Many users apply compensation at the time of data acquisition. In most cytometry acquisition software, data is written in an uncompensated format and the compensation matrix is included within the files alongside the data. Compensation matrices are often defined as keywords $Comp, $Spillover or SPILL in the raw FCS files. In FCS 3.1, the $SPILLOVER keyword is the only standardized way to specify compensation (Spidlen, Josef et al. “Data File Standard for Flow Cytometry, version FCS 3.1.” Cytometry. Part A)
The Cytobank platform can read the acquisition compensation as file-internal compensation and use it as experiment wide compensation for downstream analysis (this is the default setting). The file-internal compensation matrix can also be imported into the Cytobank platform in order for the values to be changed.
Data can still be viewed as uncompensated by changing the compensation selector to Uncompensated. You can recompute the matrix with the single staining compensation controls using the automatic compensation tool in the Cytobank platform.
You can also use other compensation tools in the Cytobank platform to create new compensation matrices. Please see Ways to create a new compensation matrix, import and export compensation matrix in the Cytobank platform.
*Spidlen, Josef et al. “Data File Standard for Flow Cytometry, version FCS 3.1.” Cytometry. Part A : the journal of the International Society for Analytical Cytology vol. 77,1 (2010): 97-100. doi:10.1002/cyto.a.20825
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892967/