Deployed 6c15eb3 with MkDocs version: 1.6.0

404.html

@@ -989,6 +989,8 @@ <h1>404 - Not found</h1>
 
         <script src="/assets/js/google-analytics.js"></script>
 
+        <script src="/js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

examples/index.html

@@ -1018,6 +1018,8 @@ <h1 id="jupyter-notebook-examples">Jupyter Notebook Examples</h1>
 
         <script src="../assets/js/google-analytics.js"></script>
 
+        <script src="../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

examples/short_notebooks/Landscape_View_Xenium/index.html

@@ -4848,6 +4848,8 @@ <h1 id="landscape-view-xenium">Landscape View Xenium<a class="anchor-link" href=
 
         <script src="../../../assets/js/google-analytics.js"></script>
 
+        <script src="../../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

gallery/gallery_xenium/index.html

@@ -1070,6 +1070,8 @@ <h2 id="bone-marrow">Bone Marrow</h2>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

gallery/gallery_xenium_mouse_brain/index.html

@@ -1032,6 +1032,8 @@ <h1 id="xenium-prime-mouse-brain-coronal-ff">Xenium Prime Mouse Brain Coronal FF
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

gallery/gallery_xenium_multi/index.html

@@ -1149,6 +1149,8 @@ <h2 id="bone-marrow">Bone Marrow</h2>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

gallery/gallery_xenium_skin_cancer/index.html

@@ -1035,6 +1035,8 @@ <h1 id="xenium-prime-human-skin-ffpe-outs">Xenium Prime Human Skin FFPE outs</h1
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

gallery/index.html

@@ -1084,6 +1084,8 @@ <h3 id="visium-hd">Visium HD</h3>
 
         <script src="../assets/js/google-analytics.js"></script>
 
+        <script src="../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

index.html

@@ -236,6 +236,15 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#whats-new" class="md-nav__link">
+    <span class="md-ellipsis">
+      What's New
+    </span>
+  </a>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#about" class="md-nav__link">
     <span class="md-ellipsis">
@@ -969,6 +978,15 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#whats-new" class="md-nav__link">
+    <span class="md-ellipsis">
+      What's New
+    </span>
+  </a>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#about" class="md-nav__link">
     <span class="md-ellipsis">
@@ -1002,14 +1020,20 @@ <h1 id="welcome-to-celldegas-documentation">Welcome to Celldega's Documentation<
     Celldega Landscape visualization of a human skin cancer Xenium dataset obtained from <a href='https://www.10xgenomics.com/datasets' target='_blank'>10X Genomics</a>.
 </div>
 
-<p>Celldega is a spatial analysis and visualization library that is being developed by the <a href='https://www.broadinstitute.org/spatial-technology-platform' target='_blank'>Spatial Technology Platform</a> at the <a href='https://www.broadinstitute.org/spatial-technology-platform' target='_blank'>Broad Institute of MIT and Harvard</a>. This project enables researchers to easily visualize large ST datasets (e.g., datasets with &gt;100M transcripts) alongside single-cell and spatial analysis notebook workflows (e.g., <a href='https://scverse.org/' target='_blank'>sverse</a> tools and novel spatial analysis approaches).</p>
+<p>Celldega is a spatial analysis and visualization library that is being developed by the <a href="https://www.broadinstitute.org/spatial-technology-platform">Spatial Technology Platform</a> at the <a href="https://www.broadinstitute.org/spatial-technology-platform">Broad Institute of MIT and Harvard</a>. This project enables researchers to easily visualize large ST datasets (e.g., datasets with &gt;100M transcripts) alongside single-cell and spatial analysis notebook workflows (e.g., <a href="https://scverse.org/">sverse</a> tools and novel spatial analysis approaches).</p>
 <ul>
 <li><a href="overview/getting_started/">Getting Started</a></li>
 <li><a href="overview/installation/">Installation</a></li>
 <li><a href="overview/usage/">Usage</a></li>
 </ul>
+<h2 id="whats-new">What's New</h2>
+<p>The project was recently presented at the Broad Retreat Data Visualization Breakout Session -</p>
+<p><a href="https://broadinstitute.github.io/Celldega-Broad-Retreat-2024/" target="_blank" rel="noopener noreferrer">
+    <img src="assets/img/Celldega_Broad-Retreat-2024.png" alt="Celldega Broad Retreat 2024" style="display:block; margin:0 auto; width:75%; border:1px solid lightgray; border-radius:5px;">
+</a></p>
 <h2 id="about">About</h2>
 <p>Celldega is named after a bodega, a small shop with all the essentials that is part of the fabric of a neighborhood.</p>
+<p><a href="https://www.nytimes.com/2025/01/03/sports/dukes-mayo-bowl.html">checking link</a></p>
 
 
 
@@ -1095,6 +1119,8 @@ <h2 id="about">About</h2>
 
         <script src="assets/js/google-analytics.js"></script>
 
+        <script src="js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

index.md

@@ -8,14 +8,22 @@
     Celldega Landscape visualization of a human skin cancer Xenium dataset obtained from <a href='https://www.10xgenomics.com/datasets' target='_blank'>10X Genomics</a>.
 </div>
 
-Celldega is a spatial analysis and visualization library that is being developed by the <a href='https://www.broadinstitute.org/spatial-technology-platform' target='_blank'>Spatial Technology Platform</a> at the <a href='https://www.broadinstitute.org/spatial-technology-platform' target='_blank'>Broad Institute of MIT and Harvard</a>. This project enables researchers to easily visualize large ST datasets (e.g., datasets with >100M transcripts) alongside single-cell and spatial analysis notebook workflows (e.g., <a href='https://scverse.org/' target='_blank'>sverse</a> tools and novel spatial analysis approaches).
-
-
-
+Celldega is a spatial analysis and visualization library that is being developed by the [Spatial Technology Platform](https://www.broadinstitute.org/spatial-technology-platform) at the [Broad Institute of MIT and Harvard](https://www.broadinstitute.org/spatial-technology-platform). This project enables researchers to easily visualize large ST datasets (e.g., datasets with >100M transcripts) alongside single-cell and spatial analysis notebook workflows (e.g., [sverse](https://scverse.org/) tools and novel spatial analysis approaches).
 
 - [Getting Started](overview/getting_started.md)
 - [Installation](overview/installation.md)
 - [Usage](overview/usage.md)
 
+## What's New
+The project was recently presented at the Broad Retreat Data Visualization Breakout Session -
+
+<a href="https://broadinstitute.github.io/Celldega-Broad-Retreat-2024/" target="_blank" rel="noopener noreferrer">
+    <img src="assets/img/Celldega_Broad-Retreat-2024.png" alt="Celldega Broad Retreat 2024" style="display:block; margin:0 auto; width:75%; border:1px solid lightgray; border-radius:5px;">
+</a>
+
+
+
 ## About
-Celldega is named after a bodega, a small shop with all the essentials that is part of the fabric of a neighborhood.
+Celldega is named after a bodega, a small shop with all the essentials that is part of the fabric of a neighborhood.
+
+[checking link](https://www.nytimes.com/2025/01/03/sports/dukes-mayo-bowl.html)

javascript/api/index.html

@@ -1797,6 +1797,8 @@ <h3 id="example-usage">Example Usage</h3>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

javascript/index.html

@@ -1018,6 +1018,8 @@ <h1 id="javascript-api-overview">JavaScript API Overview</h1>
 
         <script src="../assets/js/google-analytics.js"></script>
 
+        <script src="../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

js/open_in_new_tab.js

@@ -0,0 +1,51 @@
+// Description: Open external links in a new tab and PDF links in a new tab
+// Based on: https://jekyllcodex.org/without-plugin/new-window-fix/
+
+// Open external links in a new window
+function external_new_window() {
+    for(let c = document.getElementsByTagName("a"), a = 0; a < c.length; a++) {
+        let b = c[a];
+        if(b.getAttribute("href") && b.host !== location.host) {
+            b.target = "_blank";
+            b.rel = "noopener";
+        }
+    }
+}
+
+// Open PDF links in a new window
+function pdf_new_window() {
+    if (!document.getElementsByTagName) {
+        return false;
+    }
+
+    const extensions = ['.pdf', '.doc', '.docx', '.json', '.xls', '.xlsx', '.ppt', '.pptx', '.zip', '.rar', '.tar', '.gz', '.7z', '.bz2', '.xz', '.tgz', '.tar.gz'];
+    let links = document.getElementsByTagName("a");
+
+    for (let eleLink = 0; eleLink < links.length; eleLink++) {
+        let href = links[eleLink].href.toLowerCase(); // Convert href to lowercase for case-insensitive matching
+
+        if (extensions.some(ext => href.endsWith(ext))) {
+            links[eleLink].onclick = function() {
+                window.open(this.href);
+                return false;
+            }
+        }
+    }
+}
+
+function apply_rules() {
+    external_new_window();
+    pdf_new_window();
+}
+
+if (typeof document$ !== "undefined") {
+    // Compatibility with mkdocs-material's instant loading feature
+    document$.subscribe(function() {
+        apply_rules();
+    });
+} else {
+    // For browsers without mkdocs-material's instant loading feature
+    document.addEventListener("DOMContentLoaded", function() {
+        apply_rules();
+    });
+}

overview/file_formats/index.html

@@ -1085,6 +1085,8 @@ <h2 id="landscapefiles">LandscapeFiles</h2>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

overview/getting_started/index.html

@@ -1033,6 +1033,8 @@ <h1 id="getting-started">Getting Started</h1>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

overview/index.html

@@ -1024,6 +1024,8 @@ <h1 id="overview">Overview</h1>
 
         <script src="../assets/js/google-analytics.js"></script>
 
+        <script src="../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

overview/installation/index.html

@@ -1111,6 +1111,8 @@ <h2 id="javascript">JavaScript</h2>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

overview/usage/index.html

@@ -1085,6 +1085,8 @@ <h2 id="terrabio">Terra.bio</h2>
 
         <script src="../../assets/js/google-analytics.js"></script>
 
+        <script src="../../js/open_in_new_tab.js"></script>
+
 
   </body>
 </html>

python/api/api.md

@@ -1,5 +1,6 @@
 # Python API Reference
 
+::: celldega.nbhd
 ::: celldega.pre
 ::: celldega.viz
     handler: python