TY - JOUR
T1 - ImaCytE
T2 - Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data
AU - Somarakis, Antonios
AU - van Unen, Vincent
AU - Koning, Frits
AU - Lelieveldt, Boudewijn
AU - Hollt, Thomas
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - Visual analytics
KW - high-dimensional images
KW - imaging mass cytometry
KW - spatial omics data
UR - http://www.scopus.com/inward/record.url?scp=85096884386&partnerID=8YFLogxK
U2 - 10.1109/TVCG.2019.2931299
DO - 10.1109/TVCG.2019.2931299
M3 - Article
SN - 1077-2626
VL - 27
SP - 98
EP - 110
JO - IEEE Transactions on Visualization and Computer Graphics
JF - IEEE Transactions on Visualization and Computer Graphics
IS - 1
M1 - 8778742
ER -