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glencoesoftware / bioformats2raw

Bio-Formats image file format to raw format converter
GNU General Public License v2.0
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Convert to yx or cyx #180

Open LucaMarconato opened 1 year ago

LucaMarconato commented 1 year ago

I am converting a yx ome.tif file to NGFF. Is there an option to create a yx or cyx image? I don't need the t and z dimensions.

melissalinkert commented 1 year ago

@LucaMarconato : No, there is not an option to remove unused dimensions. bioformats2raw intentionally does not implement all features of the OME-NGFF specification, and assumes that all 5 dimensions should be preserved.

We're unlikely to implement this feature any time soon, but would be happy to look at a pull request if you (or anyone else) are interested in working on it.

LucaMarconato commented 1 year ago

Thank you for the information!

jluethi commented 7 months ago

Just adding my voice to that of @LucaMarconato & @d-v-b over here to mention that it would be very useful to avoid adding such extra dimensions. An example of the issue this raises with other tools can be found in this discussion here: https://forum.image.sc/t/fractal-framework-zarr-compatibility/92536/10?u=jluethi.

It's not our top priority, so can't provide a PR for this anytime soon. But wanted to give a +1 for its usefulness if this issue gets raised in the future.