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BodenmillerGroup / cytomapper

R package for visualization of highly multiplexed imaging data
https://bodenmillergroup.github.io/cytomapper/
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compImage function #92

Closed SchulzDan closed 7 months ago

SchulzDan commented 7 months ago

It seems that something has changed with the compensation of images. When using on disk storage and overwriting the original counts with the compensated counts and saving the h5 files then the h5 files cannot be read any more using the the loadImages function. When overwrite = FALSE, then the h5 files can still be read using the loadImages function.

However, even the h5 files than cannot be read using loadImages seem intact and can be read using rhdf5 package.

Will give you some data for reproducibility in a bit.

nilseling commented 7 months ago

What's the name argument you are using in loadImages when reading in data from the h5 files?

lassedochreden commented 7 months ago

Hi @SchulzDan, I had a look and as suggested already by @nilseling, the name argument has to be specified in your setting.

Specifically, after image compensation with overwrite = TRUE the dataset name entry of the .h5 file contains a new suffix _comp, which you now have to specify in loadImages via the name argument.

Will close this for now.

SchulzDan commented 7 months ago

thanks, indeed the mistake was somewhere upstream in our code...