Deployed 729a533 to main with MkDocs 1.6.1 and mike 2.1.3

multiview-stitcher · Oct 18, 2024 · fc653bc · fc653bc
1 parent b3f4259
commit fc653bc
Show file tree

Hide file tree

Showing 12 changed files with 802 additions and 17 deletions.
diff --git a/main/404.html b/main/404.html
@@ -367,6 +367,26 @@
 
 
 
+    <li class="md-nav__item">
+      <a href="/napari-stitcher/main/scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
+
+
     <li class="md-nav__item">
       <a href="/napari-stitcher/main/contributing/" class="md-nav__link">
 

diff --git a/main/contributing/index.html b/main/contributing/index.html
@@ -13,7 +13,7 @@
         <link rel="canonical" href="https://multiview-stitcher.github.io/napari-stitcher/main/contributing/">
 
 
-        <link rel="prev" href="../writing/">
+        <link rel="prev" href="../scripting/">
 
 
 
@@ -374,6 +374,26 @@
 
 
 
+
+
+    <li class="md-nav__item">
+      <a href="../scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
 
 
 
@@ -469,7 +489,7 @@ <h1 id="contributing">Contributing</h1>
       <nav class="md-footer__inner md-grid" aria-label="Footer" >
 
 
-          <a href="../writing/" class="md-footer__link md-footer__link--prev" aria-label="Previous: Saving fused images">
+          <a href="../scripting/" class="md-footer__link md-footer__link--prev" aria-label="Previous: Scripting and batch processing">
             <div class="md-footer__button md-icon">
 
               <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11z"/></svg>
@@ -479,7 +499,7 @@ <h1 id="contributing">Contributing</h1>
                 Previous
               </span>
               <div class="md-ellipsis">
-                Saving fused images
+                Scripting and batch processing
               </div>
             </div>
           </a>

diff --git a/main/index.html b/main/index.html
@@ -425,6 +425,26 @@
 
 
 
+    <li class="md-nav__item">
+      <a href="scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
+
+
     <li class="md-nav__item">
       <a href="contributing/" class="md-nav__link">
 
@@ -501,7 +521,7 @@ <h1 id="napari-stitcher">napari-stitcher</h1>
 <li>When working with multi-channel data, stick to the following <a href="naming_convention/">naming convention</a>: <code>{tile} :: {channel}</code>.</li>
 <li>Load either all or just a subset of the layers into the plugin.</li>
 <li>Choose registration options: registration channel, binning and more.</li>
-<li>Stitching = registration (refining the positions) + fusion (joining the tiles into a single image).</li>
+<li>Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).</li>
 <li>The registration result is shown in the viewer and the fused channels are added as new layers.</li>
 </ol>
 <h2 id="demo">Demo</h2>
@@ -510,7 +530,7 @@ <h2 id="demo">Demo</h2>
 <source src="https://github.com/multiview-stitcher/napari-stitcher/raw/refs/heads/main/docs/images/demo_3d.mp4" type="video/mp4">
 </video>
 
-<p><small>Image data: <a href="https://imagej.net/plugins/bigstitcher/">BigStitcher</a>.</small></p>
+<p><small>This demo uses the awesome <a href="https://github.com/napari-threedee/napari-threedee"><code>napari-threedee</code></a> for prepositioning the tiles. Image data: <a href="https://imagej.net/plugins/bigstitcher/">BigStitcher</a>.</small></p>
 
 
 

diff --git a/main/installation/index.html b/main/installation/index.html
@@ -469,6 +469,26 @@
 
 
 
+    <li class="md-nav__item">
+      <a href="../scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
+
+
     <li class="md-nav__item">
       <a href="../contributing/" class="md-nav__link">
 

diff --git a/main/loading/index.html b/main/loading/index.html
@@ -388,6 +388,26 @@
 
 
 
+    <li class="md-nav__item">
+      <a href="../scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
+
+
     <li class="md-nav__item">
       <a href="../contributing/" class="md-nav__link">
 

diff --git a/main/naming_convention/index.html b/main/naming_convention/index.html
@@ -388,6 +388,26 @@
 
 
 
+    <li class="md-nav__item">
+      <a href="../scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
+
+
     <li class="md-nav__item">
       <a href="../contributing/" class="md-nav__link">
 

diff --git a/main/prearrangement/index.html b/main/prearrangement/index.html
@@ -460,6 +460,26 @@
 
 
 
+    <li class="md-nav__item">
+      <a href="../scripting/" class="md-nav__link">
+
+
+  <span class="md-ellipsis">
+    Scripting and batch processing
+  </span>
+
+
+      </a>
+    </li>
+
+
+
+
+
+
+
+
+
     <li class="md-nav__item">
       <a href="../contributing/" class="md-nav__link">
 
@@ -565,7 +585,7 @@ <h1 id="prepositioning-tiles">Prepositioning tiles</h1>
 <p class="admonition-title">Prepositioning tiles</p>
 <p>As a starting point for registration, <code>napari-stitcher</code> uses the positions of the layers as they are shown in napari.</p>
 </div>
-<p>There are two ways to preoposition the layers in napari:</p>
+<p>There are two ways to preposition the layers in napari:</p>
 <h3 id="1-manual-positioning">1. Manual positioning</h3>
 <p>You can manually position the tiles by dragging and dropping them in the viewer. This is useful when you have a small number of tiles and you want to freely position them.</p>
 <div class="admonition note">