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imagej / napari-imagej

Use ImageJ functionality from napari
https://napari-imagej.readthedocs.io
BSD 2-Clause "Simplified" License
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Arrows to import layers from napari to ImageJ are missing #301

Open paulacauhy opened 6 days ago

paulacauhy commented 6 days ago

Hiya! I just installed napari-imagej but for some reason the icons that appear on the plugin panel (image attached) are different from the ones that appear in the tutorial examples. I would like to import a labels layer from napari as ROIs into FIJI, and with the icons I have that is not possible. How should I proceed?

Screenshot 2024-10-21 at 17 26 20
ctrueden commented 6 days ago

@paulacauhy The left and right arrows should allow you to send data back and forth between napari and Fiji/ImageJ. The icons match the napari-imagej 0.1.0 version, which you can see with that version of the documentation at https://napari.imagej.net/en/0.1.0/ (or https://napari.imagej.net/en/stable/). (@gselzer Should we make napari.imagej.net jump to stable by default rather than latest?)

IIRC, the left arrow brings data from Fiji/ImageJ into napari, whereas the right arrow sends data from napari to Fiji/ImageJ... right @gselzer?

gselzer commented 6 days ago

@gselzer Should we make napari.imagej.net jump to stable by default rather than latest?

This is a good idea - I updated it :+1: @paulacauhy you should now find that https://napari.imagej.net links to the documentation for 0.1.0, which is what you have installed. Please let us know if you still have questions, or any other feedback about the UI.

IIRC, the left arrow brings data from Fiji/ImageJ into napari, whereas the right arrow sends data from napari to Fiji/ImageJ... right @gselzer?

Yes, this is correct - I always thought about it as the right arrow pointing to Fiji, so the data is going to Fiji. The tooltips should also clarify this.

paulacauhy commented 5 days ago

Thanks for the quick reply! The right arrow does work to send an image layer from napari to Fiji but I'm getting the error below when trying to send a labels layer using the right arrow. Any clues on what's happening?

Screenshot 2024-10-22 at 11 07 01
gselzer commented 5 days ago

Any clues on what's happening?

I'm not terribly sure, but I can replicate it with napari-imagej version 0.1.0, with the following steps:

  1. Launch napari + napari-imagej: napari -w napari-imagej
  2. Open up the Camera sample image
  3. Click the "New shapes layer" button, and draw a shape.
  4. With the shapes layer active (highlighted blue) in napari, click the right arrow.
  5. See the same error that @paulacauhy printed above.

I then tried this again on the current main branch of napari-imagej, however I was stymied because the new data transfer buttons don't actually allow this to happen - the "transfer active layer" button that arose from the right arrow button in 0.1.0 is disabled when the shapes are selected.

I believe that this is not a problem that we can fix for you (since in a way it already has been fixed). @ctrueden I guess this is another reason to push on the 0.2.0 release...

@paulacauhy if you want to try to test out the latest main (pip install git+https://github.com/imagej/napari-imagej.git@deaeab4405969a9fa94aadbaf6595480666b19e8), it would likely solve your issue, and I'd be interested to hear about any further bugs you might find.