deploy: 7e02211

_sources/imaging/imaging.rst.txt

@@ -1,7 +1,7 @@
 .. _process-home:
 
 ###############################
-Imaging with the System
+Imaging Process
 ###############################
 
 Visualization of Axes Mapping
@@ -63,7 +63,11 @@ focused.
     :align: center
     :alt: Before and after of adjusting in Z-projections after adjusting the correction collar
 
-Processing Images - Deskewing
+###############################
+Image Post-Processing
+###############################
+
+Deskewing
 ______________________________
 
 
@@ -86,7 +90,7 @@ deskewed over. In our case, our deskew angle is equivalent to 90-60.5 degrees, w
 difference between the normal of our angle mount and the y-axis. If this value is unknown, one can use different
 values for the deskew angle until the bead PSFs are correctly aligned along the z-axis and not angled.
 
-Processing Images - Rescaling
+Rescaling
 ______________________________
 
 

_templates/custom_class.html

@@ -63,7 +63,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

_templates/custom_module.html

@@ -63,7 +63,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

design_principles/design_process.html

@@ -87,7 +87,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

design_principles/required_software.html

@@ -76,7 +76,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

genindex.html

@@ -62,7 +62,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

imaging/imaging.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Imaging with the System &mdash; navigate-hardware  documentation</title>
+  <title>Imaging Process &mdash; navigate-hardware  documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
 
@@ -65,12 +65,15 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul class="current">
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Imaging with the System</a><ul>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Imaging Process</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#visualization-of-axes-mapping">Visualization of Axes Mapping</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#finding-the-focus">Finding the Focus</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#minimizing-spherical-aberrations">Minimizing Spherical Aberrations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#processing-images-deskewing">Processing Images - Deskewing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#processing-images-rescaling">Processing Images - Rescaling</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="#image-post-processing">Image Post-Processing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#deskewing">Deskewing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#rescaling">Rescaling</a></li>
 </ul>
 </li>
 </ul>
@@ -89,7 +92,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Imaging with the System</li>
+      <li class="breadcrumb-item active">Imaging Process</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/imaging/imaging.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -99,8 +102,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <section id="imaging-with-the-system">
-<span id="process-home"></span><h1>Imaging with the System<a class="headerlink" href="#imaging-with-the-system" title="Permalink to this heading"></a></h1>
+  <section id="imaging-process">
+<span id="process-home"></span><h1>Imaging Process<a class="headerlink" href="#imaging-process" title="Permalink to this heading"></a></h1>
 <section id="visualization-of-axes-mapping">
 <h2>Visualization of Axes Mapping<a class="headerlink" href="#visualization-of-axes-mapping" title="Permalink to this heading"></a></h2>
 <p>In our system we essentially have 5 different translation stages at work: the standard x,y, and z axes, an additional
@@ -146,8 +149,11 @@ <h2>Minimizing Spherical Aberrations<a class="headerlink" href="#minimizing-sphe
 focused.</p>
 <img alt="Before and after of adjusting in Z-projections after adjusting the correction collar" class="align-center" src="../_images/SphericalExample1.png" />
 </section>
-<section id="processing-images-deskewing">
-<h2>Processing Images - Deskewing<a class="headerlink" href="#processing-images-deskewing" title="Permalink to this heading"></a></h2>
+</section>
+<section id="image-post-processing">
+<h1>Image Post-Processing<a class="headerlink" href="#image-post-processing" title="Permalink to this heading"></a></h1>
+<section id="deskewing">
+<h2>Deskewing<a class="headerlink" href="#deskewing" title="Permalink to this heading"></a></h2>
 <p>With an image stack acquired, some post processing is still required in order to remove the effects of shearing in our
 images. The root of this shearing is due to the angled method in which our sample is mounted and similarly, the angled path that
 the sample moves as the piezo is scanned. A basic visual idea of how deskewing affects the resulting image is shown
@@ -163,8 +169,8 @@ <h2>Processing Images - Deskewing<a class="headerlink" href="#processing-images-
 difference between the normal of our angle mount and the y-axis. If this value is unknown, one can use different
 values for the deskew angle until the bead PSFs are correctly aligned along the z-axis and not angled.</p>
 </section>
-<section id="processing-images-rescaling">
-<h2>Processing Images - Rescaling<a class="headerlink" href="#processing-images-rescaling" title="Permalink to this heading"></a></h2>
+<section id="rescaling">
+<h2>Rescaling<a class="headerlink" href="#rescaling" title="Permalink to this heading"></a></h2>
 <p>With a properly deskewed image set, the next step is to work to rescale the image set dimensions to properly
 represent the physical pixel sizes in every dimension. The first step to doing this involves going to the
 properties tab of the image stack (Image-&gt; Properties) and adjusting each dimension such that the x and y values

index.html

@@ -64,7 +64,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>
@@ -193,12 +194,15 @@ <h2><strong>Project Philosophy</strong><a class="headerlink" href="#project-phil
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging with the System</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging Process</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#visualization-of-axes-mapping">Visualization of Axes Mapping</a></li>
 <li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#finding-the-focus">Finding the Focus</a></li>
 <li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#minimizing-spherical-aberrations">Minimizing Spherical Aberrations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#processing-images-deskewing">Processing Images - Deskewing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#processing-images-rescaling">Processing Images - Rescaling</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html#image-post-processing">Image Post-Processing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#deskewing">Deskewing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="imaging/imaging.html#rescaling">Rescaling</a></li>
 </ul>
 </li>
 </ul>

introduction/aslm.html

@@ -65,7 +65,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

introduction/background.html

@@ -71,7 +71,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

introduction/nanospim.html

@@ -73,7 +73,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

introduction/opm.html

@@ -73,7 +73,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

introduction/principles.html

@@ -65,7 +65,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>

physical_assembly/physical_assembly.html

@@ -22,7 +22,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Imaging with the System" href="../imaging/imaging.html" />
+    <link rel="next" title="Imaging Process" href="../imaging/imaging.html" />
     <link rel="prev" title="General Design Process" href="../design_principles/design_process.html" /> 
 </head>
 
@@ -75,7 +75,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>
@@ -238,7 +239,7 @@ <h2>Physical Assembly - Installing the Piezo Angle Mount<a class="headerlink" hr
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="../design_principles/design_process.html" class="btn btn-neutral float-left" title="General Design Process" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="../imaging/imaging.html" class="btn btn-neutral float-right" title="Imaging with the System" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="../imaging/imaging.html" class="btn btn-neutral float-right" title="Imaging Process" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

search.html

@@ -65,7 +65,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Imaging with the System</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging with the System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html">Imaging Process</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
 </ul>
 
         </div>