TY - JOUR
T1 - SpaceWalker enables interactive gradient exploration for spatial transcriptomics data
AU - Li, Chang
AU - Thijssen, Julian
AU - Kroes, Thomas
AU - de Boer, Mitchell
AU - Abdelaal, Tamim
AU - Höllt, Thomas
AU - Lelieveldt, Boudewijn
PY - 2023
Y1 - 2023
N2 - In spatial transcriptomics (ST) data, biologically relevant features such as tissue compartments or cell-state transitions are reflected by gene expression gradients. Here, we present SpaceWalker, a visual analytics tool for exploring the local gradient structure of 2D and 3D ST data. The user can be guided by the local intrinsic dimensionality of the high-dimensional data to define seed locations, from which a flood-fill algorithm identifies transcriptomically similar cells on the fly, based on the high-dimensional data topology. In several use cases, we demonstrate that the spatial projection of these flooded cells highlights tissue architectural features and that interactive retrieval of gene expression gradients in the spatial and transcriptomic domains confirms known biology. We also show that SpaceWalker generalizes to several different ST protocols and scales well to large, multi-slice, 3D whole-brain ST data while maintaining real-time interaction performance.
AB - In spatial transcriptomics (ST) data, biologically relevant features such as tissue compartments or cell-state transitions are reflected by gene expression gradients. Here, we present SpaceWalker, a visual analytics tool for exploring the local gradient structure of 2D and 3D ST data. The user can be guided by the local intrinsic dimensionality of the high-dimensional data to define seed locations, from which a flood-fill algorithm identifies transcriptomically similar cells on the fly, based on the high-dimensional data topology. In several use cases, we demonstrate that the spatial projection of these flooded cells highlights tissue architectural features and that interactive retrieval of gene expression gradients in the spatial and transcriptomic domains confirms known biology. We also show that SpaceWalker generalizes to several different ST protocols and scales well to large, multi-slice, 3D whole-brain ST data while maintaining real-time interaction performance.
KW - data visualization
KW - visual analytics
KW - spatial transcriptomics
KW - gene expression gradients
UR - http://www.scopus.com/inward/record.url?scp=85179762058&partnerID=8YFLogxK
U2 - 10.1016/j.crmeth.2023.100645
DO - 10.1016/j.crmeth.2023.100645
M3 - Article
SN - 2667-2375
VL - 3
JO - Cell Reports Methods
JF - Cell Reports Methods
IS - 12
M1 - 100645
ER -