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HenriquesLab / ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
MIT License
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Unable to use the TF_SavedModel in Stardist 2D plugin in Fiji #269

Open beitea opened 1 year ago

beitea commented 1 year ago

Hi there,

Thanks for developing the ZerCostDL4Mic platform. I was able to train my StarDist 2D model using the colab notebook, however when I try to download the TF_SavedModel and use in Fiji, it doesn't work. Can I please get some advice on what could the problem be and what I can do next?

To Reproduce The TF_SavedModel was downloaded from the model folder and opened as 'Model (zip) from file' in StarDist 2D plugin in Fiji.

Expected behavior

Screenshots image image image

Desktop (please complete the following information):

guijacquemet commented 1 year ago

Hi, This is due to the fact that Fiji is not currently compatible with the latest TensorFlow version used by StarDist. You have two options: You can convert your trained model to an older TF version, as described here. You could export your model to the Bioimage.io format (in the notebook) and use DeepImageJ to run your model in Fiji.

beitea commented 1 year ago

Hi guijacquemet,

Thanks for your reply, it is very helpful. The model conversion script works perfectly for me.