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[Proposal]: Dump ReferenceFileSystem spec for ZarrTiffStore that can be read natively as zarr

See original GitHub issue

Thank you so much for your work on this project. I just came across experimental aszarr and ZarrTiffStore and am so excited! I’d written some one-off stores wrapping tifffile to read different pyramidal images as zarr (for napari), but having this in tifffile is incredible!

I’m curious if you’ve seen the proposed JSON specification for describing a ReferenceFileSystem? Asking naively, and a bit selfishly, would it be possible to detect whether a ZarrTiffStore can be natively read by zarr and “export” one of these references?

I work on web-based tools for visualizing OME-TIFF / Zarr data, and it would be really useful to quickly create these references.

Here is an example viewing a multiscale tiff on the web using zarr.js, and this is the python script I wrote with the newest version of tifffile to generate the reference. I wonder if there is some way to generalize this script, but don’t have the familiarly with the underlying formats to know if this is a silly idea.

I notice that the TiffZarrStore handles all compression, so I know at least you need to detect whether the chunk compression is supported in Zarr.

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Reactions:6
  • Comments:21 (11 by maintainers)

github_iconTop GitHub Comments

cgohlkecommented, Mar 17, 2021

One issue is that I don’t think endianness in the .zarray metadata reflects the endianness on disk.

You are right. Fixed in v2021.3.17.

martindurantcommented, Mar 17, 2021

I would love to see this functionality in a blog article somewhere

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