Dimitar Garkov, David A. Elliott, Enzo R. Porrello, Karsten Klein, Hieu T. Nim, Falk Schreiber, Mirana Ramialison: Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics, bioRxiv 2023.03.31.535025 |
|
Label: |
Documentation_VR-Omics.pdf |
|
Text: |
Download instructions and documentation of VR-OMICS. |
|
Notes: |
application/pdf |
|
Label: |
Test_Data_VR-Omics.zip |
|
Text: |
Test data generated for use with VR-Omics for different spatial transcriptomics sequencing techniqes. |
|
Notes: |
application/zip |
|
Label: |
VR_Omics.zip |
|
Text: |
Software VR-Omics (containing Python AW and Visualiser) |
|
Notes: |
application/zip |