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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 with preprocess imc images --hpf50 #255

Closed megankmckie closed 5 months ago

megankmckie commented 5 months ago

Hi there When running 'steinbock preprocess imc images --hpf 50' I get the following error for all of my files:

2024-04-25 13:11:03,380 INFO steinbock - img/file name.tiff 2024-04-25 13:11:03,382 WARNING steinbock.preprocessing.imc - Error reading acquisition 2 from file raw/file name.mcd: MCD file 'file name.mcd' corrupted: invalid acquisition image data offsets

I've never encountered this before, there are no obvious signs that my data are corrupted and I have tried re-downloading the data and I get the same error

I'm using steinbock version 0.16.1 on windows

Any help would be appreciated, Megan

Milad4849 commented 5 months ago

This error comes from readimc. Each acquisition has a start and an end position in the mcd file, this specifies where the data corresponding to the acquisition must be read from. The error above tells you that these positions for acquisition 2 do not make sense; they are either equal or the starts is after the end. The acquisition is written incorrectly into the file, redownloading would not fix it.