Deep-MI Lab Website

This is the official website for the Deep Medical Imaging (Deep-MI) Lab.

The website is built with Jekyll and hosted on GitHub Pages.

Quick Links

• Live Website: https://deep-mi.github.io
• Contributing: See CONTRIBUTING.md
• Quick Start: See QUICKSTART.md

Create News Posts

• put an .md file into the _posts directory
• name it like 2020-03-15-Short-Title.md
• have it start with the following markdown

---
title: Your Nice Title
author: First Lastname
layout: post
group: news
---
Your text goes here, with images, links etc....

See _templates/post-template.md for a complete template.

Add Members

• add member info to _data/members.yml (see file for format)
• put photos (size 365 x 365, 72 dpi) into /static/img/members (jpg compressed)

See _templates/member-template.md for a complete template.

Add Publication

• add publication info to _data/publications.yml (see file for format)
• add teaser image (size height 200 px max, jpg compressed, max 100kB) into /static/pub/paper_id.jpg
• add bibtex file into /static/pub/paper_id.bib
• link to openaccess PDF (journal) or put at /static/pub/paper_id.pdf
• paper_id is the id field in the yml

See _templates/publication-template.md for a complete template.

Validation

Before committing changes, validate your content:

# Validate YAML data files
./scripts/validate_yaml.rb

# Validate post filenames and format
./scripts/validate_posts.sh

See CONTRIBUTING.md for detailed contribution guidelines.

Tools and Scripts

Validation

# Validate YAML files (checks structure, required fields, file existence)
./scripts/validate_yaml.rb

# Validate post filenames and format
./scripts/validate_posts.sh

Image Optimization

# Optimize member photos and publication teasers
./scripts/optimize_images.sh member static/img/members/lastname.jpg
./scripts/optimize_images.sh pub static/pub/paper_id.jpg

Requirements: ImageMagick

• macOS: brew install imagemagick
• Linux: sudo apt-get install imagemagick or sudo yum install imagemagick
• Windows: See imagemagick.org

Pre-commit Hook

# Install pre-commit hook for automatic validation
cp scripts/pre-commit.sh .git/hooks/pre-commit
chmod +x .git/hooks/pre-commit

For more detailed guidelines, see CONTRIBUTING.md.

Attribution

This website was built using the Fraser Lab website as a template. James Fraser's website is open-source and available on GitHub.

Technologies Used

• Jekyll - Static site generator
• GitHub Pages - Hosting
• Bootstrap 4.4.1 - CSS framework

Local Development

Before pushing changes, please check that they will work on your system first with the plugins included in the Gemfile using the bundler tool.

Setup (First Time)

# Install bundler (without sudo for security)
gem install bundler --user-install

# Install dependencies
bundle install

Running the Site Locally

# Start the Jekyll server
bundle exec jekyll serve

# Site will be available at: http://localhost:4000
# Or: http://0.0.0.0:4000

Testing

# Check for broken links and HTML issues
bundle exec jekyll build
bundle exec htmlproofer ./_site --disable-external