core-bioimage-io-python
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bioimage-io
Python libraries for loading, running and packaging bioimage.io models
There have been some recent changes to the weight converters and it seems not everything there is up-to-date. In `weight_converter/torch/_torchscript` the function converts the weights and returns the corresponding weight...
plan: - [x] pdoc documentation for bioimageio.core API users - [x] update README.md extend and point to pdoc docs for bioimageio.core API users - [ ] add CONTRIBUTING.md for new...
Pytorch lightning model format is just a `pytorch_state_dict` with more entries. It should be quite straightforward to make a model adaptor for it, or adapt the current adaptor. Potentially a...
Hi all, Due to my stuff not working anymore complaining about some pytorch internal issue and core-dumps, I re-installed my conda environment but still my previously working code won't work...
this came up in offline discussions and was mentioned in https://github.com/bioimage-io/spec-bioimage-io/issues/579
Halo! When building a model and adding the deepImageJ config with the IJ macros, if the pre and post-processing need to use the same pipeline (e.g., scale range), there is...
Our ONNX converters could be improved. To convert from pytorch [ONNX dynamo](https://pytorch.org/docs/stable/onnx_dynamo.html) looks promising.
The following code runs into an assertion error (extracted minimum example of a previously working implementation): ``` import bioimageio.core rdf_doi = "10.5281/zenodo.7274275" model_resource = bioimageio.core.load_resource_description(rdf_doi) ``` Output: ``` /home/julian/miniconda3/envs/cebra-em-all-env2/lib/python3.9/site-packages/bioimageio/spec/shared/_resolve_source.py:437: CacheWarning:...
We should improve our network weight converters and investigate which additional weight converters we can add.
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Python libraries for loading, running and packaging bioimage.io models