CyTOF mass cytometry data is recorded in tables that list, for each cell, the signal detected per channel, which is proportional to the number of antibodies tagged with the corresponding channel's isotope bound to that cell. These data are formatted as FCS files, which are compatible with traditional flow cytometry software. Due to the high-dimensional nature of mass cytometry data, novel data analysis tools have been developed as well.
Imaging Mass Cytometry data analysis has its specificity due to different nature of data obtained. In terms of data analysis, both IMC and CyTOF generate large datasets with high dimensionality that require specialized computational methods for analysis. However, data generated by IMC can be more challenging to analyze due to additional data complexity and need for specific tools and pipelines specific for digital image analysis, whereas the data generated by CyTOF is generally analyzed using conventional flow cytometry software. A comprehensive overview of IMC data analysis techniques has been given by Milosevic in.