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AllenNeuralDynamics / aind-smartspim-stitch

Stitching and fusion pipeline in the cloud
MIT License
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Default colors for OME Zarr files do not match spectral colors #15

Closed galenlynch closed 1 year ago

galenlynch commented 1 year ago

I think the default color for an emission band, as specified in the .zattrs file, should correspond to the spectral colors if the emission wavelength is in the visible spectrum.

It would be nice if neuroglancer links were also set with these same default colors.

sharmishtaa commented 1 year ago

To view in neuroglancer, the process_output.json needs to be updated with the appropriate color. Creating a hash of viewing colors for this and running it on exisiting datasets is the first step. This can be followed by updating the neuroglancer link generation code and then updating of .zattrs.

jwong-nd commented 1 year ago

Resolved in #18! Color overlays correspond to emission wavelengths based on the CIE color arc.