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Bayer-Group / paquo

PAthological QUpath Obsession - QuPath and Python conversations
GNU General Public License v3.0
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Question Regarding Splitting Image Channels #118

Open EtashBhat opened 1 month ago

EtashBhat commented 1 month ago

Hello,

I am hoping to use QuPath interfacing through Python to split the channels of a multispectral image taken from a confocal microscope (e.g. an OIR image taken from a Confocal FV3000 microscope). In these images, each 'channel' is a separate image taken by the microscope pertaining to a specific cellular feature. It seems as though the pyvips channel methods used in Paquo all pertain to the RGB (as opposed to actual multispectral channels encoded within the image). Because QuPath can split the channels of OIRs and similar file types, I was wondering whether Paquo has the functionality to interface those capabilities in a manner different than pyvips.

I would greatly appreciate your generous guidance!

ap-- commented 3 weeks ago

Hi @EtashBhat

Doing this via paquo is currently not supported. PRs to add this functionality are welcome 😃

"OIR image taken from a Confocal FV3000 microscope"

This is important information. I don't know what libraries currently support olympus oir. I think bio-formats is one of them which explains Qupaths support.

It's best to ask you question on the www.image.sc forum. And provide very detailed information of what you want to do, and what the input data files are.