TY - JOUR
T1 - Spatially resolved transcriptomics in immersive environments
AU - Bienroth, Denis
AU - Nim, Hieu T.
AU - Garkov, Dimitar
AU - Klein, Karsten
AU - Jaeger-Honz, Sabrina
AU - Ramialison, Mirana
AU - Schreiber, Falk
N1 - Funding Information:
The authors thank the members of the Ramialison Laboratory at ARMI and MCRI and the members of Falk Schreiber?s LSI Chair for their support. The authors would also like to thank Julian Stolper for testing the application and giving feedback on the application and the manuscript, and Michael See and Natalie Charitakis for their suggestions and support as well as help with the required devices. The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government.
Funding Information:
This project was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 251654672 – TRR 161 and by DFG Center of Excellence 2117 “Centre for the Advanced Study of Collective Behaviour” (ID 422037984). M.R. was funded by an NH & MRC/Heart Foundation Career Development Fellowship and by an Australian Research Council Discovery Project DP190102771 Grant.
Funding Information:
The authors thank the members of the Ramialison Laboratory at ARMI and MCRI and the members of Falk Schreiber’s LSI Chair for their support. The authors would also like to thank Julian Stolper for testing the application and giving feedback on the application and the manuscript, and Michael See and Natalie Charitakis for their suggestions and support as well as help with the required devices. The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information. Upon data acquisition, one major hurdle is the subsequent interpretation and visualization of the datasets acquired. To address this challenge, VR-Cardiomicsis presented, which is a novel data visualization system with interactive functionalities designed to help biologists interpret spatially resolved transcriptomic datasets. By implementing the system in two separate immersive environments, fish tank virtual reality (FTVR) and head-mounted display virtual reality (HMD-VR), biologists can interact with the data in novel ways not previously possible, such as visually exploring the gene expression patterns of an organ, and comparing genes based on their 3D expression profiles. Further, a biologist-driven use-case is presented, in which immersive environments facilitate biologists to explore and compare the heart expression profiles of different genes.
AB - Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information. Upon data acquisition, one major hurdle is the subsequent interpretation and visualization of the datasets acquired. To address this challenge, VR-Cardiomicsis presented, which is a novel data visualization system with interactive functionalities designed to help biologists interpret spatially resolved transcriptomic datasets. By implementing the system in two separate immersive environments, fish tank virtual reality (FTVR) and head-mounted display virtual reality (HMD-VR), biologists can interact with the data in novel ways not previously possible, such as visually exploring the gene expression patterns of an organ, and comparing genes based on their 3D expression profiles. Further, a biologist-driven use-case is presented, in which immersive environments facilitate biologists to explore and compare the heart expression profiles of different genes.
KW - Fish tank virtual reality
KW - Head-mounted display
KW - Immersive analytics
KW - Immersive environment
KW - Spatial transcriptomics
KW - Spatially-resolved transcriptomics
KW - Virtual reality
UR - http://www.scopus.com/inward/record.url?scp=85122825495&partnerID=8YFLogxK
U2 - 10.1186/s42492-021-00098-6
DO - 10.1186/s42492-021-00098-6
M3 - Article
C2 - 35001220
AN - SCOPUS:85122825495
SN - 2524-4442
VL - 5
JO - Visual Computing for Industry, Biomedicine, and Art
JF - Visual Computing for Industry, Biomedicine, and Art
IS - 1
M1 - 2
ER -