Fiji error when runnnig n2v-sem demo model with bioimage.io

[maweigert]

Hi,

I am trying to get the n2v bioimage.io demo model to run from inside Fiji, yet without success.

Ways to reproduce:

• clean Fiji install with java tensorflow 1.15, java-bioimage-io-0.3.5.jar
• download https://github.com/bioimage-io/fiji-bioimage-io/releases/download/v0.1.4/n2v-sem-demo.zip
• open blobs.gif + bioimage.io prediction

Any ideas?

[tomburke-rse]

Hi @maweigert,

I manage to reproduce the error, but so far could not find the exact source of the problem. It seems that the image is not set as input data for the tensor, resulting in the NPE.

Since the model you use is a very old one (and I guess it's for testing purposes only?) a workaround would be to use one of the test models from imagej-modelzoo:
https://github.com/imagej/imagej-modelzoo/raw/master/src/test/resources/net/imagej/modelzoo/consumer/denoise2D/dummy-0.3.0.model.bioimage.io.zip

[maweigert]

Hi @tomburke-rse ,

thanks for the quick reply!

Since the model you use is a very old one (and I guess it's for testing purposes only?)

Ah, ok. I used the one directly from https://bioimage.io , so good to know that its outdated ;)

a workaround would be to use one of the test models from imagej-modelzoo:
https://github.com/imagej/imagej-modelzoo/raw/master/src/test/resources/net/imagej/modelzoo/consumer/denoise2D/dummy-0.3.0.model.bioimage.io.zip

Ok, that worked, thanks!

[tomburke-rse]

Post Edit:
I uploaded a new release for the most recent version to the repo, but unfortunately 0.3.0 is hardcoded (and we're at 0.3.1). I'll have that fixed and hopefully released by tomorrow, so that the sem-demo also works from bioimage.io.