core-bioimage-io-python
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bioimage-io
Python libraries for loading, running and packaging bioimage.io models
going from model class/instance in code to the spec is indeed not trivial. we could try to write the file automatically with `inspect.getsource` we'd have to somehow make sure to...
Tiled prediction seems to not be implemented for v0.4 models: ```python import bioimageio.core import imageio.v3 as imageio from xarray import DataArray from bioimageio.spec.model.v0_5 import AxisId image = imageio.imread("/home/pape/.cache/micro_sam/sample_data/livecell-2d-image.png") model =...
It's unclear how to pass the value for `input_block_shape` in order to specify a fixed tiling shape. The code ```python import bioimageio.core import imageio.v3 as imageio from xarray import DataArray...
... to support "live" editing. This needs more a closer look. Not sure this is working or even desired.
Thanks @mese79 for brining up bandit today.. I thought if we are evaluating to check contributed model source code with bandit we ought to check our own code too...
The new xarray version(2025.3.0) removed ops from their core, and it now cause this error: ``` 20_578821_1/runtime_resources/pip/a5f1874eaf70cb0ae9ccdcf572824a4d19ad4882/virtualenv/lib/python3.11/site-packages/bioimageio/core/_magic_tensor_ops.py", line 9, in from xarray.core import nputils, ops ImportError: cannot import name 'ops'...
Hello, Please feel free to redirect me to the Image.sc forum if this is not the right place to discuss about licensing. We are in the process of uploading a...
If I want to use `core` for inference, the model will be downloaded along with the sample input and output, which are unnecessary.
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Python libraries for loading, running and packaging bioimage.io models