Bfconvert: merge n channels

Hi (possibly @dgault)
is it possible to merge n>3 channels (8bit or 16bit) with bfconvert into a multi-channel ome.tiff file?

If not, should be able to do it with the QuPath OME.TIFF writer. I have used that fairly often.

It is brought up in a few of the Image Alignment threads, so you could use those scripts except you would not need any alignment (matrix would be all 0s, or default).

Also this, in case they don’t get back to you soon.

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@Research_Associate Thank you! This is an important hint.

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If you haven’t checked out the pattern file option in Bio-Formats, have a look here: to see if that may do what you want. Note that this works both with bfconvert and with the Glencoe tools (Converting Whole Slide Images to OME-TIFF: A New Workflow).


@dsudar Thank you for the link to the pattern file information.
Yes, that is exactly what I want to do with bfconvert.

However, I had no success using the following command

bfconvert ..\converted\Test_c<0-4:1>.tif ..\series_output.ome.tif

with the files

CLI message (not an error message) is: “System can not find the specified file”

The files exist and the path definitions are ok.
As a test, the following works

bfconvert ..\converted\Test_c0.tif ..\series_output.ome.tif

@phaub, The pattern needs to be in a file named blahblah.pattern in that directory where you have your single channel .tif files.

Then you can issue the command:

bfconvert …\converted\blahblah.pattern …\series_output .ome.tif



Thanks @dsudar. The blahblah pattern made it work :ok_hand:

is a solution and

is one too.

Only one can be selected as solution.
But :+1: :+1: :+1: for both of you.

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