core-bioimage-io-python

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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_

FynnBe

bioimageio.core should be able to make sense of bioimageio datasets programatically!

FynnBe

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.

constantinpape

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.

oeway

Better default io names in build_model()

12

... 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

validate markdown documentation

5

> @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...

FynnBe

MONAI translation to BioImage format

1

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...

IvanHCenalmor

Workflow RDF

6

needs https://github.com/bioimage-io/spec-bioimage-io/pull/478 Implements resolved nodes for the workflow RDF.

FynnBe

@FynnBe In the meeting today we discussed that the sha256 check should be enforced in the core package.

oeway

WIP: Write higher dimensional imagej friendly tiff files. And (possibly) incorporate changes from imageio v2 to imageio v3

FynnBe