Spatially resolved transcriptomics in immersive environments

Denis Bienroth; Hieu T Nim; Dimitar Garkov; Karsten Klein; Sabrina Jaeger-Honz; Mirana Ramialison; Falk Schreiber

doi:10.1186/s42492-021-00098-6

Spatially resolved transcriptomics in immersive environments

Vis Comput Ind Biomed Art. 2022 Jan 10;5(1):2. doi: 10.1186/s42492-021-00098-6.

Authors

Denis Bienroth^{1

2}, Hieu T Nim^{2

3

4}, Dimitar Garkov¹, Karsten Klein¹, Sabrina Jaeger-Honz¹, Mirana Ramialison^{5

6

7}, Falk Schreiber^{8

9}

Affiliations

¹ Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
² Cell Biology, Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia.
³ Australian Regenerative Medicine Institute, Monash University, Clayton, Melbourne, VIC, Australia.
⁴ Systems Biology Institute Australia, Clayton, Melbourne, VIC, Australia.
⁵ Cell Biology, Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia. [email protected].
⁶ Australian Regenerative Medicine Institute, Monash University, Clayton, Melbourne, VIC, Australia. [email protected].
⁷ Systems Biology Institute Australia, Clayton, Melbourne, VIC, Australia. [email protected].
⁸ Department of Computer and Information Science, University of Konstanz, Konstanz, Germany. [email protected].
⁹ Faculty of Information Technologies, Monash University, Melbourne, Australia. [email protected].

Abstract

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-Cardiomics is 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.

Keywords: Fish tank virtual reality; Head-mounted display; Immersive analytics; Immersive environment; Spatial transcriptomics; Spatially-resolved transcriptomics; Virtual reality.

Abstract

Grants and funding