update layout

README.md

@@ -1,30 +1,18 @@
-# Becoming a medical imaging AI expert with nitrain
+# Becoming a medical imaging AI expert with Python
 
-This book will take you through the entire medical imaging AI workflow from data to deployment.
+This book will take you through the entire medical imaging AI workflow from data to deployment using the nitrain framework and pytorch.
 
-## Usage
+## About the book
 
-### Building the book
+By going through this book, you will learn how to tackle any medical imaging AI problem in Python. That includes building regression, classification, or image-to-image models for any type of medical imaging processing task. It is split up into the following sections that operate more-or-less independently in case you want to sharpen your skills in one particular area:
 
-If you'd like to develop and/or build the Becoming a medical imaging AI expert with nitrain book, you should:
-
-1. Clone this repository
-2. Run `pip install -r requirements.txt` (it is recommended you do this within a virtual environment)
-3. (Optional) Edit the books source files located in the `book/` directory
-4. Run `jupyter-book clean book/` to remove any existing builds
-5. Run `jupyter-book build book/`
-
-A fully-rendered HTML version of the book will be built in `book/_build/html/`.
-
-### Hosting the book
-
-Please see the [Jupyter Book documentation](https://jupyterbook.org/publish/web.html) to discover options for deploying a book online using services such as GitHub, GitLab, or Netlify.
-
-For GitHub and GitLab deployment specifically, the [cookiecutter-jupyter-book](https://github.com/executablebooks/cookiecutter-jupyter-book) includes templates for, and information about, optional continuous integration (CI) workflow files to help easily and automatically deploy books online with GitHub or GitLab. For example, if you chose `github` for the `include_ci` cookiecutter option, your book template was created with a GitHub actions workflow file that, once pushed to GitHub, automatically renders and pushes your book to the `gh-pages` branch of your repo and hosts it on GitHub Pages when a push or pull request is made to the main branch.
-
-## Contributors
-
-We welcome and recognize all contributions. You can see a list of current contributors in the [contributors tab](https://github.com/ncullen93/book/graphs/contributors).
+- Handling medical images
+- Loading imaging datasets
+- Creating batches of images
+- Training models
+- Fine-tuning models
+- Explaining model results
+- Sharing and deploying models
 
 ## Credits
 

book/_toc.yml

@@ -4,24 +4,27 @@
 format: jb-book
 root: intro
 parts:
-  - caption: Handling medical images
+  - caption: 1. Handling medical images
     chapters:
       - file: 01-01-installing-libraries
       - file: 01-02-reading-and-writing-images
       - file: 01-03-visualizing-images
       - file: 01-04-operating-on-images
-  - caption: Loading imaging datasets
+  - caption: 2. Loading imaging datasets
     chapters:
       - file: markdown
-  - caption: Creating batches of images
+  - caption: 3. Creating batches of images
     chapters:
       - file: markdown-notebooks
-  - caption: Training models
+  - caption: 4. Training models
     chapters:
       - file: markdown-copy
-  - caption: Explaining model results
+  - caption: 5. Explaining model results
     chapters:
       - file: markdown-copy2
-  - caption: Sharing and deploying models
+  - caption: 6. Sharing and deploying models
     chapters:
       - file: markdown-copy3
+  - caption: Appendix
+    chapters:
+      - file: markdown-copy5

book/markdown-copy4.md

@@ -0,0 +1,55 @@
+# Markdown Files
+
+Whether you write your book's content in Jupyter Notebooks (`.ipynb`) or
+in regular markdown files (`.md`), you'll write in the same flavor of markdown
+called **MyST Markdown**.
+This is a simple file to help you get started and show off some syntax.
+
+## What is MyST?
+
+MyST stands for "Markedly Structured Text". It
+is a slight variation on a flavor of markdown called "CommonMark" markdown,
+with small syntax extensions to allow you to write **roles** and **directives**
+in the Sphinx ecosystem.
+
+For more about MyST, see [the MyST Markdown Overview](https://jupyterbook.org/content/myst.html).
+
+## Sample Roles and Directives
+
+Roles and directives are two of the most powerful tools in Jupyter Book. They
+are kind of like functions, but written in a markup language. They both
+serve a similar purpose, but **roles are written in one line**, whereas
+**directives span many lines**. They both accept different kinds of inputs,
+and what they do with those inputs depends on the specific role or directive
+that is being called.
+
+Here is a "note" directive:
+
+```{note}
+Here is a note
+```
+
+It will be rendered in a special box when you build your book.
+
+Here is an inline directive to refer to a document: {doc}`markdown-notebooks`.
+
+## Citations
+
+You can also cite references that are stored in a `bibtex` file. For example,
+the following syntax: `` {cite}`holdgraf_evidence_2014` `` will render like
+this: {cite}`holdgraf_evidence_2014`.
+
+Moreover, you can insert a bibliography into your page with this syntax:
+The `{bibliography}` directive must be used for all the `{cite}` roles to
+render properly.
+For example, if the references for your book are stored in `references.bib`,
+then the bibliography is inserted with:
+
+```{bibliography}
+
+```
+
+## Learn more
+
+This is just a simple starter to get you started.
+You can learn a lot more at [jupyterbook.org](https://jupyterbook.org).

book/markdown-copy5.md

@@ -0,0 +1,55 @@
+# Markdown Files
+
+Whether you write your book's content in Jupyter Notebooks (`.ipynb`) or
+in regular markdown files (`.md`), you'll write in the same flavor of markdown
+called **MyST Markdown**.
+This is a simple file to help you get started and show off some syntax.
+
+## What is MyST?
+
+MyST stands for "Markedly Structured Text". It
+is a slight variation on a flavor of markdown called "CommonMark" markdown,
+with small syntax extensions to allow you to write **roles** and **directives**
+in the Sphinx ecosystem.
+
+For more about MyST, see [the MyST Markdown Overview](https://jupyterbook.org/content/myst.html).
+
+## Sample Roles and Directives
+
+Roles and directives are two of the most powerful tools in Jupyter Book. They
+are kind of like functions, but written in a markup language. They both
+serve a similar purpose, but **roles are written in one line**, whereas
+**directives span many lines**. They both accept different kinds of inputs,
+and what they do with those inputs depends on the specific role or directive
+that is being called.
+
+Here is a "note" directive:
+
+```{note}
+Here is a note
+```
+
+It will be rendered in a special box when you build your book.
+
+Here is an inline directive to refer to a document: {doc}`markdown-notebooks`.
+
+## Citations
+
+You can also cite references that are stored in a `bibtex` file. For example,
+the following syntax: `` {cite}`holdgraf_evidence_2014` `` will render like
+this: {cite}`holdgraf_evidence_2014`.
+
+Moreover, you can insert a bibliography into your page with this syntax:
+The `{bibliography}` directive must be used for all the `{cite}` roles to
+render properly.
+For example, if the references for your book are stored in `references.bib`,
+then the bibliography is inserted with:
+
+```{bibliography}
+
+```
+
+## Learn more
+
+This is just a simple starter to get you started.
+You can learn a lot more at [jupyterbook.org](https://jupyterbook.org).