Unable to build a whole slide server error Qupath

Hello,

I am trying to open a .qpdata file and I am not being able to do so.

First, qupath asks me to “set path to missing file” so I choose the .qpdata file that I want to open, but then it shows me this error:

Unable to build a whole slide server for…(files name) and then: unable to build ImageServer for file (files name) (args=) with requested provider qupath.imagej.images.servers.ImageJServerBuilder).

The thing is that a pathologist did some annotations in whole slide images and then he sent the .qpdata files to me so I can open the files with Qupath and see the anotations, but I cannot open the files.

If I draw some annotations myself and then I open the .qpdata files I don’t have problems; the files can be opened. But not the ones that he sent me.

I appreciate all the help.

Thank you very much

Sofía

The missing file is the image file - qpdata just contains the objects and data for the overlays. Since no image file is included with the qpdata file, you need to find it for QuPath.

For example, if you are in a project (and you should always be in a project), you would navigate to the folder for a given image, then replace the qpdata file in that folder with the edited one from the pathologist.
image
More information on projects here:
https://qupath.readthedocs.io/en/latest/docs/tutorials/projects.html

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Ok, thank you very much.

So, if the pathologist creates a project with the tiff and with the tiff plus annotations, should I be able to open it with Qupath on my computer?

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I was able to see the annotations. Thank you for your help!

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Hi,

I am encountering another problem now,

apart from the HE slides (which have the original annotations) I have several IHC slides with different markers. When I try to apply the annotations to these IHC slides, the annotations are not in the exact same positions as the originals, they are a little bit displaced.

Do you have any idea of why is this happening?

Thank you very much and sorry if this has been already asked.

If you have the same annotations for different sequential slices or different restainings, the annotations will be in the same place (assuming the same file), but the images will not be. There are entire threads on attempting registration (alignment) between similar images. Depending on how similar your pieces of tissue are (sequential slices will never really work except in very general terms, strip-stains can work but not perfectly), this may or may not be useful.

OK, thank you very much!!

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