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I was looking more into this and Nanostring has an export module in github that might format the files similar to the demo dataset they put out, with flat file...
Also, take a look at proseg, another image-free method, seems already handling well cosmx, merfish and xenium datasets. https://github.com/dcjones/proseg
That's great, looks very promising.
Wanted to add that for getting the data in similar format to previous datasets, it has to be exported as a flatfile in AtoMX.
I believe it is the same format. The problem with CosMX data output is that is very poorly documented, and there might be some little changes here and there, as...
> Ah I just saw your other thread about this: #65 > > It might be good to add a parameter to set an ID name for the data. I...
Just checking, I'm not seeing a difference when using z-score as adjustment in dittodimhex. relative.to.max is working thought, so not sure best way to compose.