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BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
49 stars 14 forks source link

Error message when executing "steinbock measure intensities" #177

Closed marleneweiss closed 1 year ago

marleneweiss commented 1 year ago

Hi,

I have been working with steinbock since the workshop and it has been great. However, when executing "steinbock measure intensities" for new samples, I got the error message copied below. Could you maybe hint me towards what the problem might be? The commands for preprocessing, measuring neighbors and regionprops for the same samples worked without an issue. Thank you, Marlene Error_measure intensities

Milad4849 commented 1 year ago

Hi Marlene,

Thanks for posting this issue. The error you get indicates that you have more channels in your panel file than acquired channels in your tiff (one extra channel in this case, 38 vs 37). Could you please check that the acquired channels are the same for all ROIs and that they match the panel file?

marleneweiss commented 1 year ago

Hi Milad,

thank you for your answer and for hinting me towards the underlying issue. I am not sure what was wrong with the old panel file (it did not have an extra channel in it), but I exchanged it and then it worked.

Best, Marlene