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Set default channel color to grey for single channel images #171

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melissalinkert
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Fixes #170

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@sbesson sbesson left a comment

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Tested by converting a minimal test.fake with bioformats2raw 0.5.0 and with this PR included. The only metadata difference is the channel color which is now grey rather than red

(java11) sbesson@Sebastiens-MacBook-Pro-2 bioformats2raw % diff test.zarr/0/.zattrs ~/Downloads/test.zarr/0/.zattrs 
41c41
<       "color" : "808080",
---
>       "color" : "FF0000",
(java11) sbesson@Sebastiens-MacBook-Pro-2 bioformats2raw % diff test.zarr/.zattrs ~/Downloads/test.zarr/.zattrs 
(java11) sbesson@Sebastiens-MacBook-Pro-2 bioformats2raw % diff test.zarr/OME/.zattrs test.zarr/OME/.zattrs 

This is inline with the current behavior of the OMERO import logic. The extension of the color unit test should cover the most common combinations including single-channel with/without color metadata and multi-channel.

From my side this should be amenable to an immediate patch release of bioformats2raw 0.5.1, maybe alongside #167 and optionally #169.

@chris-allan chris-allan merged commit e04af0b into glencoesoftware:master Nov 3, 2022
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Color metadata & single-channel use case
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