Pixel classifier!

Hello! I am using pixel classifier for H&E slide and the detection was great and I love it! My question: Is there any way I can save the annotations somehow and apply them to a project that contains 20 H&E slides and be able to view my results?
BTW, I am using Qupath m1
Thanks in advance!!

You can always save the annotations, and even save the same annotations to multiple images, but the pixel classifier is one of the experimental functions and cannot be saved or applied across a project. You would need to create a new pixel classifier for each image. As far as I know, most people doing area classification are still using
superpixel classification
of some sort
for repeatability across a project.

Ok great! Thanks. I will go ahead and try it and hopefully I can come up with the solution.

1 Like

I tried the superpixel classification and I got to where I created tiles and then segmented the tissue which was great. But now how do I go about setting up the classes (stroma vs tumor) using Superpixel classifier and being able to save the annotation and load the classifier to a different image?
Thanks!!

A trained classifier for superpixels works just like a trained classifier for cells, except that you need to add some measurements before you create the annotations indicating which superpixels are which class. Then you save the classifier, and run that classifier after creating the same superpixels and measurements on each image.

1 Like

Thanks for getting back to me…
The picture I attached is right after when I created tiles for the whole image. The one on the left is a manual annotation that was done by using the brush tool which is on top of the tiles and it allowed me to set up the class, but the one on the right is just the tiled annotation. By double clicking on a portion of the tiled annotation, the annotation gets selected but it does not allow me to set up the class as you can see on the right side of the image.
My question: How can I set the class for the one on the right side? because when I right click on each those boxes, it does not allow me to set up the class as you can see on the right side of the image.
I hope my question is clear. please let me know if you need more clarification.
Thanks

I believe manually setting the class for detections is a feature in newer versions of QuPath, but originally it was expected that you train a classifier or have some other method of calculating an unbiased (less biased) classifier. Lots of classifier options available in the links at the top of this post.

Note that you will want to add some kind of features to your tile objects if you want to create a machine learning or other type of classifier.

I have already tried all the above but I still have issues.
My goal is to make a classifier using the “SuperPixel” classifier and be able to load that classifier to my project which contains 20 H&E slides. Am I able to do this? Thanks

Yes, but it may help to be more specific as to what is going wrong. The standard workflow listed here has not really changed as far as generating annotations, though Pete’s comments were a definite improvement as long as you aren’t using M4 where that function (tiles to annotations) doesn’t work.
https://groups.google.com/d/msg/qupath-users/gm0YYJxSriA/FE3hNBS3BAAJ
If you could point out at which step you are running into problems, or what specifically you are trying, I might be able to be more specific.

Although not by design… should be fixed in the next milestone.

Thanks for getting back to me Research_Associate!
I looked at the website but the instruction is not really clear at least for someone like me who is a beginner. I was wondering if there is another documentation/website that explains the same process step by step. We are definitely in the right track!!
Thanks

I took a quick shot in another post, but as I said there, I’m not going into to much detail as there are far too many options depending on the project, and the whole process will hopefully become obsolete in the future.