Merge pull request #6 from AtlasAnalyticsLab/feature/atlaspatch-release-2026-02-06

Feature/atlaspatch release 2026 02 06

Author: chengjiahao1234

DEVELOPMENT.md

@@ -2,7 +2,7 @@
 
 **Internal documentation for Atlas Analytics Lab website developers**
 
-**Last Updated:** December 2, 2025  
+**Last Updated:** February 6, 2026  
 **Repository:** https://github.com/AtlasAnalyticsLab/AtlasAnalyticsLab.github.io  
 **Status:** Actively maintained
 
@@ -714,8 +714,9 @@ headline: "Text with [link](OPENINGS_LINK)"
 ### Notes
 
 - All page content now uses `{{ site.url }}{{ site.baseurl }}/path` or `{{ site.baseurl }}/path` patterns
-- No hardcoded URLs exist in templates, includes, or page content (as of November 27, 2025)
-- Hardcoded URLs only in configuration files (`_config.yml`, `robots.txt`) and documentation
+- No hardcoded *internal* URLs exist in templates, includes, or page content (as of November 27, 2025)
+- External links (e.g., project websites) may use full `https://...` URLs as needed
+- Hardcoded URLs should otherwise be limited to configuration files (`_config.yml`, `robots.txt`) and documentation
 - Repository URL structure follows GitHub Pages naming conventions
 
 ---

README.md

@@ -211,6 +211,12 @@ This setting affects the entire site including header, footer, and content areas
 
 ---
 
+## Project Sites
+
+- **AtlasPatch:** https://atlasanalyticslab.github.io/AtlasPatch/ (linked from the header -> Projects dropdown)
+
+---
+
 ## Deployment
 
 The site automatically deploys via **GitHub Actions** when you push to the `main` branch.
@@ -388,4 +394,4 @@ Concordia University, Montreal, QC, Canada
 
 ---
 
-**Last Updated:** December 2, 2025
+**Last Updated:** February 6, 2026

_data/alumni_members.yml

@@ -59,6 +59,6 @@
   linkedin: "https://ca.linkedin.com/in/cassandre-notton-69ba6a131"
 
 - name: Denisha Thakkar
-  info_current: MSc Graduate, ML Egnineer @ CIBC
+  info_current: MSc Graduate, ML Engineer @ CIBC
   linkedin: "https://ca.linkedin.com/in/denisha-thakkar"
 

_data/news.yml

@@ -115,6 +115,9 @@
 #     headline: '🎂 <strong>Happy Birthday</strong> to Omar Abdelwahed!'
 #==============================================================================
 
+- date: February 5, 2026
+  headline: "We've released **AtlasPatch**! Visit the project page [here](https://atlasanalyticslab.github.io/AtlasPatch/)."
+
 - date: November 27, 2025
   headline: "**We are hiring PhD students!** Join our lab for cutting-edge research in computational pathology. [See details](OPENINGS_LINK)"
 

_data/publications.yml

@@ -38,6 +38,19 @@
 #     list_image: "images/pubpic/survey.jpg"
 #==============================================================================
 
+- id: "Alagha_arXiv2025_AtlasPatch"
+  title: "AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing in Computational Pathology"
+  authors: "Ahmed Alagha, Christopher Leclerc, Yousef Kotp, Omar Abdelwahed, Calvin Moras, Peter Rentopoulos, Rose Rostami, Bich Ngoc Nguyen, Jumanah Baig, Abdelhakim Khellaf, Vincent Quoc-Huy Trinh, Rabeb Mizouni, Hadi Otrok, Jamal Bentahar, Mahdi S. Hosseini"
+  year: 2026
+  status: "under_review"
+  type: "article"
+  journal: "arxiv:2602.03998"
+  url: "https://atlasanalyticslab.github.io/AtlasPatch/"
+  arxiv: "2602.03998"
+  github: "https://github.com/AtlasAnalyticsLab/AtlasPatch"
+  list_image: "images/pubpic/atlaspatch.png"
+  highlight: 0
+
 - id: "He_IPMI2025_PathTTT"
   title: "PathTTT: Test-Time Training with Meta-auxiliary Learning for Pathology Image Classification"
   authors: "Haoyu He, Mahdi S. Hosseini, Yang Wang"

_includes/footer.html

@@ -17,7 +17,7 @@
   
   Dependencies:
     - Bootstrap 5 grid system and icons
-    - theme-toggle.js script
+    - JavaScript loaded by _layouts/default.html
 -->
 <!-- Global footer containing institutional links and contact details. -->
 <footer id="footer" class="py-4">
@@ -75,6 +75,3 @@
     </div>
   </div>
 </footer>
-
-<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
-<script src="{{ site.url }}{{ site.baseurl }}/js/theme-toggle.js"></script>

_includes/header.html

@@ -11,7 +11,7 @@
     - Persistent theme preference via localStorage
   
   Navigation Pages:
-    - Home, News, Team, Openings, Publications, Funding, Lab Life, Contact
+    - Home, News, Team, Openings, Publications, Projects, Funding, Lab Life, Contact
   
   Dependencies:
     - Bootstrap 5 navbar component
@@ -38,6 +38,20 @@
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/team/">Team</a></li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/openings">Openings</a></li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/publications/">Publications</a></li>
+        <li class="nav-item dropdown">
+          <a class="nav-link dropdown-toggle dropdown-toggle-no-caret" href="#" id="projectsDropdown" role="button"
+             data-bs-toggle="dropdown" aria-expanded="false">
+            Projects
+          </a>
+          <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="projectsDropdown">
+            <li>
+              <a class="dropdown-item" href="https://atlasanalyticslab.github.io/AtlasPatch/" target="_blank"
+                 rel="noopener noreferrer">
+                AtlasPatch
+              </a>
+            </li>
+          </ul>
+        </li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/funding/">Funding</a></li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/gallery/">Lab Life</a></li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/contact/">Contact</a></li>

css/main.scss

@@ -102,7 +102,6 @@ p.byline {
   border-bottom: 1px solid var(--atlas-border-color);
   min-height: var(--atlas-nav-height);
   transition: background-color 0.3s ease, border-color 0.3s ease;
-  overflow-x: hidden;
 }
 
 .navbar .container-fluid {
@@ -126,6 +125,10 @@ p.byline {
   color: var(--atlas-link-color);
 }
 
+.navbar .dropdown-toggle-no-caret::after {
+  display: none;
+}
+
 .navbar .navbar-toggler {
   border-color: var(--atlas-border-color);
   color: var(--atlas-body-text);

googlecf337ccf1dc755f1.html

@@ -0,0 +1 @@
+google-site-verification: googlecf337ccf1dc755f1.html