Slide label of scn files

[Martin Hoehne]

Hi Pete,

I just started to play around with QuPath and think it might be very useful for us! Thanks for sharing this with the world.

We have files in Leica´s SCN format. When we open them with the Aperio ImageScope viewer, we also get an image of the actual slide label (see attachment).

Is there a way to get this label also with QuPath? I checked View > Show Slide Label, but this tells me "no label available".

Thanks in advance

Martin

[Pete]

Hi Martin,

I don't have any SCN files, so have never looked to see where the label lurks - however, if you go to the 'Image' tab in QuPath (left of the screen), you should see a table of properties, and below that two other options: 'Image list' and 'Associated images'.

If QuPath was able to find any other images in the file, they should be listed here.  You should also be able to view each image by double-clicking on its name in either of these lists.

Does that work?  If so, can you tell me the name of the image containing the label?  It may be that it is just called something different from what QuPath expects.

If it doesn't work, and you haven't installed it already, you could try adding the Bio-Formats extension to QuPath from here: https://github.com/qupath/qupath-bioformats-extension

I believe Bio-Formats also supports SCN images as an alternative to OpenSlide (which QuPath uses to read whole slide images by default)... however, I have not tested the combination of QuPath + Bio-Formats for SCN files, and it is possible that QuPath + OpenSlide handles that particularly format more reliably.

Thanks,

Pete

[Martin Hoehne]

Hi Pete,

I tried both suggestions. Both work, bu the results are somewhat different.

Without the BioFormats installed, `Image list´ is empty (but the images are displayed nevertheless). And I find the overview image of the complete slide (including the label) in ´Associated images´ with the name "macro" (the only image in this list). I can view by double clicking, but see only the upper part of the image -- saving the images and opening with e.g. IrfanView shows the whole slide.

With BioFormats its different. The whole slide including label is shown in the main window directly. And the `image list´ is no longer empty.

It´s probably difficult to understand how it really looks without seing it .... I uploaded an SCN file if you want to have a look yourself.

https://gigamove.rz.rwth-aachen.de/d/id/3Yr3546gPQUkf9

Thanks for the help

Martin

[Pete]

Hi Martin,

Thanks, this is really helpful.  What you describe makes sense, and there is definitely room for improvement on the QuPath side.

Originally, QuPath expected each file to contain one image - although there may be several ‘associated images’ with it (including the label).  This is basically how OpenSlide handles things, and QuPath depends on OpenSlide to read the images and handle all the format-specific issues.  You can see more information about OpenSlide and SCN at http://openslide.org/formats/leica/

For SCN, OpenSlide gives one associated image called ‘macro’.  For other formats (you can check which ones at http://openslide.org ) it also gives an image called ‘label’.  Currently QuPath’s 'Show slide label’ command only looks for an image called ‘label’, but it would be better if it also looks for ‘macro’ as well.  I have logged this as an issue at https://github.com/qupath/qupath/issues/40

Only the top of the image is displayed because I assumed associated images/labels would always be small… and just displayed them very simply without rescaling.  If you open the macro image and go to Edit -> Copy you can copy the image and paste it into another software application, where you should see the full image.  Therefore I’ve mentioned the need to resize macro/label images properly within QuPath in the same issue mentioned above.

Regarding Bio-Formats, this works quite differently from OpenSlide and can support much more complicated file formats… including microscopy files that may contain very large numbers of full-resolution images, as well as z-stacks and time series.  The idea of an ‘Image list’ was added to QuPath to support these more complicated files, and give the option of displaying every image that the file contains.

The disadvantage of this is that currently QuPath doesn’t try to figure out what the different images mean, and so likely just displays them in the order that they are found.  Therefore you need to go into the ‘Image list’ to select the image you want.  For your example file, you should find 3 images - the first being the macro, and the other two being the high resolution data for different regions.

One last thing: if you create a Project first - https://github.com/qupath/qupath/wiki/Projects - and then open your SCN file using Bio-Formats, all images should be added separately to the project.  This means you can access them easily from the ‘Project’ tab, without needing to go into the image list.  This may be more convenient.

Overall I’m not sure which option is best in your case, but hopefully that helps find the information you need in the meantime.

Thanks again,

Pete

[Martin Hoehne]

Hi Pete,

thanks for the reply. I think I´m completely fine for the moment with the BioFormats option. 

I need some more time to explore the functionalities of QuPath like projects and automated detection of nuclei and so on .... 

Best

Martin