Visual cohort comparison for spatial single-cell omics-data

• Published in: IEEE transactions on visualization and computer graphics Vol. 27; no. 2; pp. 733 - 743
• Main Authors: Somarakis, Antonios, Ijsselsteijn, Marieke E., Luk, Sietse J., Kenkhuis, Boyd, de Miranda, Noel F.C.C., Lelieveldt, Boudewijn P.F., Hollt, Thomas
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.02.2021; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Biomarkers; Biomedical imaging; Cohort Studies; Computer Graphics; Data analysis; Domains; Humans; Image segmentation; Imaging Mass Cytometry; Outliers (statistics); single-cell omics-data; Spatial data; Spatial databases; spatially-resolved data; Subject specialists; Task analysis; Vectra; Visual analytics; Visual comparison; Visualization; Workflow
• ISSN: 1077-2626; 1941-0506; 2160-9306; 1941-0506
• DOI: 10.1109/TVCG.2020.3030336

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.