Will Moore
Will Moore
It would be great to support ome-zarr labels data. This is a zarr image where values of 0 are transparent (no label) and colour of each label may be specified...
Add changelog 0.6.0. Do we call this `0.6.0rc1`, or should we just go for `0.6.0` release?
Fixes #65. This refactors `PlateLabels`: - Doesn't assume that a Well exists at `row:0 column:0`. - Doesn't assume that there is a label named `"0"` at `image/labels/0/`. Reads `image/labels/.zattrs` for...
Work in progress... I am testing the JSON schemas from ngff repo, downloading them to a cache with https://github.com/allenai/cached_path. This PR adds a `validate` command that validates the JSON at...
See https://github.com/ome/ome_zarr_test_suite/pull/11 Currently `ome-zarr-py` doesn't validate data, e.g. checking that essential metadata is present or that data is expected dimensions. Maybe add this functionality to the `info` command by default...
Hi, I would like to create a menu where each MenuItem is a link (using svelte). Something like Github's options to filter pull requests: ...
Started to look again at #71 View page at https://github.com/will-moore/ngff/blob/ngff_tools_table/ngff-tools.md Aims of this table/documentation: - Allow data producers and consumers to know whether a particular feature is supported in their...
Currently, when viewing an NGFF Plate in vizarr or napari, the pyramid is created by using 1 down-sampled tile from the first Image of every Well. In vizarr (https://github.com/hms-dbmi/vizarr/pull/119) we...
It seems that `ome_zarr download` is writing chunks with `"dimension_separator": "."`, even when downloading v0.4 data: ``` $ ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0138A/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/ --output MMStack_Pos0.ome.zarr $ ls -al MMStack_Pos0.ome.zarr/0/ total 250256 drwxr-xr-x...
This code provides a way to "set active channels" for a NGFF image, similar to omero-py [image.set_active_channels()](https://github.com/ome/omero-py/blob/7f979ce44b1fcbebfceb92cf51bf7c354a28ec57/src/omero/gateway/__init__.py#L8793) to render chosen channels with colours and min/max levels. Having written this code...