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eyurtsev / FlowCytometryTools

A python package for visualization and analysis of high-throughput flow cytometry data
https://eyurtsev.github.io/FlowCytometryTools/
MIT License
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LMD to FCS #3

Open yoavram opened 9 years ago

yoavram commented 9 years ago

It would be cool to open LMD files (generated for example by Gallios machines). Its possible to do it in R, so one could in principle reimplement in python or just use the R implementation and call it from python via Rpy2.

Here's an R script that does it: https://gist.github.com/yoavram/198493cebbf0b323a9d8

eyurtsev commented 9 years ago

My knowledge of R is basically 0, but from the code it looks like it's only necessary to rename the file extension? (i.e., is the lmd format different from the fcs format?)

yoavram commented 9 years ago

Wait, from which code? The gist I sent?

eyurtsev commented 9 years ago

Yes, (I did say that my knowledge is basically 0!) ;)

yoavram commented 9 years ago

Oh I see. This R function read.FCS knows how to read LMD. Then write.FCS writes a standard FCS. From what I understand LMD (list mode data) is a wrapper around FCS. See: https://github.com/RGLab/flowCore/blob/3f63a2e0ba8ebcccd9340ddbfda5d1807806c037/man/read.FCS.Rd https://github.com/RGLab/flowCore/blob/trunk/R/IO.R

jxramos commented 5 years ago

What's special about the Gallios machine? Do the lmd files follow the flow cytometry standard format? You can read about that format from the wikipedia page. https://en.wikipedia.org/wiki/Flow_Cytometry_Standard

Can you please upload an example lmd file to this issue?

Digging around a bit it seems that there's is some FCS intersection...

Beckman-Coulter Gallios produces LMD files that contain an FCS 3.0 compliant portion. They display the data as collected, if “True View” is used. If standard view is used, linear parameters are scaled 1-1024 and log parameters to four decades with a range of 1-1024. This is a display similar to FCS 2.0 data. Preferences in FlowJo control the scaling of the exported FCS 3.0 file. Data can be scaled identical to their acquisition display in true view OR standard view. http://docs.flowjo.com/vx/workspaces-and-samples/flowjo-and-your-cytometer/ws-cytometer-beckman/cxp/

SreejaMukherjee commented 1 year ago

Hello! I have some lmd files generated from a BC Navios machine. Can I use R to change it to a fcs file and further use it through flowjo for post acquisition and formatting some of the gates? If yes, which version of R studio is compatible with the flowcore package?