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Add support for multi-channel .ome.tiff #13

Closed ArtemSokolov closed 3 years ago

ArtemSokolov commented 3 years ago

Consider adding support for multi-channel .ome.tiff, by re-parameterizing --nuclear-image <file.tif> --membrane-image <file.tif> to --image <file.ome.tif> --nuclear-channel <int> --membrane-channel <int>

As a possible feature, allow for multiple indices to be specified, renaming the parameters to --nuclear-channels and --membrane-channels accordingly.

Example code for reading .ome.tiff and other formats: https://github.com/HMS-IDAC/UnMicst/blob/340a31de8873fa247ea502e778ef14acee56984e/UnMicst2.py#L754-L764

willgraf commented 3 years ago

This issue is fixed in the first release 0.1.0.

--nuclear-channel and --membrane-channel default to 0 (expecting --nuclear-image and --membrane-image to be single channel), but both can accept multiple channels which get summed together into a single channel (e.g. "membrane" channel).

For images that contain both membrane and nuclear channels, just pass the same file path to both --nuclear-image and --membrane-image and set the corresponding channel(s).

Please re-open this issue if you don't think it's closed. And please make a new issue for anything you'd like to see added or improved!

FloWuenne commented 2 years ago

Hi @willgraf ,

I would like to re-open this issue and suggest the following change:

Change the default for --membrane-image to : "If not passed, and --membrane-channel is not -1, --nuclear-image is used instead.

Instead of the current way of reading two separate files (one for nuclear and one for membrane), this would only read a large multi-channel image once and would be more in line with the idea of using large, multi-channel images.