From cf459b24c58d4fb71d40d14115e406e837ef06c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Wed, 22 Jan 2025 14:30:58 +0100 Subject: [PATCH] rearange sections --- README.md | 66 +++++++++++++++++++++++++++++-------------------------- 1 file changed, 35 insertions(+), 31 deletions(-) diff --git a/README.md b/README.md index 95b345f3..6da9f693 100644 --- a/README.md +++ b/README.md @@ -288,17 +288,33 @@ The package is also available via pip pip install "bioimageio.core[onnx,pytorch]" ``` -### Set up Development Environment +## 🐍 Use in Python -To set up a development conda environment run the following commands: +`bioimageio.core` is a python package that implements prediction with bioimageio models +including standardized pre- and postprocessing operations. +These models are described by---and can be loaded with---the bioimageio.spec package. -```console -conda env create -f dev/env.yaml -conda activate core -pip install -e . --no-deps -``` +In addition bioimageio.core provides functionality to convert model weight formats. -There are different environment files available that only install tensorflow or pytorch as dependencies, see [dev folder](https://github.com/bioimage-io/core-bioimage-io-python/tree/main/dev). +### Documentation +[Here you find the bioimageio.core documentation.](https://bioimage-io.github.io/core-bioimage-io-python/bioimageio/core.html) + +#### Presentations +- [Create a model from scratch](https://bioimage-io.github.io/core-bioimage-io-python/presentations/create_ambitious_sloth.slides.html) ([source](https://github.com/bioimage-io/core-bioimage-io-python/tree/main/presentations)) + +#### Examples +
+
Notebooks that save and load resource descriptions and validate their format (using bioimageio.spec, a dependency of bioimageio.core)
+
load_model_and_create_your_own.ipynb + Open In Colab +
+
dataset_creation.ipynb + Open In Colab +
+
Use the described resources in Python with bioimageio.core
+
model_usage.ipynb + Open In Colab +
## 💻 Use the Command Line Interface @@ -309,6 +325,9 @@ You can list all the available commands via: bioimageio ``` +For examples see [Getting started](#get-started). + + ### CLI inputs from file For convenience the command line options (not arguments) may be given in a `bioimageio-cli.json` @@ -323,33 +342,18 @@ blockwise: true stats: inputs/dataset_statistics.json ``` -## 🐍 Use in Python - -`bioimageio.core` is a python package that implements prediction with bioimageio models -including standardized pre- and postprocessing operations. -These models are described by---and can be loaded with---the bioimageio.spec package. -In addition bioimageio.core provides functionality to convert model weight formats. +## Set up Development Environment -### Documentation -[Here you find the bioimageio.core documentation.](https://bioimage-io.github.io/core-bioimage-io-python/bioimageio/core.html) +To set up a development conda environment run the following commands: -#### Presentations -- [Create a model from scratch](https://bioimage-io.github.io/core-bioimage-io-python/presentations/create_ambitious_sloth.slides.html) ([source](https://github.com/bioimage-io/core-bioimage-io-python/tree/main/presentations)) +```console +conda env create -f dev/env.yaml +conda activate core +pip install -e . --no-deps +``` -#### Examples -
-
Notebooks that save and load resource descriptions and validate their format (using bioimageio.spec, a dependency of bioimageio.core)
-
load_model_and_create_your_own.ipynb - Open In Colab -
-
dataset_creation.ipynb - Open In Colab -
-
Use the described resources in Python with bioimageio.core
-
model_usage.ipynb - Open In Colab -
+There are different environment files available that only install tensorflow or pytorch as dependencies, see [dev folder](https://github.com/bioimage-io/core-bioimage-io-python/tree/main/dev). ## Logging level