diff --git a/Gemfile b/Gemfile index 8e3aa4e..0d5b42e 100644 --- a/Gemfile +++ b/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" diff --git a/README.md b/README.md index e7ce733..d2ec489 100644 --- a/README.md +++ b/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 diff --git a/_config.yml b/_config.yml index 356dcb0..72943f4 100644 --- a/_config.yml +++ b/_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 diff --git a/_data/navigation.yml b/_data/navigation.yml new file mode 100644 index 0000000..1e06be0 --- /dev/null +++ b/_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/ + diff --git a/index.md b/index.md index 925a336..b185678 100644 --- a/index.md +++ b/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 %}