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biovault / ImaCytE

ImaCytE is an interactive tool for data-driven exploration of Imaging Mass Cytometry data as presented in the paper "ImaCytE: Visual Exploration of Cellular Micro-environments for Imaging Mass Cytometry Data".
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# ImaCytE

DOI

ImaCytE is a tool developed for the interactive and data-driven exploration of Imaging Mass Cytometry data as presented in the paper "ImaCytE: Visual Exploration of Cellular Micro-environments for Imaging Mass Cytometry Data". It is focused on the identification of the cell phenotypes that exist in the samples and the interactive exploration of their microenvironment.

Cite

If you use ImaCytE within the scope of a scientific article you must cite the original publication:

Somarakis A., van Unen V., Koning F., Lelieveldt B., and Höllt T., ImaCytE: Visual Exploration of Cellular Microenvironments for Imaging Mass Cytometry Data, IEEE Transactions on Visualization and Computer Graphics, pp. 1-1, 2019. DOI: 10.1109/TVCG.2019.2931299

In case you use the Cohort Comparison feature of ImaCytE you must cite also the following publication: Somarakis A., Ijsselsteijn, M.E., Luk, S.J., Kenkhuis, B., de Miranda, N.F., Lelieveldt B., and Höllt T., Visual cohort comparison for spatial single-cell omics-data, IEEE Transactions on Visualization and Computer Graphics, pp. 1-1, 2020. DOI: 10.1109/TVCG.2020.3030336

Getting started

In case you have a Matlab 2016b or newer you can run ImaCytE from source code.

If you have an older version or you don't have a Matlab installed in your PC you can download and install the executable from the release page .

Using ImaCytE from source code

Loading data for analysis

Detailed step-by-step instructions for the analysis of Imaging Mass Cytometry data, as has been written by our Imaging Mass Cytometry analysis expert, Marieke Ijsselsteijn, Immunogenomics group, Leiden University Medical Center

Detailed Tutorial

ImaCytE tutorial, kindly written by ImaCytE user,
Juan Manuel Ojeda García, Flow Cytometry Core Facility, Newcastle University

Video

video

Video describing main functionalities of ImaCytE through the case study described in the paper.

Video presenting our paper in PacificVis 2020.

Video presenting the main functionalities of our Visual Cohort comparison tool (SpaCeCo), which is integrated in ImaCytE.

Video presenting an overview of our work (preprocessing, ImaCytE, SpaCeCo) in EuroVis 2021.

Contact

Antonios Somarakis antonis.som@gmail.com