ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data
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-cellul...
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| Veröffentlicht in: | IEEE transactions on visualization and computer graphics 2021-01, Vol.27 (1), p.98-110 |
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| container_title | IEEE transactions on visualization and computer graphics |
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| creator | Somarakis, Antonios Van Unen, Vincent Koning, Frits Lelieveldt, Boudewijn Hollt, Thomas |
| description | 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. |
| doi_str_mv | 10.1109/TVCG.2019.2931299 |
| format | Article |
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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. 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| subjects | Cellular Microenvironment - physiology Computational Biology - methods Cytometry Data analysis high-dimensional images Image Cytometry - methods Image Processing, Computer-Assisted Imaging imaging mass cytometry Phenotype Proteins Software spatial omics data Spatial resolution Task analysis Visual analytics Visualization Workflow |
| title | ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data |
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