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I have an implementation which uses the metadata CATMAID stores about N5 stacks to build an xarray.DataArray (wrapping a dask.Array wrapping a zarr.Array...), which users can then query using project coordinates and fetch in parallel. Here, the heavy lifting is done by other libraries so it's only really metadata-wrangling; it can also be extended to other tile source types fairly easily (I'm working on supporting JPEG stacks, where you just need a shim which looks like a zarr.Store).
Would pymaid be the right place for this? It is obviously useful to the same people, but it also brings in some heavy dependencies: zarr, fsspec[http], pydantic>=2, xarray[parallel], imageio (these are currently tucked behind an extra, and the module isn't loaded on first import). Alternatively, I have another package which builds xarray.DataArrays out of chunked stores with different metadata standards (currently OME-NGFF zarr, bigdataviewer n5, n5-viewer, neuroglancer n5), so I could add it there, adding pymaid as a dependency. Much less discoverable for pymaid users, though, even if pointed to in the docs.
The text was updated successfully, but these errors were encountered:
I have an implementation which uses the metadata CATMAID stores about N5 stacks to build an
xarray.DataArray
(wrapping adask.Array
wrapping azarr.Array
...), which users can then query using project coordinates and fetch in parallel. Here, the heavy lifting is done by other libraries so it's only really metadata-wrangling; it can also be extended to other tile source types fairly easily (I'm working on supporting JPEG stacks, where you just need a shim which looks like azarr.Store
).Would pymaid be the right place for this? It is obviously useful to the same people, but it also brings in some heavy dependencies: zarr, fsspec[http], pydantic>=2, xarray[parallel], imageio (these are currently tucked behind an extra, and the module isn't loaded on first import). Alternatively, I have another package which builds xarray.DataArrays out of chunked stores with different metadata standards (currently OME-NGFF zarr, bigdataviewer n5, n5-viewer, neuroglancer n5), so I could add it there, adding pymaid as a dependency. Much less discoverable for pymaid users, though, even if pointed to in the docs.
The text was updated successfully, but these errors were encountered: