QuPath 0.2.0m3 pixel classifier export image

[lesolorzanov (Leslie Solorzano)]

After trying a lot. I see that in QuPath 0.2.0 m3 there is an option to output the image of the classifier in an instance of what seems imageJ. How can I save this image? I try all the commands from imageJ and nothing happens and I don’t see any options in QuPath itself to save this image. Can I do it via script?

The image show what I mean.

If it can’t be saved, then I would like to save a region using a request with a ROI but I want the classification colors not the original slide colors.

Using a very low resolution in the classifier I managed to create the polygons of the classified objects, but when I send it to imageJ I only see the outlines eventhough the fill option is 100%.

[Research_Associate (MicroscopyRA)]

If you want to save what is shown onscreen with the Live Prediction, you can Send snapshot to ImageJ, and then save the file there.

Export Live Pixel Classifier Prediction as Image

Whenever I use the pixel classifier, I just report the class area numbers for each annotation given by the live prediction. I rarely use the “Create objects” button, because then it deletes all of my annotations and I can’t change things afterwards. I’d like to export images of the classified regions to demonstrate what was considered positive and negative. This would ideally be something like https://petebankhead.github.io/qupath/scripting/2018/03/13/script-export-import-binary-masks.html, but…

Reminded me that the Show option should be savable, but you may have to create an ImageJ instance first. So send some random region to ImageJ first, then “Show” your result, then save the file.

[lesolorzanov (Leslie Solorzano)]

Thanks. The thing is that I don’t want to send a snapshot because it doesn’t have the correct size, I want that image that is being shown, of the size it is being shown, the image inside the red square.

If I click on the imagej button it sends the snapshot of the qupath view and sends only lines of polygons, not the filled (green, magenta, blue).

[Research_Associate (MicroscopyRA)]

Snapshot can have the right size if you set the magnification as the same as the microscope magnification. I actually ran into this yesterday when I wanted to run Snapshots through an R script and needed 1:1 pixel size.

[lesolorzanov (Leslie Solorzano)]

What is saved is the original data with no annotations even if I ask it to send the annotations, in which case it only sends lines, painted on top of the image. This nice beautiful image in greyscale with the mask (which is exactly what I need) I can’t get, it’s right there and I can’t save it. I can’t send it to imageJ, or I don’t know how, because the button sends the qupath view, not the IJ instance.

[Research_Associate (MicroscopyRA)]

I’m not sure what is going on then, maybe it is system dependent. As long as I have ImageJ already running, the image is save-able.
For no ImageJ open I see:

Once I click Extensions->ImageJ-Send snapshot to ImageJ, and then close the useless snapshot but leave ImageJ running, I see:

At that point, I can go to the ImageJ window and save it.

[Research_Associate (MicroscopyRA)]

I suppose I should emphasize, the QuPath ImageJ, not some other ImageJ or FIJI.