Semi-Automated Background Removal Limits Loss of Data and Normalises the Images for Downstream Analysis of Imaging Mass Cytometry Data

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.

@Article { ISLHM20,
  author       = "Ijsselsteijn, Marieke E and Somarakis, Antonios and Lelieveldt, Boudewijn P.F. and H\öllt, Thomas and
                  Miranda, Noel de",
  title        = "Semi-Automated Background Removal Limits Loss of Data and Normalises the Images for Downstream Analysis of
                  Imaging Mass Cytometry Data",
  journal      = "bioRxiv",
  year         = "2020",
  doi          = "10.1101/2020.11.26.399717",
  url          = "http://graphics.tudelft.nl/Publications-new/2020/ISLHM20"
}