Recently I’ve read an interesting webinar and a paper that using image cytometry for cell phenotyping. The idea is that, the cell segmentation algorithm can generate an output file that is analog to the FCS file format: each row represents a single-cell and columns represents the mean intensity of biomarkers (channels).
I realized that when I performed the multiplexed analysis using QuPath, the build-in algorithm can also give me the estimated intensity of each channel for each cell, which makes them great candidates for image cytometry analysis. However, I am stuck here as I am not sure how to exploit the QuPath output for FCS Express software. Obviously, FCS Express requires a specific file format - FCS to perform the image cytometry. I noticed that in Pete’s blog, there is a ShinnyApp that seems do the job, link:https://gabrielascui.shinyapps.io/qupath_to_fcs/
But when I upload the measurement file and eliminate the columns with names as requested, the system told me there is an error and I cannot download the FCS file and I am not able to see the dot plot.
I am expecting something like this eventually:
(source: PMID: 28380359)
Anyone has some exprience with this topic? Thank you in advance!