set Channel names

[rebecca...@googlemail.com]

Hello,

being very new with qupath and image analysis I am trying to get  into v0.1.3.. Therefore, I would like to know if there is a way to change the server type of an image. Is it even necessary  have the server type set to Bio-Formats in order to chance Channel names?(which is my original goal at this point). Does "these names can now be seen using the Brightness/Contrast command:" mean, there is no script necessary in order to change channel names with v0.1.3?

Thanks!

[micros...@gmail.com]

In general, you can change the names of the brightfield channels by editing the Stain1 and Stain2 entries in the Image tab.

Openslide uses RGB in place of channels, I think, so you cannot rename or recolor Openslide channels.

You can't exactly set the server type after the image is open, but you can set the type of images that QuPath will use BioFormats for by default. You do this in the Preferences dialog.

I am not sure about the naming of channels in 1.3, hopefully someone else with a current install can check that :)

[Pete]

I'm not sure why the last post was deleted - it happened while I was in the process of replying.

Anyway, for fluorescence/multiplexed images it depends whether Bio-Formats is able to read the channel names.  If it can, then QuPath v0.1.3 will display the channel names (previous versions didn't try) - but not all file formats will necessarily store the names, or at least not store them in a way that Bio-Formats can recognize.  In the case of TIFF images, it would depend on what software wrote the TIFF itself.

(I'm not actively working on v0.1.3 any more, but am using it as the basis for a bigger update that will further improve the way images with multiple channels can be viewed)

[rebecca...@googlemail.com]

OK. All I  know (and I will know more after the holidays when people return to the office) is, the original file is a lif-file. All I get is a tiff file generated by fiji. So for now, I will play around with fiji and see what I can get.

[Pete]

In that case, with QuPath you would almost certainly be better using the LIF file - and not converting to TIFF in Fiji first.

The LIF may contain multiple images.  If you create a project in QuPath, then add the LIF, all images will become available in the QuPath project - giving a convenient way to switch between them.

[rebecca...@googlemail.com]

Hello Pete,

converting the lif file in Fiji results in multiple tif files, that we then , after some contrast adjustments, open with qupath. Opening  the lif file in qupath offers the same options. 

However, channel names still are channel 1, channel 2.... , That changing to CD3, CD8 .. would be a nicce-to-have.  Does it maybe mean, the channel information is not transferred?

Thanks!

[Pete]

Any channel names that Bio-Formats can find in the .lif should be available in the upcoming QuPath release (I've already written code for that bit): https://petebankhead.github.io/qupath/2018/08/03/bioformats-update.html#support-for-32-bit-multichannel-images

That might be all you need here.  In case it isn't, I'd also like to add the ability to also set the channel names if they are missing (or incorrect), but that remains on my todo list.

[rebecca...@googlemail.com]

I am using the v0.1.3 beta version already. I will look into  the small script later and check if that work for me. Thanks for getting back to my issue so fast!