No display of data in Colab Notebook

imjoy-team / imjoy-interactive-segmentation

MIT License

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No display of data in Colab Notebook #25

Closed Romain-Laine closed 3 years ago

Romain-Laine commented 3 years ago

Hi Wei, Thanks again for the amazing tool! I'd like to train a CellPose segmentation model using the interactive tool in Google Colab, so I am trying to get it to work on the example dataset first. Following the steps of the video, I do not manage to get images to be displayed in Kaibu. See below. Any ideas what I may be doing wrong?

I have simply done the following:

upload the tutorial.jpynb notebook to Colab
run the install
restart the session
re-run the install cell
run the cell starting up the interactive tool
play around trying to get images

Thanks a lot!

Romain

oeway commented 3 years ago

Hey @Romain-Laine Thanks for testing this!

I see, I cannot see an immediate issue, from the screen, it appears you have got the file list and you are using Safari?

We haven't test it in Safari, could you try it in Chrome or Firefox? Also you don't need to restart the runtime (ignore the warning would be fine). So basically:

upload the notebook
open it in Chrome or firefox (latest version)
change the runtime type to GPU
install and run

Romain-Laine commented 3 years ago

Works a dream in Chrome! I feel embarrassed to have fallen for that silly mistake, especially since the paper does mention Chrome and Firefox explicitly. Thanks a lot, Wei.

Romain

oeway commented 3 years ago

Great! @Romain-Laine No worries. I now recall why it doesn't work, it's related to the safari bug I reported a few days ago: https://github.com/Kitware/itk-vtk-viewer/issues/386 Which should be fixed soon.