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1 | 1 | # core-bioimage-io-python
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2 | 2 |
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3 |
| -Python specific core utilities for running models in the [BioImage Model Zoo](https://bioimage.io). |
| 3 | +Python specific core utilities for [bioimage.io]("https://bioimage.io") resources (in particular models). |
4 | 4 |
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5 | 5 | ## Installation
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6 | 6 |
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@@ -67,7 +67,7 @@ mamba activate core
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67 | 67 | pip install -e . --no-deps
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68 | 68 | ```
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69 | 69 |
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70 |
| -There are different environment files that only install tensorflow or pytorch as dependencies available. |
| 70 | +There are different environment files available that only install tensorflow or pytorch as dependencies. |
71 | 71 |
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72 | 72 | ## 💻 Command Line
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73 | 73 |
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@@ -106,12 +106,15 @@ bioimagei predict-images -m <MODEL> -i <INPUT_PATTERN> - o <OUTPUT_FOLDER>
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106 | 106 |
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107 | 107 | ## From python
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108 | 108 |
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109 |
| -`bioimageio.core` is a python library that implements loading models, running prediction with them and more. |
110 |
| -To get an overview of this functionality, check out the example notebooks: |
| 109 | +`bioimageio.core` is a python package that implements prediction with bioimageio models |
| 110 | +including standardized pre- and postprocessing operations. |
| 111 | +These models are described by---and can be loaded with---the bioimageio.spec package. |
111 | 112 |
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112 |
| -* [example/model_usage](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_usage.ipynb) for how to load models and run prediction with them |
113 |
| -* [example/model_creation](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_creation.ipynb) for how to create bioimage.io compatible model packages |
114 |
| -* [example/dataset_statistics_demo](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/dataset_statistics_demo.ipynb) for how to use the dataset statistics for advanced pre-and-postprocessing |
| 113 | +In addition bioimageio.core provides functionality to convert model weight formats. |
| 114 | + |
| 115 | +To get an overview of this functionality, check out these example notebooks: |
| 116 | + |
| 117 | +* [model creation/loading with bioimageio.spec](https://github.com/bioimage-io/spec-bioimage-io/blob/main/example_use/load_model_and_create_your_own.ipynb) |
115 | 118 |
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116 | 119 | ## Model Specification
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117 | 120 |
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