tidy up doc files

README.md

@@ -2,22 +2,147 @@
 
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
-This file will become your README and also the index of your
-documentation.
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+![Python Version](https://img.shields.io/badge/python-3.7+-blue.svg)
+![Jupyter
+Notebook](https://img.shields.io/badge/jupyter-%23f37626.svg?style=flat&logo=jupyter&logoColor=white)
 
-## Install
+## Overview
 
-``` sh
-pip install bioMONAI
-```
+bioMONAI is a collaborative platform for developing and deploying deep
+learning models in medical imaging using the MONAI framework and Jupyter
+notebooks. This project aims to facilitate interoperability,
+reproducibility, and community collaboration in biomedical research.
 
+## Table of Contents
 
-## How to use
+- [bioMONAI](#biomonai)
+  - [Overview](#overview)
+  - [Table of Contents](#table-of-contents)
+  - [Installation](#installation)
+  - [Getting Started](#getting-started)
+  - [Usage](#usage)
+  - [Contributing](#contributing)
+  - [License](#license)
+  - [Contact](#contact)
 
-Fill me in please! Don’t forget code examples:
+## Installation
 
-``` python
-1+1
-```
+To install the BioMONAI nbs environment, follow these steps:
 
-    2
+1.  **Clone the repository:**
+
+    ``` bash
+    git clone https://github.com/bmandracchia/biomonai.git
+    cd biomonai-nbs
+    ```
+
+2.  **Create a new Conda environment (recommended):**
+
+    ``` bash
+    conda create -n biomonai python=3.7
+    conda activate biomonai
+    ```
+
+3.  **Install dependencies:**
+
+    ``` bash
+    pip install -r requirements.txt
+    ```
+
+4.  **Install MONAI and other necessary packages:**
+
+    ``` bash
+    pip install bioMONAI
+    ```
+
+## Getting Started
+
+To get started with BioMONAI nbs, follow these steps:
+
+1.  **Clone the repository:**
+
+    ``` bash
+    git clone https://github.com/your_username/biomonai-nbs.git
+    cd biomonai-nbs
+    ```
+
+2.  **Activate your Conda environment:**
+
+    ``` bash
+    conda activate biomonai
+    ```
+
+3.  **Open Jupyter Notebook:**
+
+    ``` bash
+    jupyter notebook
+    ```
+
+4.  **Navigate to the notebooks directory and open a sample notebook:**
+
+    - You should see a list of available notebooks in your browser. Open
+      one to start exploring!
+
+## Usage
+
+To use BioMONAI nbs for your own projects, follow these steps:
+
+1.  **Create a new Jupyter notebook or open an existing one.**
+
+2.  **Import necessary modules:**
+
+    ``` python
+    import bioMONAI
+    ```
+
+3.  **Start coding! You can now leverage MONAI’s capabilities alongside
+    the interactive features of Jupyter notebooks.**
+
+## Contributing
+
+We welcome contributions from the community! To contribute to BioMONAI
+nbs, follow these steps:
+
+1.  **Fork the repository on GitHub.**
+
+2.  **Clone your fork:**
+
+    ``` bash
+    git clone https://github.com/your_username/biomonai-nbs.git
+    cd biomonai-nbs
+    ```
+
+3.  **Create a new branch for your changes:**
+
+    ``` bash
+    git checkout -b feature/new-feature
+    ```
+
+4.  **Make your changes and commit them:**
+
+    ``` bash
+    git add .
+    git commit -m "Add new feature: <feature description>"
+    ```
+
+5.  **Push to your fork and create a pull request on GitHub.**
+
+6.  **Wait for the review, and merge if everything looks good!**
+
+## License
+
+BioMONAI nbs is released under the Apache 2.0 license. See
+[LICENSE](https://github.com/your_username/biomonai-nbs/blob/main/LICENSE)
+for more details.
+
+------------------------------------------------------------------------
+
+## Contact
+
+If you have any questions or need further assistance, please open an
+issue on GitHub or contact us directly at:
+
+- Project Lead: [Biagio Mandracchia](mailto:biagio.mandracchia@uva.es)
+- Contributors: [Contributor
+  Names](mailto:contributor1@example.com,%20contributor2@example.com)

_proc/.quarto/xref/INDEX

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_proc/00_core.ipynb

@@ -81,22 +81,10 @@
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_proc/01_data.ipynb

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@@ -820,22 +820,10 @@
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