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tlnagy / OMETIFF.jl

I/O operations for OME-TIFF files in Julia
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Something up with MicroManager OMEs? #16

Closed rsrock closed 6 years ago

rsrock commented 6 years ago

I'm debugging some code involving reading MicroManager OME files, and I think I stumbled on something weird here. If I open the test image singles/background_1_MMStack.ome.tif using this package, you'll see that it's transposed. However, other ome.tiff images are not transposed. For example, the neutrophil image is correct.

Do you know if there is something funny about MicroManager files?

[edit] Sure enough, if I add that file to the ""TIFF value verifications" test block, that test fails.

tlnagy commented 6 years ago

Yeah, I had noticed that I had to transpose the data with the micromanager files (e.g. the neutrophil one), but not with the simpler tiffs (everything else). I wasn't able to track down what was different about them. I ended up just transposing everything by default till I figure it out

I think the offending line is here:

https://github.com/tlnagy/OMETIFF.jl/blob/10586a0156300f4ac3c09549df18160a6efbce65/src/loader.jl#L88

It's a nasty hack and something that I want to fix. I haven't noticed any details in the OME TIFF spec that would make it disagree with the standard TIFF one, which is what I based my reader on.

[edit] Sure enough, if I add that file to the ""TIFF value verifications" test block, that test fails.

Yeah, this is expected. :/