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BIOP / qupath-extension-biop-omero

QuPath extension to work with images through OMERO's Java API (raw)
GNU General Public License v3.0
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3 channel fluorescence images open as RGB #28

Closed RAHoebe closed 6 months ago

RAHoebe commented 9 months ago

When I open a 3 channel fluorescence image from OMERO into QuPath 5.0 it converts it to RGB. A 4 channel image opens correctly as 4 channels.

Rdornier commented 9 months ago

Hello @RAHoebe

Thanks for reporting this issue. I already correct for a similar bug on .vsi files in the version 0.8.1. This is a known bug as there is no explicit information on whether the image, coming from OMERO, is RGB or not.

Could you please tell me

If you are not using the latest version of the extension, try to update to the latest one and see if it solves the issue. Thanks,

Rémy.

RAHoebe commented 9 months ago

Test-3-4-Channels.zip

Hi Rémy,

The image is from a LIF file (see attached ZIP). In the LIF a 3 channel uint8 image and 4 channel uint16 image. The 3 channel image is seen as RGB. This is not correct.

Best, Ron

Rdornier commented 9 months ago

Hello,

I see... It is due to the name of the channels that are not set (the default channel names are 0,1,2 on OMERO) ; this is the reason why it detects the image as RGB. I suggest you to rename the channels for the 3-channels image and it should fix the bug. You can rename the channels directly on OMERO.

Currently, and because there is no obvious way to state which image is RGB, I try to classify as best as I can the images, and every images which have 3 unit8-channels, without any names or with default RED, GREEN, BLUE names are set to RGB in QuPath.

Best, Rémy.

RAHoebe commented 8 months ago

Hi,

When I import/open an image from Omero I have-to/can set a Type. Maybe make it a channel Image when you set this type to Fluorescence? And otherwise to RGB. Seems to me very logical that a Fluorescence image is (in 99.9% of the cases) a channel image and not RGB.

Best, Ron

Rdornier commented 8 months ago

Hello,

This is not a bad idea and I didnt' thought about using it. However, the Type is somehow decoupled from the imageServer. I do not have access to the Type information when the RGB state is set.

The only way I have to get rid of it at that point is to rename at least one channel of the image. On OMERO, it is easy to set the name of all the channels at once, with the option Apply to all. I know this is not the best solution ; I'm still looking at improving this point.

Best, Rémy.

Rdornier commented 6 months ago

This is now fixed in the version 1.0.0 by looking at the image histogram. If a majority of pixels are dark, then it is a fluoresent image. Otherwise, it is an RGB image.