Will Moore

Leica spectral scans - wavelength misinterpreted as time

1

See https://forum.image.sc/t/leica-spectral-scans/59762 for report and sample file.

See https://github.com/ome/omero-py/pull/196#issuecomment-642446600 AdminService methods for loading Experimenters and Groups could allow options for loading the GroupExperimenterMap.

Shapes

4

Add support for Polygons, Polylines, Lines, Ellipses etc. See https://napari.org/tutorials/fundamentals/shapes.html for ways of representing nD shapes. Prompted by request for viewing Shapes in vizarr: https://github.com/hms-dbmi/vizarr/issues/127 Related to #33 (Mesh specification).

Investigate OpenMINDS as an option for ngff validation

4

See Intro video at https://vimeo.com/605602233 (start at 9 minutes) It seems that OpenMINDS has a way of describing schemas, and tools that can convert those schemas into JSON-ld, html doc,...

document client feature support

4

As the spec evolves, it's increasing likely that there will be parts of it that are not supported by all the clients, either because of technical limitations or the work...

I found it spec slightly confusing, based on this wording: 3.4. "image-label" metadata Groups containing the image-label dictionary represent an image segmentation in which each unique pixel value represents a...

json-ld, "omero" metadata and labels paths

10

A couple of outstanding issues with the current spec from https://github.com/ome/omero-ms-zarr/issues/76#issuecomment-722279765 that we may want to fix before "v0.2" since they are breaking changes. - Plate has `"plate":{}` and a...

Support bioformats2raw layout

11

Bioformats2raw exports a "Fileset" of 1 or more Images for some formats, as described at https://github.com/ome/ngff/pull/112 with the paths to them as `0/`, `1/`, etc and names and other metadata...

View OME-NGFF collection of Images

8

We are making progress with defining a specification for a collection of Images at https://github.com/ome/ngff/issues/31 and with generating a collection of OME-NGFF Images (export from OMERO) at https://github.com/ome/omero-cli-zarr/pull/83 so I'm...

resolution levels not a factor of 2

2

When using OMERO to provide a OME-Zarr interface via https://github.com/will-moore/omero-web-zarr the size of each pyramid resolution is determined by the pyramid in the original file. For svs images, the resolution...