Skip to content

Commit 28f9a20

Browse files
m-reuterm-reuter
committed
switch to minimal mistakes theme
1 parent 4c63d96 commit 28f9a20

5 files changed

Lines changed: 201 additions & 27 deletions

File tree

‎Gemfile‎

Lines changed: 5 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,10 @@
11
source 'https://rubygems.org'
22

3-
# Specify Ruby version for consistency
4-
ruby '>= 2.7.0'
3+
# Use GitHub Pages gem which includes Jekyll and compatible plugins
4+
gem "github-pages", group: :jekyll_plugins
55

6-
# GitHub Pages gem (includes Jekyll and plugins used by GitHub Pages)
7-
gem 'github-pages'
8-
# HTML validation and link checking for CI/CD
9-
gem "html-proofer"
6+
# Additional plugins for Minimal Mistakes theme
7+
gem "jekyll-include-cache", group: :jekyll_plugins
108

11-
# Required for Ruby 3.x to run Jekyll server
9+
# Required for Ruby 3.x+ to run Jekyll server
1210
gem "webrick"

‎README.md‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -95,13 +95,16 @@ For more detailed guidelines, see [CONTRIBUTING.md](CONTRIBUTING.md).
9595

9696
## Attribution
9797

98-
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).
98+
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).
99+
100+
The original Deep-MI website was built using the [Fraser Lab website](http://fraserlab.com/) as a template.
99101

100102
### Technologies Used
101103

102104
- Jekyll - Static site generator
105+
- Minimal Mistakes - Modern responsive theme
103106
- GitHub Pages - Hosting
104-
- Bootstrap 4.4.1 - CSS framework
107+
- Ruby - Programming language
105108

106109
## Local Development
107110

‎_config.yml‎

Lines changed: 133 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,140 @@
1+
# Site Settings
2+
title: "Deep Medical Imaging Lab"
13
name: "Deep Medical Imaging Lab"
2-
description: "This is the official web page for the Deep Medical Imaging Lab at DZNE and MGH/HMS."
4+
description: "Advancing medical imaging through deep learning and AI - research at DZNE, MGH/HMS, and MIT CSAIL"
5+
url: "https://Deep-MI.github.io"
6+
baseurl: ""
7+
repository: "Deep-MI/Deep-MI.github.io"
38

4-
url: "https://Deep-MI.org"
9+
# Theme - using remote_theme for GitHub Pages compatibility
10+
remote_theme: "mmistakes/minimal-mistakes@4.24.0"
11+
minimal_mistakes_skin: "default" # "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise"
512

6-
paginate: 5
7-
plugins: [jekyll-paginate]
8-
paginate_path: "news/page:num"
13+
# Site Author
14+
author:
15+
name: "Deep MI Lab"
16+
avatar: "/static/img/logos/deepmi.png"
17+
bio: "Deep learning and AI for medical imaging and computational neuroimaging"
18+
location: "Bonn, Germany & Boston, USA"
19+
links:
20+
- label: "GitHub"
21+
icon: "fab fa-fw fa-github"
22+
url: "https://github.com/Deep-MI"
23+
- label: "Website"
24+
icon: "fas fa-fw fa-link"
25+
url: "https://Deep-MI.github.io"
926

10-
permalink: pretty
27+
# Site Footer
28+
footer:
29+
links:
30+
- label: "GitHub"
31+
icon: "fab fa-fw fa-github"
32+
url: "https://github.com/Deep-MI"
33+
- label: "DZNE"
34+
icon: "fas fa-fw fa-link"
35+
url: "https://www.dzne.de"
36+
37+
# Reading Files
38+
include:
39+
- .htaccess
40+
- _pages
41+
exclude:
42+
- vendor
43+
- .asset-cache
44+
- .bundle
45+
- .jekyll-assets-cache
46+
- .sass-cache
47+
- assets/js/plugins
48+
- assets/js/_main.js
49+
- assets/js/vendor
50+
- Capfile
51+
- CHANGELOG
52+
- config
53+
- Gemfile
54+
- Gruntfile.js
55+
- gulpfile.js
56+
- LICENSE
57+
- log
58+
- node_modules
59+
- package.json
60+
- Rakefile
61+
- README
62+
- tmp
63+
keep_files:
64+
- .git
65+
- .svn
66+
encoding: "utf-8"
67+
markdown_ext: "markdown,mkdown,mkdn,mkd,md"
68+
69+
# Conversion
1170
markdown: kramdown
12-
kramdown:
71+
highlighter: rouge
72+
lsi: false
73+
excerpt_separator: "\n\n"
74+
incremental: false
75+
76+
# Markdown Processing
77+
kramdown:
78+
input: GFM
79+
hard_wrap: false
80+
auto_ids: true
81+
footnote_nr: 1
82+
entity_output: as_char
83+
toc_levels: 1..6
84+
smart_quotes: lsquo,rsquo,ldquo,rdquo
85+
enable_coderay: false
1386
parse_block_html: true
1487

15-
exclude: [vendor]
88+
# Sass/SCSS
89+
sass:
90+
sass_dir: _sass
91+
style: compressed
92+
93+
# Outputting
94+
permalink: /:categories/:title/
95+
paginate: 10
96+
paginate_path: /news/page:num/
97+
timezone: Europe/Berlin
98+
99+
# Plugins
100+
plugins:
101+
- jekyll-paginate
102+
- jekyll-sitemap
103+
- jekyll-gist
104+
- jekyll-feed
105+
- jekyll-include-cache
106+
107+
# Archives
108+
category_archive:
109+
type: liquid
110+
path: /categories/
111+
tag_archive:
112+
type: liquid
113+
path: /tags/
114+
115+
# HTML Compression
116+
compress_html:
117+
clippings: all
118+
ignore:
119+
envs: development
120+
121+
# Defaults
122+
defaults:
123+
# _posts
124+
- scope:
125+
path: ""
126+
type: posts
127+
values:
128+
layout: single
129+
author_profile: true
130+
read_time: true
131+
comments: false
132+
share: true
133+
related: true
134+
# _pages
135+
- scope:
136+
path: "_pages"
137+
type: pages
138+
values:
139+
layout: single
140+
author_profile: false

‎_data/navigation.yml‎

Lines changed: 15 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
# Main Navigation
2+
main:
3+
- title: "Research"
4+
url: /research/
5+
- title: "Publications"
6+
url: /publications/
7+
- title: "Team"
8+
url: /members/
9+
- title: "News"
10+
url: /news/
11+
- title: "Join Us"
12+
url: /join/
13+
- title: "Contact"
14+
url: /contact/
15+

‎index.md‎

Lines changed: 43 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,20 +1,53 @@
11
---
2-
title: Deep MI Lab
3-
layout: home
4-
group: home
2+
layout: splash
3+
title: "Deep Medical Imaging Lab"
4+
permalink: /
5+
header:
6+
overlay_color: "#000"
7+
overlay_filter: "0.5"
8+
overlay_image: /static/img/deepmi.png
9+
actions:
10+
- label: "Our Research"
11+
url: "/research/"
12+
- label: "Publications"
13+
url: "/publications/"
14+
excerpt: "Advancing medical imaging through deep learning and AI"
15+
intro:
16+
- 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."
17+
feature_row:
18+
- image_path: /static/img/research/fastsurfer/01_teaser_white.png
19+
alt: "FastSurfer"
20+
title: "FastSurfer"
21+
excerpt: "Fast and accurate deep-learning based neuroimaging pipeline"
22+
url: "/research/fastsurfer/"
23+
btn_label: "Learn More"
24+
btn_class: "btn--primary"
25+
- image_path: /static/img/research/brainprint/brainprint_teaser.png
26+
alt: "BrainPrint"
27+
title: "BrainPrint"
28+
excerpt: "Shape analysis and asymmetry quantification of neuroanatomical structures"
29+
url: "/research/brainprint/"
30+
btn_label: "Learn More"
31+
btn_class: "btn--primary"
32+
- image_path: /static/img/research/fatsegnet/fatsegnet_teaser.png
33+
alt: "FatSegNet"
34+
title: "FatSegNet"
35+
excerpt: "Automated adipose tissue segmentation in Dixon MRI"
36+
url: "/research/fatsegnet/"
37+
btn_label: "Learn More"
38+
btn_class: "btn--primary"
539
---
640

7-
# Welcome to Deep MI Lab!
8-
{: .display-4}
41+
{% include feature_row id="intro" type="center" %}
942

10-
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.
11-
{: .welcomefont}
43+
## Our Affiliations
1244

1345
We are part of the:
14-
{: .welcomefont}
1546

1647
- [German Center for Neurodegenerative Diseases, Bonn, Germany](https://www.dzne.de/en/research/research-areas/population-health-sciences/forschungsgruppen/reuter/research-areasfocus/)
1748
- [Martinos Center for Biomedical Imaging, MGH/HMS Boston, USA](https://www.martinos.org/investigator/martin-reuter/)
18-
- and associated to [MIT CSAIL](http://reuter.mit.edu).
19-
{: .welcomefont}
49+
- and associated to [MIT CSAIL](http://reuter.mit.edu)
50+
{: .notice--info}
51+
52+
{% include feature_row %}
2053

0 commit comments

Comments
 (0)