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IEEE Transactions on Visualization and Computer Graphics

ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data

Antonios Somarakis, Vincent van Unen, Frits Koning, Boudewijn P. F. Lelieveldt, and Thomas Höllt

ImaCytE. Screenshot of our integrated system including the settings panels (a,b), the embedding view (c), the heatmap view (d) for cluster visualization, the image view (e), the interactions heatmap (f), and the motif view (g).

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Tissue functionality is determined by the characteristics of tissue-resident cells and their interactions within their microenvironment. Imaging Mass Cytometry offers the opportunity to distinguish cell types with high precision and link them to their spatial location in intact tissues at sub-cellular resolution. This technology produces large amounts of spatially-resolved high-dimensional data, which constitutes a serious challenge for the data analysis. We present an interactive visual analysis workflow for the end-to-end analysis of Imaging Mass Cytometry data that was developed in close collaboration with domain expert partners. We implemented the presented workflow in an interactive visual analysis tool; ImaCytE. Our workflow is designed to allow the user to discriminate cell types according to their protein expression profiles and analyze their cellular microenvironments, aiding in the formulation or verification of hypotheses on tissue architecture and function. Finally, we show the effectiveness of our workflow and ImaCytE through a case study performed by a collaborating specialist.

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Antonios Somarakis, Vincent van Unen, Frits Koning, Boudewijn P. F. Lelieveldt, and Thomas Höllt, ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data, IEEE Transactions on Visualization and Computer Graphics, 27, pp. 98–110, 2021.

BibTex 

@article{bib:somarakis:2021,
    author       = { Somarakis, Antonios and van Unen, Vincent and Koning, Frits and Lelieveldt, Boudewijn P. F. and Höllt, Thomas },    
    title        = { ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data },
    journal      = { IEEE Transactions on Visualization and Computer Graphics },
    volume       = { 27 },
    year         = { 2021 },
    pages        = { 98--110 },
    doi          = { 10.1109/TVCG.2019.2931299 },
    pubmedid     = { 31369380 },
    url          = { https://publications.graphics.tudelft.nl/papers/134 },
}