Support OME-zarr labels layers about vizarr HOT 7 OPEN

Another example of showing / hiding / coloring labels: https://downloads.openmicroscopy.org/presentations/2020/community-call-2020-10-29/OMERO%20Plus,%20PathViewer%20and%20NGFF%202020-10-27.mp4

from vizarr.

Ah, I wasn't aware that the labels data were dense arrays. What are the non-zero elements for the labels (value wise)? I think we should be able to reuse the loader modules (to fetch data tiles), but I think transparaent for 0 values will require a new layer (or shaders at minimum) perhaps @ilan-gold has some input.

from vizarr.

Having just been reading #32, I can imagine that an API for showing/hiding or setting colors on masks would be very cool. Similar to what you're doing in vitessce http://vitessce.io/?dataset=linnarsson-2018

I think we use a deck.gl polygon layer for the segmentation in vitessce because the data are in a columnar format (not dense pixel arrays). Both @keller-mark and @ilan-gold have more experience with writing custom layers in deck.gl, and hopefully they have some ideas of how to do something similar for dense array masks

With that said, I like the idea of having different layers because then we can render UI elements based on different layerProps for each layer.

from vizarr.

Yes we use selectable polygon layers from deck.gl which requires pre-processing the data to get polygons but likely will not require any sort of pyramid/multi-resolution handling.

We could certainly write shaders to handle this concept of value-per-color, raster/pixel-based-storage, segmentation mask, especially if this is the direction OMERO is headed - it would be very straightforward to do and could scale very well to lots of different labels if what I have in my head is right for the implementation. I agree @manzt that we should be able to reuse the loaders for it - we would change the layer (or really just the shaders) used by XRLayer to accommodate this new data and reuse the MultiscaleImageLayer with a few tweaks to the APIs.

from vizarr.

We could certainly write shaders to handle this concept of value-per-color, raster/pixel-based-storage, segmentation mask, especially if this is the direction OMERO is headed

See Will's link above (https://github.com/ome/omero-ms-zarr/blob/master/spec.md#image-label-metadata). The OME-Zarr specification uses (dense) zarr arrays for masks.

from vizarr.

@will-moore

Ilan and I talked about this today and I think we have an idea for implementation (likely a new layer with custom shaders). I would be useful to have an example dataset with these arrays to work with. I can't seem to find the an image with "image-label" metadata? Is this different from "masks"?

I've tried opening the examples in ome/ome-zarr-py#30 with the ome-zarr-py plugin and the masks don't seem to load the masks layers. Again, I'm not sure if mask / image-label are different.

$ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr # just opens image layers

from vizarr.

Yeah, I had to ask around to find an image with labels. (we are planning a directory page to list all our ome-zarr images soon).
This one has labels:

napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr

The presence of labels is specified by the existence of https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr/labels/.zattrs

Labels are multi-resolution arrays (same as pixel data) but tiles may be missing if they are all zeros to save space when you have sparsely-populated labels.

from vizarr.