switch to minimal mistakes theme

Gemfile

@@ -1,12 +1,13 @@
 source 'https://rubygems.org'
 
-# Specify Ruby version for consistency
-ruby '>= 2.7.0'
+# Use GitHub Pages gem which includes Jekyll and compatible plugins
+gem "github-pages", group: :jekyll_plugins
+
+# Additional plugins for Minimal Mistakes theme
+gem "jekyll-include-cache", group: :jekyll_plugins
 
-# GitHub Pages gem (includes Jekyll and plugins used by GitHub Pages)
-gem 'github-pages'
 # HTML validation and link checking for CI/CD
 gem "html-proofer"
 
-# Required for Ruby 3.x to run Jekyll server
+# Required for Ruby 3.x+ to run Jekyll server
 gem "webrick"

README.md

@@ -95,13 +95,16 @@ For more detailed guidelines, see [CONTRIBUTING.md](CONTRIBUTING.md).
 
 ## Attribution
 
-This website was built using the [Fraser Lab website](http://fraserlab.com/) as a template. James Fraser's website is open-source and available on [GitHub](https://github.com/fraser-lab/fraser-lab.github.io).
+This website uses the [Minimal Mistakes Jekyll theme](https://mmistakes.github.io/minimal-mistakes/) by Michael Rose, which is open-source and available on [GitHub](https://github.com/mmistakes/minimal-mistakes).
+
+The original Deep-MI website was built using the [Fraser Lab website](http://fraserlab.com/) as a template.
 
 ### Technologies Used
 
 - Jekyll - Static site generator
+- Minimal Mistakes - Modern responsive theme
 - GitHub Pages - Hosting
-- Bootstrap 4.4.1 - CSS framework
+- Ruby - Programming language
 
 ## Local Development
 

_config.yml

@@ -1,15 +1,140 @@
+# Site Settings
+title: "Deep Medical Imaging Lab"
 name: "Deep Medical Imaging Lab"
-description: "This is the official web page for the Deep Medical Imaging Lab at DZNE and MGH/HMS."
+description: "Advancing medical imaging through deep learning and AI - research at DZNE, MGH/HMS, and MIT CSAIL"
+url: "https://Deep-MI.github.io"
+baseurl: ""
+repository: "Deep-MI/Deep-MI.github.io"
 
-url: "https://Deep-MI.org"
+# Theme - using remote_theme for GitHub Pages compatibility
+remote_theme: "mmistakes/minimal-mistakes@4.24.0"
+minimal_mistakes_skin: "default" # "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise"
 
-paginate: 5
-plugins: [jekyll-paginate]
-paginate_path: "news/page:num"
+# Site Author
+author:
+  name: "Deep MI Lab"
+  avatar: "/static/img/logos/deepmi.png"
+  bio: "Deep learning and AI for medical imaging and computational neuroimaging"
+  location: "Bonn, Germany & Boston, USA"
+  links:
+    - label: "GitHub"
+      icon: "fab fa-fw fa-github"
+      url: "https://github.com/Deep-MI"
+    - label: "Website"
+      icon: "fas fa-fw fa-link"
+      url: "https://Deep-MI.github.io"
 
-permalink: pretty
+# Site Footer
+footer:
+  links:
+    - label: "GitHub"
+      icon: "fab fa-fw fa-github"
+      url: "https://github.com/Deep-MI"
+    - label: "DZNE"
+      icon: "fas fa-fw fa-link"
+      url: "https://www.dzne.de"
+
+# Reading Files
+include:
+  - .htaccess
+  - _pages
+exclude:
+  - vendor
+  - .asset-cache
+  - .bundle
+  - .jekyll-assets-cache
+  - .sass-cache
+  - assets/js/plugins
+  - assets/js/_main.js
+  - assets/js/vendor
+  - Capfile
+  - CHANGELOG
+  - config
+  - Gemfile
+  - Gruntfile.js
+  - gulpfile.js
+  - LICENSE
+  - log
+  - node_modules
+  - package.json
+  - Rakefile
+  - README
+  - tmp
+keep_files:
+  - .git
+  - .svn
+encoding: "utf-8"
+markdown_ext: "markdown,mkdown,mkdn,mkd,md"
+
+# Conversion
 markdown: kramdown
-kramdown: 
+highlighter: rouge
+lsi: false
+excerpt_separator: "\n\n"
+incremental: false
+
+# Markdown Processing
+kramdown:
+  input: GFM
+  hard_wrap: false
+  auto_ids: true
+  footnote_nr: 1
+  entity_output: as_char
+  toc_levels: 1..6
+  smart_quotes: lsquo,rsquo,ldquo,rdquo
+  enable_coderay: false
   parse_block_html: true
 
-exclude: [vendor]
+# Sass/SCSS
+sass:
+  sass_dir: _sass
+  style: compressed
+
+# Outputting
+permalink: /:categories/:title/
+paginate: 10
+paginate_path: /news/page:num/
+timezone: Europe/Berlin
+
+# Plugins
+plugins:
+  - jekyll-paginate
+  - jekyll-sitemap
+  - jekyll-gist
+  - jekyll-feed
+  - jekyll-include-cache
+
+# Archives
+category_archive:
+  type: liquid
+  path: /categories/
+tag_archive:
+  type: liquid
+  path: /tags/
+
+# HTML Compression
+compress_html:
+  clippings: all
+  ignore:
+    envs: development
+
+# Defaults
+defaults:
+  # _posts
+  - scope:
+      path: ""
+      type: posts
+    values:
+      layout: single
+      author_profile: true
+      read_time: true
+      comments: false
+      share: true
+      related: true
+  # _pages
+  - scope:
+      path: "_pages"
+      type: pages
+    values:
+      layout: single
+      author_profile: false

_data/navigation.yml

@@ -0,0 +1,15 @@
+# Main Navigation
+main:
+  - title: "Research"
+    url: /research/
+  - title: "Publications"
+    url: /publications/
+  - title: "Team"
+    url: /members/
+  - title: "News"
+    url: /news/
+  - title: "Join Us"
+    url: /join/
+  - title: "Contact"
+    url: /contact/
+

index.md

@@ -1,20 +1,53 @@
 ---
-title: Deep MI Lab
-layout: home
-group: home
+layout: splash
+title: "Deep Medical Imaging Lab"
+permalink: /
+header:
+  overlay_color: "#000"
+  overlay_filter: "0.5"
+  overlay_image: /static/img/deepmi.png
+  actions:
+    - label: "Our Research"
+      url: "/research/"
+    - label: "Publications"
+      url: "/publications/"
+excerpt: "Advancing medical imaging through deep learning and AI"
+intro:
+  - excerpt: "Our research focuses on the development of novel computational methods (deep learning, AI) for the automated analysis, segmentation, classification, diagnosis, and prognosis of medical imaging data to support the study of neurodegenerative diseases."
+feature_row:
+  - image_path: /static/img/research/fastsurfer/01_teaser_white.png
+    alt: "FastSurfer"
+    title: "FastSurfer"
+    excerpt: "Fast and accurate deep-learning based neuroimaging pipeline"
+    url: "/research/fastsurfer/"
+    btn_label: "Learn More"
+    btn_class: "btn--primary"
+  - image_path: /static/img/research/brainprint/brainprint_teaser.png
+    alt: "BrainPrint"
+    title: "BrainPrint"
+    excerpt: "Shape analysis and asymmetry quantification of neuroanatomical structures"
+    url: "/research/brainprint/"
+    btn_label: "Learn More"
+    btn_class: "btn--primary"
+  - image_path: /static/img/research/fatsegnet/fatsegnet_teaser.png
+    alt: "FatSegNet"
+    title: "FatSegNet"
+    excerpt: "Automated adipose tissue segmentation in Dixon MRI"
+    url: "/research/fatsegnet/"
+    btn_label: "Learn More"
+    btn_class: "btn--primary"
 ---
 
-# Welcome to Deep MI Lab!
-{: .display-4}
+{% include feature_row id="intro" type="center" %}
 
-Our research focuses on the development of novel computational methods (deep learning, AI) for the automated analysis, segmentation, classification, diagnosis, and prognosis of medical imaging data to support the study of neurodegenerative diseases.
-{: .welcomefont}
+## Our Affiliations
 
 We are part of the:
-{: .welcomefont}
 
 - [German Center for Neurodegenerative Diseases, Bonn, Germany](https://www.dzne.de/en/research/research-areas/population-health-sciences/forschungsgruppen/reuter/research-areasfocus/)
 - [Martinos Center for Biomedical Imaging, MGH/HMS Boston, USA](https://www.martinos.org/investigator/martin-reuter/)
-- and associated to [MIT CSAIL](http://reuter.mit.edu).
-{: .welcomefont}
+- and associated to [MIT CSAIL](http://reuter.mit.edu)
+{: .notice--info}
+
+{% include feature_row %}