SpaceWalker enables interactive gradient exploration for spatial transcriptomics data

Cell Reports Methods, vol. 3, pp. 100645

Abstract

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.

Authors 7

1. Chang Li Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands

2. Julian Thijssen Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands

3. Thomas Kroes Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands

4. Mitchell M. de Boer Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands

5. Tamim Abdelaal Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Delft Bioinformatics Lab, INSY, TU Delft, 2628 XE Delft, the Netherlands

   Delft Bioinformatics Lab, INSY, TU Delft, 2628 XE Delft, the Netherlands

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands

6. Thomas Höllt

   Delft University of Technology

   Affiliation as printed

   Computer Graphics and Visualization, INSY, TU Delft, 2628 XE Delft, the Netherlands

7. Boudewijn P. F. Lelieveldt corresponding Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Delft Bioinformatics Lab, INSY, TU Delft, 2628 XE Delft, the Netherlands. Electronic address: b.p.f.lelieveldt@lumc.nl

   Delft Bioinformatics Lab, INSY, TU Delft, 2628 XE Delft, the Netherlands

   Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands