Project Details

Description

Humans have approximately 20,000 genes, and each cell-type in the body such as a neurone or a skin cell is defined by which of these genes are switched on, and by how much (it’s expression level). With advances in microfluidics and DNA sequencing technology we can now measure the output of each gene (called the transcriptome) within a single cell, and for many thousands of cells in one experiment. This is called single-cell RNAseq (scRNAseq). The large number of cells we can process poses significant challenges regarding the visualisation and analysis of this complex data. To make it human comprehensible, cells are mathematically projected into two or three dimensional space using reduction methods such as UMAP and tSNE to provide a visual overview cellular composition (or heterogeneity).

Projecting cells into 3D space is often more informative for large complex experiments. There is less information loss as the extra dimension avoids excessive collapsing of the cells, however, current methods to navigate 3D maps are very limited. To address this we are developing CellexalVR, a virtual reality (VR) environment for the visualisation and analysis of single-cell experiments (www.cellexalvr.med.lu.se).

The overarching aim of this proposal is to significantly extend the capabilities of CellexalVR to encompass spatial transcriptomics. We will develop an immersive 3D environment and tool-set to concurrently dissect ST and scRNAseq data in VR while allowing the user to simultaneously visualise tissue/organ structure to provide greater context for the expression data they are seeing.

A second aim is to develop a cloud system to centrally distribute scRNAseq and ST data directly into CellexalVR. We call this CellexalNet, and will enable researchers across the world to pull scRNAseq/ST data directly into VR, removing the need for data downloads and subsequent scripting/programming which is beyond the scope of many.
Short titleeSSENCE@LU 7:2
StatusActive
Effective start/end date2021/01/012022/12/31