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benediktrauscher / ICS

Supplementary computer code to reproduce analyses and figures in the manuscript "High speed fluorescence image-enabled cell sorting".
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FCS3.2 not supported #1

Open gabrielpan147 opened 10 months ago

gabrielpan147 commented 10 months ago

Hello, I am trying to reproduce the analysis workflow of the paper. I tried to generate a table using R and import it to the Fiji plugin to generate processed images. I just noticed that currently the BD image cytometer generates fcs3.2 format, which is not supported in flowCore module in R. Thus the whole R program can not work properly. Do you have any ideas or suggestions?

Thanks!

schraivo commented 10 months ago

Hi Gabriel, we also faced that issue recently. I couldn't find a solution yet, but are working on it. If you find a solution in the meanwhile, please let me know, maybe yours is better than mine.

gabrielpan147 commented 10 months ago

Hello, thanks for your reply! Actually I did not find any current packages in R which support FCS3.2. I don't know if there are tools that can easily convert FCS3.1 into FCS3.2, I will take a look at FCS3.2 standard when I have time and see if we can do it by ourselves. Or maybe, we should contact BD to see if they have any solutions, as they are the only known company who apply FCS3.2 in industry.

schraivo commented 10 months ago

Hi Gabriel, the BD file type can't be changed. If you can contact the guys from the flowcore package, I'll check if we can do something from here in the meanwhile.

gabrielpan147 commented 10 months ago

Thanks for you reply, I am contacting BD for solutions. I will let you know if I hear any updates from them. By the way, I have another question: how do you determine the scale bar of the images extracted from the machine?

gitdemont commented 9 months ago

Hi, If it can help IFC package has been updated and should hopefully allow FCS files parsing according to recent 3.2 specifications. Still need to test with real-world files, see https://github.com/gitdemont/IFC/issues/4

gabrielpan147 commented 8 months ago

Hi, If it can help IFC package has been updated and should hopefully allow FCS files parsing according to recent 3.2 specifications. Still need to test with real-world files, see gitdemont/IFC#4

Hello Demont,

Thank you for your suggestion! I would test if the package works on my side and let you know asap!

Gabriel

gitdemont commented 7 months ago

Hi @gabrielpan147 ,

So, did you manage to try things out ?

Best

gabrielpan147 commented 7 months ago

Hello @gitdemont ,

Sorry I did not work on this project these days, I will find a time to do that!

Best, Gabriel

gitdemont commented 7 months ago

Thanks for your reply @gabrielpan147 Don't hesitate to comment / submit issue about FCS3.2 support in IFC Best

alefrol638 commented 5 months ago

Latest version of flowcore supports FCS 3.2. However, CytoML, which is required for the line below, does not support FCS 3.2. Any update?

 flowjo_to_gatingset(open_flowjo_xml(wsp, sample_names_from="sampleNode"))
schraivo commented 5 months ago

Hi alefrol. We depend on the CytoML update as well and hope for the update happening soon. The Flowcore (as you mentioned) has been updated.

schraivo commented 5 months ago

Correction to my previous comment: Works now, you just need to install it from their github directly.

For all versions, you must have dependencies installed. library(BiocManager) This should pull all dependencies. BiocManager::install("openCyto")

Then install latest dependencies from github, using devtools. _install.packages("devtools") library(devtools) #load it

install_github("RGLab/flowWorkspace") install_github("RGLab/openCyto") installgithub("RGLab/CytoML")