imwrite() error with StarDist3D 6.1 generate predictions

HenriquesLab / ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy

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imwrite() error with StarDist3D 6.1 generate predictions #229

Closed GeorginaSV closed 1 year ago

GeorginaSV commented 1 year ago

Hello, when I try to generate predictions in the StarDist3D notebook v1.15.1 using Chrome browser I get the following error

Screenshot 2022-12-15 at 13 10 37

Thank you for your help with this, and for making these notebooks available!

esgomezm commented 1 year ago

Dear @GeorginaSV

Yes, the packages have been updated and this function does not work like that anymore. Could you please download the last version of the notebook?

If you already have a model working and you don't want to update the notebook, would you mind changing the function as follows?

Where it sais imsave(FILEnames[i], labels, polygons) please substitute by imwrite(FILEnames[i], labels)

Thanks!

GeorginaSV commented 1 year ago

Thank you. I found I had to substitute imsave(FILEnames[i], labels, polygons) with imsave(FILEnames[i], labels) instead of imwrite(FILEnames[i], labels)