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feat: open webKnossos datasets (x, y, z axes, URLs without .zarr) - #28

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feat/webknossos-axes
Oct 1, 2026
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MPanknin merged 1 commit into
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feat/webknossos-axes

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@MPanknin MPanknin commented Oct 1, 2026

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webKnossos publishes OME-Zarr layers as c, x, y, z with a transpose codec, under URLs without .zarr. The compatibility sweep showed every reachable webKnossos dataset failing for these two reasons.

  • Axis order: x, y and z may come in any order within the last three dimensions. Shape, chunks, scale, chunk coordinates and strides are read through that order; nothing is transposed.
  • Format detection: a URL is Kiln's sharded format only when it serves a volume.json. Anything else is read as OME-Zarr, with or without .zarr in it.

To test on the preview, Neuromast_WT1 (9216 × 9216 × 1024, uint8, 6 × 6 × 30 nm):
app/?dataset=https%3A%2F%2Fdata-humerus.webknossos.org%2Fdata%2Fzarr3_experimental%2F5b3ce7bb1d0000340240b921%2Fcolor

Tests: metadata and native pyramid from the real Neuromast layer metadata, voxel identity through zarrita with the transpose codec, and the URL detection.


Generated by Claude Code

webKnossos publishes OME-Zarr layers as c, x, y, z with a transpose
codec, under URLs without ".zarr". Kiln rejected the axis order and
never tried Zarr for such URLs.

- The spatial axes may come in any order within the last three
  dimensions; shape, chunks, scale, chunk coordinates and strides are
  read through that order. Nothing is transposed.
- A URL is Kiln's sharded format only when it serves a volume.json;
  anything else is read as OME-Zarr.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@MPanknin
MPanknin merged commit 03aa662 into main Oct 1, 2026
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