Interactive Annotator will not read images correctly

I am trying to use the Interactive Annotator to mark features for FIJI Trainable Segmentation but the Interactive Annotator will not read a specific set of my images so that I can mark them. It seems to get corrupted in some manner when this set of images is input It will not open up the image annotation window in a way to allow me to view the images and work with them to mark areas for labeling. It opens in several different ways: the most recent - the annotator opens to either a completely black window in the image area or sometimes a completely white window with a black rectangle along the bottom. Other times, it gives black and white lines, and other times it gives hash marks, and other times - rectangles, etc. As I said previously, it opens up in various different ways, and the actual image shows up in one of the windows from time to time, but it never opens with the actual image available in both of the annotator windows (Minimap window, and Image window). Consequently, I am unable to annotate my images to prepare them for the Segmentation Training and application. It does have a couple of other quirks, but I will avoid being too wordy here and summarize with stating it cannot handle this set of images for some reason. Of significance: This Interactive Annotator and Trainable Segmentation work fine when I input a different set of images - there is something out this particular set of images that is causing this node to wig out on me. Any suggestions are appreciated.

Hi @C_Sharp,
That’s very unfortunate that your are experiencing these issues. Are you able to share your workflow and one of those problematic images with us? Then I can take a look and figure out what is going wrong here.

Best,
Gabriel

This is my workflow (first part of it that includes this portion and the nodes around it):

The inside of the metanode is:

Not sure if that will work. I do not know how to upload a workflow onto this forum.

I am splitting out the green channel and attempting to segment the cells. This is where the problem occurs - trying to mark the image for segmentation training.

And this is what I get when I open up “Configuration” in the Interactive Annotator:

OK, now, that one is even more odd than the other ones I have been getting all day. Those are parts of cars! - it is quite obvious from the wheel, headlamps & grill, and top seen in parts of that mottled image. SOOOO weird???

This is more typical of what I get when I open up the configuration of the Interactive Annotator

Ok wow this is really weird, I have never seen somtehing like this before.
Can you please give us some details about your version of KNIME AP and your operating system. Also did you try switching to a new workspace and importing your images from there?

Also when sharing the workflow it is best if you export the workflow (right click on it in the Explorer view and select export).
best,
Gabriel

KNIME version is 3.5.3
Operating system is macOS High Sierra Ver 10.13.4
I have tried switching to a new workspace - same issue occurs.

I see how to export a workflow, but I do not know how to upload them here on the forum.
I guess I do not know what to do with it after I click on export. I will try this:

Interactive Annotator problem.knwf (30.8 KB)

Hmm, Looks like that worked.

I cannot reproduce the issue with KNIME 3.5.3 on Windows 7.
Annotation works just fine:

Can anyone get it to open correctly on a macOS High Sierra?

I can’t reproduce the issue on macOS High Sierra.

I uninstalled KNIME on another mac and did a fresh install of KNIME and I can now get the Interactive Annotator to open correctly.

3 Likes

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.