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ImmuneDynamics / Spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
https://immunedynamics.github.io/spectre/
MIT License
56 stars 21 forks source link

‘simple’ discovery analysis workflow #125

Closed sailseem closed 2 years ago

sailseem commented 2 years ago

Dear developer,

I am just wondering that can I analyze the IMC data using simple discovery analysis workflow? If so, how can I deal with the x and y position information as data input?

Thanks a lot, fan

ghar1821 commented 2 years ago

Yes you can, but you will need to first do image segmentation. We have a protocol that you can try: https://wiki.centenary.org.au/display/SPECTRE/Protocol%3A+multi-cut+cell+segmentation+using+Ilastik

After that you can load the data into R and run the discovery workflow. We have some sample scripts to do this in the repository: https://github.com/ImmuneDynamics/Spectre/tree/master/workflows/Spatial%20-%20advanced/Spectre%20advanced%20spatial.

We've started writing out a guided tutorial, but haven't finished them yet (https://immunedynamics.io/spectre/spatial-advanced). Finding time to do it is not easy these days.

sailseem commented 2 years ago

Thank you very much, that's so cool and we are looking forward to the complete tutorials. What a nice package!!! Thanks

sailseem commented 2 years ago

sorry, one more question. What are the major differences between these two segmentation methods, or they are actually the same? Which one do you recommend? Protocol: multi-cut cell segmentation using Ilastik

Protocols: modified Bodenmiller segmentation pipeline (IMCtools, CellProfiler, Ilastik, HistoCat) Skip to end of metadata

sailseem commented 2 years ago

By using the protocol here Protocols: modified Bodenmiller segmentation pipeline (IMCtools, CellProfiler, Ilastik, HistoCat)

I got an error when I execute the sample data, image And we don't have the access to the troubleshooting page image image

And the data folder only has the MCD file in zip file, no txt file at all, is this the problem? Thanks a lot and sorry for so many questions for this.

ghar1821 commented 2 years ago

Sorry for not getting back sooner. @tomashhurst can you fix the permission to the troubleshooting page?

I recommend trying the ilastik protocol - it's our preferred one these days.

tomashhurst commented 2 years ago

@sailseem the 'multicut' option is our go-to option these days, and in general it should be easier to user. Have you had a go at that one?

tomashhurst commented 2 years ago

For that troubleshooting page, I have updated the link on the protocol page, and you can access it here: https://wiki.centenary.org.au/x/hSDmCw.