Modelzoo exporter command about imagej-modelzoo HOT 8 OPEN

What do you think about joining forces and combine our efforts in this repo?

Cool idea!

from imagej-modelzoo.

I would suggest that we setup a call within the next two weeks where we can synch our two projects. After this we should be able to create a list of github issues which we can assign and implement.

Perfect. How do you want to proceed?

from imagej-modelzoo.

I think @oeway and @FynnBe can help with this.

We were working in the update to YAML while N2V was being published so now we need to merge all the specifications. Does it make sense to create this file from Java or is it better to create it from Python (DeepImageJ only works with TF models)?

What about parsing an official template located in imagej-modelzoo?

from imagej-modelzoo.

We are already working closely together with @oeway and @FynnBe regarding the yaml-specification. But this project here should be a consumer of the modelzoo and is purely on the Java side.

The published N2V uses the modelzoo format and is available here as a demo. As you can see in the n2v-sem-demo.model.yaml not all fields are filled out. Especially a link to the used training data is missing. Also author and documentation is currently added by hand editing the generated yaml file.

What do you think about joining forces and combine our efforts in this repo?

from imagej-modelzoo.

How do you want to proceed?

This is just an idea:

• Create a new general plugin for the imagej-modelzoo, let's say "modelzoo importer"
• Through a GUI similar to DeepImageJ's one, this plugin parses the YAML file specified here and completes it with all the required information.
• Should we try to define the YAML here here, according to the description given in bioimage-io/configuration? I'd say yes.

The main difference between current n2v-sem-demo and the version DeepImageJ needs is the integration of macros for the preprocessing and post-processing. What do you think is the best way to integrate them?

from imagej-modelzoo.

I would suggest that we setup a call within the next two weeks where we can synch our two projects. After this we should be able to create a list of github issues which we can assign and implement.

I think the three points you mentioned are part of the required features and should all live in this repo.

The main difference between current n2v-sem-demo and the version DeepImageJ needs is the integration of macros for the preprocessing and post-processing. What do you think is the best way to integrate them?

In my opinion macro-integration is another layer on top of this layer.

from imagej-modelzoo.

As discussed with @esgomezm and @dasv74 during NEUBIAS, we think it would be a nice addition to provide a web based BioEngine app for making model packages directly on bioimage.io.

We can basically generate fields from a schema file for the model config, we have a little experiment here.

The generated web interface will have all the parameters included in the yaml, they will be generated from the schema, so we make sure the generated yaml will be compatible with the specification.

Not only the yaml, but we can also add files and build the zip file within the bioengine app.

Further more, when the zip file with weights and yaml are made, the bioengine app can spin up a remote server and run a test with the model directly.

Of course, in the meantime, you can implement the same in Java natively. For longer term, a more centralized web based bioengine app would require less maintenance efforts, especially when we change the specification.

from imagej-modelzoo.

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/compatibility-of-imagej-tensorflow-with-imagej1/41295/6

from imagej-modelzoo.