Load a csv file into FlowCytometryTools

[IreneRobles]

Hi,
I am currently working with image analysis data. There I would love to be able to gate the cells as I could do in fcs. The problem is that they are not a .fcs file and I try to load it as a pandas dataframe with no success. I would really appreciate if you could help me to analyse my .csv file that is not from flow cytometry as if it were.
Thanks!
Irene

[eyurtsev]

I am currently working with image analysis data. -- is this microscopy data rather than flowcytometry data?

If you could attach an example CSV I can take a look to at the data to figure out whether this is feasible

Won't be able to respond very quickly (my day job has nothing to do with flow cytometry :))

[IreneRobles]

example.txt

Hi,
Thanks a lot for answering. Here is the text file.
(It is a csv file, but I had to change the extension to be able to upload it)

The two columns that should be plotted together to be gated are:
Intensity_UpperQuartileIntensity_FilteredGreen and Intensity_UpperQuartileIntensity_FilteredRed

Thank you so much!

Irene

[eyurtsev]

I suspect that there might already be something out there for dealing with the data that you have -- so you may be better off not using this library

If you do want to try and use it -- you'll need to fork the code locally and write a bit of logic for this class:

https://github.com/eyurtsev/FlowCytometryTools/blob/master/FlowCytometryTools/gui/fc_widget.py#L579

Similar to the load_fcs, you can load a csv file

You'll need to create a Sample object that contains your data and mimics the interface that's used for fcs files -- specifically, it'll need information about the "channels" (columns) that you have

https://github.com/eyurtsev/FlowCytometryTools/blob/master/FlowCytometryTools/gui/fc_widget.py#L702

Make corresponding changes here (in the GUILauncher)

https://github.com/eyurtsev/FlowCytometryTools/blob/master/FlowCytometryTools/gui/webagg_backend/gui.py#L204

And you'll be able to launch your application by Launching GUILauncher