Visual cohort comparison for spatial single-cell omics-data

IEEE Transactions on Visualization and Computer Graphics, vol. 27, pp. 733–743

Abstract

Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease and identify related biomarkers, clinical researchers regularly perform large-scale cohort studies, requiring the comparison of such data at cellular level. In such studies, with little a-priori knowledge of what to expect in the data, explorative data analysis is a necessity. Here, we present an interactive visual analysis workflow for the comparison of cohorts of spatially-resolved omics-data. Our workflow allows the comparative analysis of two cohorts based on multiple levels-of-detail, from simple abundance of contained cell types over complex co-localization patterns to individual comparison of complete tissue images. As a result, the workflow enables the identification of cohort-differentiating features, as well as outlier samples at any stage of the workflow. During the development of the workflow, we continuously consulted with domain experts. To show the effectiveness of the workflow, we conducted multiple case studies with domain experts from different application areas and with different data modalities.

Authors 7

1. Antonios Somarakis Aachen Division of Image Processing (LKEB)

   Leiden University Medical Center

   Affiliation as printed

   Division of Image Processing, Leiden University Medical Center, The Netherlands

2. Marieke E. Ijsselsteijn Aachen Immunogenomics group

   Leiden University Medical Center

   Affiliation as printed

   Immunogenomics group, Leiden University Medical Center, The Netherlands

3. Sietse J. Luk Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, The Netherlands

4. Boyd Kenkhuis Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, The Netherlands

5. Noel F.C.C. de Miranda Aachen Immunogenomics group

   Leiden University Medical Center

   Affiliation as printed

   Immunogenomics group, Leiden University Medical Center, The Netherlands

6. Boudewijn P. F. Lelieveldt Aachen Division of Image Processing (LKEB)

   Leiden University Medical Center

   Affiliation as printed

   Division of Image Processing, Leiden University Medical Center, The Netherlands

7. Thomas Höllt Aachen Computer Graphics and Visualization Group Leiden Computational Biology Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Computer Graphics and Visualization Group, TU Delft, Leiden Computational Biology Center, Leiden University Medical Center, The Netherlands