Imjoy [WIP]

[FynnBe]

add an imjoy plugin

[oeway]

@Fynn Could you point me to an example image? And which model should I try? I have been working on the bioimage.io website and made some progress, now it’s time to put some real model there. Would be great if you can start to send PR to the models repo. My next plan is to make the Ilastik bioengine app work.

[oeway]

@FynnBe I just tried the code, however, I got an error when I try to load the Unet2D model from bioimage.io: https://bioimage.io/?model=2D%20UNet%20Nuclei%20Broad

ParserError: while parsing a block mapping
  in "/tmp/tmp3eelvz6m/Sigmoid.transformation.yaml", line 1, column 1
expected <block end>, but found '<block mapping start>'
  in "/tmp/tmp3eelvz6m/Sigmoid.transformation.yaml", line 4, column 7

Full stack trace here: https://gist.github.com/oeway/7f32db7384f242cab64fe5e81faf6ce6

[FynnBe]

@FynnBe I just tried the code, however, I got an error when I try to load the Unet2D model from bioimage.io: https://bioimage.io/?model=2D%20UNet%20Nuclei%20Broad

ParserError: while parsing a block mapping
  in "/tmp/tmp3eelvz6m/Sigmoid.transformation.yaml", line 1, column 1
expected <block end>, but found '<block mapping start>'
  in "/tmp/tmp3eelvz6m/Sigmoid.transformation.yaml", line 4, column 7

Full stack trace here: https://gist.github.com/oeway/7f32db7384f242cab64fe5e81faf6ce6

I fixed the released unet2d model zip. it should work now

[oeway]

ok, great, will try.

BTW, do you have a test image included in the zip?

[FynnBe]

not yet, I thought I'll add one two in today. would it be sufficient if they are in the zip and the covers field would point to them to show them on the website?

[oeway]

Great, I think the test image and the covers should be different images. test image is full resolution , perhaps 16bits, which we use to feed into the network, ideally also provide a ground-truth image to validate the result with CI. The cover image is only for display on the website, so it should have low-resolution, small size, sometimes in artistic style.

[FynnBe]

sure, but where do we host the cover images? one option would be to add them into the zip as well, another to just make covers a list of urls.
It would be convenient to have them in the zip as well, but I suspect you don't want to unpack the zip packages for the website, so maybe the latter?

[FynnBe]

ok, great, will try.

BTW, do you have a test image included in the zip?

no, I suppose we should though... I'm on it

[oeway]

Right, I would host the cover images together with the yaml (same folder or at least in the same github repo), then get a raw url from github to fill in the yaml.

We will generate the zip file so it will have the cover images in the zip in the near future.

For now, I would add the cover images + test images in the zip file manually.

[FynnBe]

would it be possible to construct that raw github link on the fly, from the raw github model.yaml link and the relative file path within that yaml... ?
https://github.com/bioimage-io/pytorch-bioimage-io/tree/master/specs/models/unet2d/nuclei_broad

[oeway]

Yes, we are doing that, in the yaml you can use relative path to the cover image/readme etc., we have code to resolve it.

[oeway]

FYI: I made a BioEngine App based on your example, and it runs smoothly in ImJoy with MyBinder: bioimage-io/bioimage-io-resources#7