core-bioimage-io-python

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Difficulty accessing torch module from a zipped model

2

I want to have direct access to the `torch.nn.Module` of a model from the model zoo (if available), but having difficulty accessing it. *Approach 1* 1) `pip install bioimageio.core>=0.7` 2)...

pattonw

Invalid model description from rdf on model zoo

2

I am trying to load a model from the model zoo. Steps: *Approach 1* 1) `pip install bioimageio.core>=0.7` 1) I went to download [this](https://bioimage.io/#/?id=10.5281%2Fzenodo.5764892) model 2) I downloaded the rdf...

pattonw

Is there a build model_creation example?

15

Previously, there was a model_creation example notebook. It is also referenced in the [Bioimagezoo developers guide](https://bioimage.io/docs/#/guides/developers-guide) as being [here](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_creation.ipynb). If not, is there another such example of how to create...

davidackerman

[This presentation](https://github.com/bioimage-io/core-bioimage-io-python/tree/main/presentations) [slides](https://bioimage-io.github.io/core-bioimage-io-python/presentations/create_ambitious_sloth.slides.html) are a good start for another example on how to create a model description from scratch.

FynnBe

ValueError when creating prediction pipeline with locally created model

3

When I try to run a prediction from a zip source file that I created locally I get a `ValueError` (full traceback below). The model was created from scratch locally...

ElpadoCan

Minimal inference script with `bioimage.io.core.prediction()` fails

1

To allow the following script to run without errors: ```python import numpy as np from bioimageio.core.prediction import predict from bioimageio.core.sample import Sample from bioimageio.core.tensor import Tensor from bioimageio.spec.model.v0_5 import TensorId...

qin-yu

Move 'get started' to bioimageio.core.__init__.py and maybe execute example commands with subprocess to have them validated with ptyest... >>>import subprocess >>>subprocess.run("bioimageio predict impartial-shrimp --example=True".split()) Maybe use https://docs.pytest.org/en/stable/how-to/doctest.html#doctest-namespace-fixture to provide some...

FynnBe

https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#example-10-miniforge

FynnBe

We need an example to create a model from scratch like happening in https://github.com/bioimage-io/core-bioimage-io-python/blob/main/presentations/create_ambitious_sloth.ipynb but for a simple 2D Unet. https://github.com/bioimage-io/spec-bioimage-io/blob/main/example/load_model_and_create_your_own.ipynb falls short as it first loads an existing model....

FynnBe

Add testcase for blocking with optional inputs

1

We have not had this use case (SAM-like models are currently the only ones with optional inputs. However, they cannot be processed blockwise, because we have not implemented the required...

FynnBe