Feature request: default view for multichannel OME-Zarr images
krokicki opened this issue · comments
Currently, Neuroglancer will not load a multichannel OME-Zarr unless the user provides a lot of manual configuration. I'm aware of two configuration possibilities and they are both rather difficult to execute:
- Manually set up the individual channels as layers. I've done that for the following image but it was a lengthy iterative process and required manual editing of the JSON: https://neuroglancer-demo.appspot.com/#!s3://janelia-flylight-imagery-dev/Fly-eFISH/NP01_1_1_SS00790.json
- You can create a renderer which combines the channel information and exposes channel parameters as user controls (#533). This requires unchunked channels (#284) which is not supported by bioformats2raw. It's also not yet clear if the unchunked channel scheme would be compatible with other tools.
Other tools that are compatible with OME-Zarr are able to provide a default view of a multichannel image with just a URL:
- https://allen-cell-animated.github.io/website-3d-cell-viewer/?url=https://janelia-flylight-imagery-dev.s3.amazonaws.com/Fly-eFISH/NP01_1_1_SS00790_AstA546_CCHa1_647_1x_LOL.chunked.zarr/0
- https://avivator.gehlenborglab.org/?image_url=https://janelia-flylight-imagery-dev.s3.amazonaws.com/Fly-eFISH/NP01_1_1_SS00790_AstA546_CCHa1_647_1x_LOL.chunked.zarr/0
It would be extremely useful if Neuroglancer could be made to work in a similar way so that providing a URL to a multichannel OME-Zarr loads all of the channels and displays some default view of the data that could then be customized.