Hey thanks, I tend to agree. Although if I read this right, OME-zarr punted on lossy compression (which is all that really matters) so IMHO it doesn't have much use in the real world yet even though people evidently put a lot of work into it:
https://github.com/ome/ome-zarr-py
https://ngff.openmicroscopy.org/latest/
https://zarr.readthedocs.io/en/v2.1.0/api/codecs.html
https://www.researchgate.net/publication/356622607_OME-NGFF_...
https://www.biorxiv.org/content/10.1101/2023.02.17.528834v1....
i.munro (Ian Munro) August 15, 2023, 8:54am
On the original point about size I suspect your answer is compression.
I have found that a lot of image formats use lossy compression.
I’m not sure about CZI specifically.
AFAIK ome-zarr (sensibly IMO) uses only lossless compression.
Best
Ian
and:
sebi06 (Sebi06) August 15, 2023, 1:42pm
Hi all,
for CZI we offer currentyl two compression methods:
JPG-XR
ZSTD
So we have lossless and lossy options depending on your needs. All of them are implemented in our C++, #NET or Python APIs and also supported from BioFormats.
Looks like CZI is a competitor:
https://www.zeiss.com/microscopy/en/products/software/zeiss-...
https://github.com/cgohlke/czifile
http://www.physics.hmc.edu/~gerbode/wppriv/wp-content/upload...
CZI is basically JPEG compression and is probably missing the multidimensional compressor which is the secret sauce missing from the various formats. It also mentions licensing and legal so is maybe lost in the weeds and not open source.
Without more info, it feels like this is still an open problem.
My interest in this is for video games, since so many are multiple GB in size but are also missing this multidimensional compressor. If we had it, I'd guess a 10:1 to 100:1 reduction in size over what we have now, with no perceptual loss in quality.
https://github.com/ome/ome-zarr-py
https://ngff.openmicroscopy.org/latest/
https://zarr.readthedocs.io/en/v2.1.0/api/codecs.html
https://www.researchgate.net/publication/356622607_OME-NGFF_...
https://www.biorxiv.org/content/10.1101/2023.02.17.528834v1....
and: Looks like CZI is a competitor:https://www.zeiss.com/microscopy/en/products/software/zeiss-...
https://github.com/cgohlke/czifile
http://www.physics.hmc.edu/~gerbode/wppriv/wp-content/upload...
CZI is basically JPEG compression and is probably missing the multidimensional compressor which is the secret sauce missing from the various formats. It also mentions licensing and legal so is maybe lost in the weeds and not open source.
Without more info, it feels like this is still an open problem.
My interest in this is for video games, since so many are multiple GB in size but are also missing this multidimensional compressor. If we had it, I'd guess a 10:1 to 100:1 reduction in size over what we have now, with no perceptual loss in quality.