Omero Loading issue

[todd-fallesen]

Hi, we've got an issue trying to do loading from Omero into Napari.

I've installed napari 2 different ways to give it a go:

conda create -n omero -c ome python=3.7 omero-py
conda activate omero
pip install napari-omero

and

conda create -n omero39 -c ome python=3.9 omero-py
conda activate omero
pip install napari[all]

and then install napar-omero from the plugin browser

in both cases, I'm getting the menu to login to Omero, can do so without an issue, see thumbnails of the images, but then get the 'AttributeError': 'NoneType' object has no attribute 'layers'

I saw that there was a similar issue earlier in February, but seems that the fix from then isn't working for us.

Cheers

[will-moore]

Hi @todd-fallesen, I haven't used this in a while, but I just tried to pip install napari-omero in a similar way to your first example (although not on a completely clean env) and I couldn't reproduce your issue.

I noticed that $ napari_omero from the README should be $ napari-omero (see #37). Is that what you found? Is napari functioning OK otherwise?

Can you try other ways of opening Images. E.g. command-line $ omero napari view Image:1 (look the Image ID up via a different OMERO client).

[todd-fallesen]

Hi @will-moore Sorry for the late response. We're running both Napari and Omero on our linux cluster, and I was unsure of what OS we were using in the background, it's CentOS 7.9. It fails while trying to load from the command line as well.

Napari seems to be ok otherwise, we're loading images just fine from the file menu. Thanks for looking into this!

[will-moore]

I'm afraid I don't have access to a similar system with an aim to reproduce this. @tlambert03 Any ideas what might be going on here?

One less-than-ideal workaround is to export images from OMERO as OME-NGFF using https://pypi.org/project/omero-cli-zarr/ and then open with the napari-ome-zarr plugin:

pip install omero-cli-zarr
pip install napari-ome-zarr

# exports to 123.zarr
omero zarr export Image:123

napari --plugin napari-ome-zarr 123.zarr

Obviously it's a pain to have to look-up the Image:ID elsewhere and takes longer to export the Image first (may be impracticable for larger images) but you will get faster viewing in napari once you have the data locally

[DrKenHo-crick]

Hi @will-moore I have tried to do a fresh install and also got the same problem on my MacBook. I used to have a version that works.

napari-ome-zarr is working ok separately, but our images are stored within OMERO, so it is not much of a solution for our users.

I believe the problem is related to this or even the same bug:

https://github.com/tlambert03/napari-omero/issues/13

[DrKenHo-crick]

Hi @will-moore and @tlambert03

My colleague @RoccoDAntuono found that the following works:

conda create -n nap-omero -c ome python=3.7 omero-py
conda activate nap-omero
pip install napari-omero
pip install napari==0.4.10

Presumably some changes between 0.4.10 and 0.4.15 the latest release.

[jo-mueller]

I'm having the same issue as described here. Strangely, it works, when I load images from the command line with viewer.open("omero://Image:XXX")

System information:

napari: 0.4.15
Platform: Windows-10-10.0.17763-SP0
Python: 3.9.12 (main, Apr 4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
Qt: 5.15.3
PyQt5: 5.15.4
NumPy: 1.22.4
SciPy: 1.8.1
Dask: 2022.7.0
VisPy: 0.9.6

OpenGL:
- GL version: 4.6.0 NVIDIA 516.59
- MAX_TEXTURE_SIZE: 32768

Screens:
- screen 1: resolution 1920x1080, scale 1.0
- screen 2: resolution 1680x1050, scale 1.0

Plugins:
- PlatyMatch: 0.0.3
- RedLionfish: 0.5
- animation: 0.0.2
- clEsperanto: 0.18.0
- console: 0.0.4
- devbio_napari: 0.5.9
- napari-3d-ortho-viewer: 0.0.1
- napari-accelerated-pixel-and-object-classification: 0.8.1
- napari-assistant: 0.3.10
- napari-brightness-contrast: 0.1.7
- napari-clusters-plotter: 0.5.1
- napari-crop: 0.1.5
- napari-curtain: 0.1.1
- napari-folder-browser: 0.1.3
- napari-layer-details-display: 0.1.4
- napari-mouse-controls: 0.1.3
- napari-plot-profile: 0.2.1
- napari-plugin-search: 0.1.3
- napari-segment-blobs-and-things-with-membranes: 0.3.0
- napari-simpleitk-image-processing: 0.4.0
- napari-tabu: 0.1.5
- napari-time-slicer: 0.4.9
- napari-tools-menu: 0.1.15
- napari-workflow-inspector: 0.2.2
- napari-workflow-optimizer: 0.1.4
- napari_skimage_regionprops1: 0.5.3
- napari_skimage_regionprops2: 0.5.3
- omero: 0.1.1
- scikit-image: 0.4.15
- svg: 0.1.6
- the-segmentation-game: 0.1.0

[zoccoler]

Hi everyone, I am having the same error when using the plugin. I can see thumbnails, which is very nice to have, but no image is loaded into the viewer and the same error as @todd-fallesen 's pops up when I click on any of the thumbnails.

Similarly to @jo-mueller , if I run through the command line, it works, but then I don;t have the nice navigation interface. I am on Windows 10.

Platform: Windows-10-10.0.17763-SP0
Python: 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:17:03) [MSC v.1929 64 bit (AMD64)]
Qt: 5.15.2
PyQt5: 5.15.4
NumPy: 1.22.4
SciPy: 1.8.1
Dask: 2022.05.2
VisPy: 0.9.6

OpenGL:
- GL version: 4.6.0 - Build 27.20.100.8729
- MAX_TEXTURE_SIZE: 16384

Screens:
- screen 1: resolution 1280x720, scale 3.0

Plugins:
- console: 0.0.4
- omero: 0.1.1
- scikit-image: 0.4.15
- svg: 0.1.6```