deploy: 51e0c93

_sources/imaging/imaging.rst.txt

@@ -64,7 +64,7 @@ focused.
     :alt: Before and after of adjusting in Z-projections after adjusting the correction collar
 
 ###############################
-Image Post-Processing
+Image Stack Processing
 ###############################
 
 Deskewing
@@ -93,19 +93,44 @@ values for the deskew angle until the bead PSFs are correctly aligned along the
 Rescaling
 ______________________________
 
-
 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-> Properties) and adjusting each dimension such that the x and y values
 correspond to the xy pixel size based on the system magnification and camera sensor size, and the z value
-corresponding to the z step size. While using our angled piezo configuration, the z step size :math:`\delta _z`
-doesn't directly correspond to the step size chosen for the piezo via navigate. Depicted graphically below, the
-actual z step size is related to both the angle for the piezo and the piezo step size :math:`\delta _p` .
+corresponding to the z step size as an effective z pixel size. While using our angled piezo configuration, the z step
+size :math:`\delta_z` doesn't directly correspond to the step size chosen for the piezo via navigate. Depicted
+graphically below, the actual z step size is related to both the angle for the piezo and the piezo step size
+:math:`\delta _p` .
 
 .. image:: Images/CalculatingZstep.png
     :align: center
     :alt: Depiction of how :math:`\delta _z` is derived
 
 An example of what these values can be is shown below, where for our camera and system magnification our xy pixel
-size is the same at 130 nm, while we used a piezo step size of 200 nm. Using the relationship shown above to find
-:math:`\delta _z`, we find our actual z-step size is roughly 98.5 nm.
+size is the same at 130 nm, while we used a piezo step size of 200 nm in Navigate. Using the relationship shown above
+to find :math:`\delta _z`, we find our actual z-step size is roughly 98.5 nm. Then we can adjust the image stack
+properties panel as follows:
+
+.. image:: Images/PropertiesPanel.png
+    :align: center
+    :alt: Properties Panel for our system
+
+With the properties panel adjusted, the next step is to open the rescaling panel in ImageJ (Image-> Scale). In this
+panel, the relative ratios of each of the pixel sizes to each other needs to be established. As an example for our
+system, our x and y pixel sizes are the same at 130 nm and our z-step size :math:`\delta _z` is 98.5 nm. The ratio
+between these values is roughly 0.757, so our rescaling panel looks like the following:
+
+.. image:: Images/RescalePanel.png
+    :align: center
+    :alt: Rescaling Panel for our system
+
+After selecting OK, ImageJ will then rescale the dimensions of the image stack relative to the values entered in the
+rescaling panel. In our case, there would be no adjustments to x or y, but z would be rescaled from it's original
+value.
+
+.. image:: Images/HighlightofRescale.png
+    :align: center
+    :alt: Difference in z-stack size after rescaling
+
+Reslicing
+______________________________

_sources/index.rst.txt

@@ -60,7 +60,7 @@ evaluated in their entirety through time.
    :maxdepth: 2
 
 .. toctree::
-   :caption: Hardware and Physical Assembly
+   :caption: Physical Assembly and Hardware
    :maxdepth: 5
 
    physical_assembly/physical_assembly

_sources/physical_assembly/physical_assembly.rst.txt

@@ -1,5 +1,68 @@
 .. _process-home:
 
+###############################
+Physical Assembly
+###############################
+
+Note on Difference in Simulated and Physical Coordinate Definitions
+______________________________
+
+It should be noted briefly that when discussing our physical microscope systems using Navigate software, the definitions
+for the coordinate axes is different than that of our simulations. This is due to a difference in standardized
+definitions for the axes in our previous systems and how Zemax defines these same axes. This difference is depicted in
+the picture below:
+
+.. image:: Images/CoordinateSchemeChange.png
+    :align: center
+    :alt: Difference in coordinate axes for simulation and physical setup
+
+Baseplate Assembly Process
+______________________________
+
+
+Our baseplate design was made with ease of assembly in mind. The basic process involves aligning Polaris posts with
+dowell pins and screwing them using 1/4"-20 Screws in at the predetermined hole locations on the breadboard.
+This general process is depicted below:
+
+.. image:: Images/BaseplateAssembly.png
+    :align: center
+    :alt: General process to place posts on baseplate
+
+We used various different Polaris post sizes in our assembly based on what element was being mounted on them.
+Also worth noting is that three elements are designed to be placed on 0.5" posts and as such require 0.5" post holders at
+their designated locations: the L1 focus iris, the rectangular aperture after L2, and the ND filter after the 45 degree mirror.
+The overal breakdown of which size posts went with each hole location is listed below:
+
+.. image:: Images/PostHeightBreakdown.png
+    :align: center
+    :alt: Schematic of which holes use which post heights
+
+To either mount the baseplate onto an optical table or onto separate posts, the process is similar in that
+just requires screwing 1/4"-20 screws into either an optical breadboard or onto separate posts at the four corner holes.
+
+.. image:: Images/BaseplateAssembly_Corners.png
+    :align: center
+    :alt: General process to place posts on baseplate corners
+
+Physical Assembly - Visualization of Axes Mapping
+______________________________
+
+
+In our system we essentially have 5 different translation stages at work: the standard x,y, and z axes, an additional
+stage along the z axis to control the focus of the detection path (f), and and axis associated with the piezo positioned
+such that its normal is 60.5 degrees away from the y-axis.
+
+.. image:: Images/PhysicalAxesMaps.png
+    :align: center
+    :alt: Layout of how the axis of the system are mapped
+
+Physical Assembly - How to Mount a Lens in a Polaris Holder
+______________________________
+
+
+Physical Assembly - Installing the Piezo Angle Mount
+______________________________
+
 ###############################
 Hardware
 ###############################
@@ -80,68 +143,3 @@ for Navigate looks like the following for setting up our piezo:
 .. image:: Images/Piezo_Config.png
     :align: center
     :alt: How to find the Test Panels panel
-
-
-###############################
-Physical Assembly
-###############################
-
-Note on Difference in Simulated and Physical Coordinate Definitions
-______________________________
-
-It should be noted briefly that when discussing our physical microscope systems using Navigate software, the definitions
-for the coordinate axes is different than that of our simulations. This is due to a difference in standardized
-definitions for the axes in our previous systems and how Zemax defines these same axes. This difference is depicted in
-the picture below:
-
-.. image:: Images/CoordinateSchemeChange.png
-    :align: center
-    :alt: Difference in coordinate axes for simulation and physical setup
-
-Baseplate Assembly Process
-______________________________
-
-
-Our baseplate design was made with ease of assembly in mind. The basic process involves aligning Polaris posts with
-dowell pins and screwing them using 1/4"-20 Screws in at the predetermined hole locations on the breadboard.
-This general process is depicted below:
-
-.. image:: Images/BaseplateAssembly.png
-    :align: center
-    :alt: General process to place posts on baseplate
-
-We used various different Polaris post sizes in our assembly based on what element was being mounted on them.
-Also worth noting is that three elements are designed to be placed on 0.5" posts and as such require 0.5" post holders at
-their designated locations: the L1 focus iris, the rectangular aperture after L2, and the ND filter after the 45 degree mirror.
-The overal breakdown of which size posts went with each hole location is listed below:
-
-.. image:: Images/PostHeightBreakdown.png
-    :align: center
-    :alt: Schematic of which holes use which post heights
-
-To either mount the baseplate onto an optical table or onto separate posts, the process is similar in that
-just requires screwing 1/4"-20 screws into either an optical breadboard or onto separate posts at the four corner holes.
-
-.. image:: Images/BaseplateAssembly_Corners.png
-    :align: center
-    :alt: General process to place posts on baseplate corners
-
-Physical Assembly - Visualization of Axes Mapping
-______________________________
-
-
-In our system we essentially have 5 different translation stages at work: the standard x,y, and z axes, an additional
-stage along the z axis to control the focus of the detection path (f), and and axis associated with the piezo positioned
-such that its normal is 60.5 degrees away from the y-axis.
-
-.. image:: Images/PhysicalAxesMaps.png
-    :align: center
-    :alt: Layout of how the axis of the system are mapped
-
-Physical Assembly - How to Mount a Lens in a Polaris Holder
-______________________________
-
-
-Physical Assembly - Installing the Piezo Angle Mount
-______________________________
-

_templates/custom_class.html

@@ -56,15 +56,15 @@
 <li class="toctree-l1"><a class="reference internal" href="../design_principles/required_software.html">Required Software and Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../design_principles/design_process.html">General Design Process</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Hardware and Physical Assembly</span></p>
+<p class="caption" role="heading"><span class="caption-text">Physical Assembly and Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Hardware</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#physical-assembly">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#hardware">Hardware</a></li>
 </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 Process</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-stack-processing">Image Stack Processing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
 <ul>

_templates/custom_module.html

@@ -56,15 +56,15 @@
 <li class="toctree-l1"><a class="reference internal" href="../design_principles/required_software.html">Required Software and Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../design_principles/design_process.html">General Design Process</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Hardware and Physical Assembly</span></p>
+<p class="caption" role="heading"><span class="caption-text">Physical Assembly and Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Hardware</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#physical-assembly">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#hardware">Hardware</a></li>
 </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 Process</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-stack-processing">Image Stack Processing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
 <ul>

design_principles/design_process.html

@@ -23,7 +23,7 @@
     <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="Hardware" href="../physical_assembly/physical_assembly.html" />
+    <link rel="next" title="Physical Assembly" href="../physical_assembly/physical_assembly.html" />
     <link rel="prev" title="Required Software and Packages" href="required_software.html" /> 
 </head>
 
@@ -80,15 +80,15 @@
 </ul>
 </li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Hardware and Physical Assembly</span></p>
+<p class="caption" role="heading"><span class="caption-text">Physical Assembly and Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Hardware</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#physical-assembly">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#hardware">Hardware</a></li>
 </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 Process</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-stack-processing">Image Stack Processing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
 <ul>
@@ -517,7 +517,7 @@ <h2>Processing Images - Rescaling<a class="headerlink" href="#processing-images-
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="required_software.html" class="btn btn-neutral float-left" title="Required Software and Packages" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="../physical_assembly/physical_assembly.html" class="btn btn-neutral float-right" title="Hardware" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="../physical_assembly/physical_assembly.html" class="btn btn-neutral float-right" title="Physical Assembly" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

design_principles/required_software.html

@@ -69,15 +69,15 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="design_process.html">General Design Process</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Hardware and Physical Assembly</span></p>
+<p class="caption" role="heading"><span class="caption-text">Physical Assembly and Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Hardware</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#physical-assembly">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../physical_assembly/physical_assembly.html#hardware">Hardware</a></li>
 </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 Process</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../imaging/imaging.html#image-stack-processing">Image Stack Processing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
 <ul>

genindex.html

@@ -55,15 +55,15 @@
 <li class="toctree-l1"><a class="reference internal" href="design_principles/required_software.html">Required Software and Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="design_principles/design_process.html">General Design Process</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Hardware and Physical Assembly</span></p>
+<p class="caption" role="heading"><span class="caption-text">Physical Assembly and Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="physical_assembly/physical_assembly.html">Hardware</a></li>
-<li class="toctree-l1"><a class="reference internal" href="physical_assembly/physical_assembly.html#physical-assembly">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="physical_assembly/physical_assembly.html">Physical Assembly</a></li>
+<li class="toctree-l1"><a class="reference internal" href="physical_assembly/physical_assembly.html#hardware">Hardware</a></li>
 </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 Process</a></li>
-<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html#image-post-processing">Image Post-Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="imaging/imaging.html#image-stack-processing">Image Stack Processing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
 <ul>