core-bioimage-io-python
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Python libraries for loading, running and packaging bioimage.io models
Have you seen this library? https://allencellmodeling.github.io/aicsimageio/ Seems to work very nicely with the metadata of tiff files both for the import and export _Originally posted by @esgomezm in https://github.com/bioimage-io/core-bioimage-io-python/issues/329#issuecomment-1451916207_
bioimageio.core should be able to make sense of bioimageio datasets programatically!
this should be done for both core and [spec](https://github.com/bioimage-io/spec-bioimage-io). We discussed this with @FynnBe and @jdeschamps. @jdeschamps agreed to look into this.
It would be nice if we can add a new CI task to automatically release our CI testing environment as docker containers, to be used by HPC or server users.
... Does it check for the names of the input&output layers when writing the rdf.yaml? _Originally posted by @esgomezm in https://github.com/bioimage-io/collection-bioimage-io/issues/571#issuecomment-1485578142_ We could inspect the (TF) weights for better `tensor_inputs`...
> @FynnBe: can we somehow check this more explicitly? (If not I think this is not so important if we have bioimage-io/spec-bioimage-io#501 working, then it's easy to check manually). Quick...
Hi, I have been working with the script to translate the MONAI models to BioImage format. I already have some of them working with pre and post processing: - BraTS...
needs https://github.com/bioimage-io/spec-bioimage-io/pull/478 Implements resolved nodes for the workflow RDF.
@FynnBe In the meeting today we discussed that the sha256 check should be enforced in the core package.
WIP: Write higher dimensional imagej friendly tiff files. And (possibly) incorporate changes from imageio v2 to imageio v3