More Changes to various sections

docs/source/design_principles/design_process.rst

@@ -20,8 +20,8 @@ From there, determine the resulting FoV of the detection path by dividing the to
 
 FoV (in microns) = (W :subscript:`Sensor` /M)*1000
 
-For our system, this resulted in a FoV of ~266 μm, meaning that we want to select lenses in our illumination path
-to produce a light sheet as close to 266 μm in length as we can achieve.
+For our system, this resulted in a FoV of ~266 :math:`\mu m`, meaning that we want to select lenses in our illumination path
+to produce a light sheet as close to 266 :math:`\mu m` in length as we can achieve.
 
 The overarching goal of a standard optical system is to both mold light into a particular shape and direct it to a
 particular location. In our case, our optical system works to convert an input gaussian beam into a thin light sheet that illuminates our sample.
@@ -67,7 +67,7 @@ and set up our simulation.
 
 Here, we use Zemax as a tool to find the optimal placement of all the lenses of our system
 based on whether or not the input beam should be focusing or collimated after each lens.
-As a general rule of thumb, one should build optical systems in Zemax element-by-element
+As a general rule of thumb, one should build optical systems in Zemax in an element-by-element
 manner instead of adding all the optical elements and trying to then optimize aspects of it.
 Our general flow involves adding a lens to the system and then optimizing for either
 either a focused or collimated beam, and then adding in the next lens and doing the same process until all lenses are
@@ -125,26 +125,55 @@ Through Focus Spot analysis allows us to essentially see the evolution of the li
 where we can then estimate a sort of range where we expect the width of the light sheet to be thin enough for our
 imaging purposes, where the maximum usable light sheet width is the FWHM at the focus multiplied by sqrt(2).
 
+Zemax Tolerancing Analysis
+-----------------
+
+When considering building physical systems using Zemax, an additional analysis tool known as tolerancing becomes
+increasingly important. Tolerancing is essentially the process of understanding how sensitive different elements in a
+system are to various perturbations. This can be along the lines of how sensitive the collimation or magnification of a
+4F system is to small physical displacements of the two lenses that comprise it. Similarly to Zemax's optimization
+process, tolerancing also utilizes a merit function. This merit function is fully customizable, and serves to define
+how well a particular system is performing. In the case of our system, we chose our merit function to factor in both the
+size and displacement of the output light sheet relative to the perfectly optimized instance.
+
+.. image:: docs/source/design_principles/Images/ToleranceMF.png
+    :align: center
+    :alt: Tolerance Merit Function
+
+
+
 Baseplate Design
 -----------------
 
 When satisfied with the results of simulations, the optimized values in Zemax can then be used to design
 our baseplate. This process involves taking the optimized distances between our various optical elements
 and then considering how each of those elements are mounted in a physical system, as in Zemax all of the elements are
-effectively suspended in midair.
+effectively suspended in midair like below:
+
+.. image:: docs/source/design_principles/Images/CylindricalDesign6_30_90_75_250flip4.png
+    :align: center
+    :alt: Zemax Elements Floating
 
 For mounting our elements, we utilize the `Polaris <https://www.thorlabs.com/navigation.cfm?guide_id=2368>`_ line from
 Thorlabs, which are designed with long-term stability and alignment in mind. Each component is characterized in part by
 two dowell pin alignment holes to ensure subsequent mounted elements are aligned along a specific axis. In the baseplate
 design, we are essentially deciding on the location for the mounting holes of the Polaris posts we're using, which is
 not the same as the locations of the elements themselves from Zemax.
 
+.. image:: docs/source/design_principles/Images/PolarisScheme.png
+    :align: center
+    :alt: Polaris Scheme
+
 While we are able to use most of our element mounts from the Polaris line, for the cylindrical lens L3 we needed a mount
 capable of rotating the lens, which at this time is not something available from Thorlabs. In our case we designed an
 additional mounting element that allows the use of a basic Thorlabs
 `RSP1 rotation mount <https://www.thorlabs.com/thorproduct.cfm?partnumber=RSP1>`_, but still ensures alignment with the
 other Polaris elements. The CAD file for this mount is available for download here (INSERT DOWNLOAD LINK FOR ELEMENT?)
 
+.. image:: docs/source/design_principles/Images/RotationMount.png
+    :align: center
+    :alt: Rotation Mount Adapter
+
 With the method in which each of the elements needs to be mounted decided upon, we then went over the product schematics
 for each mount to understand the z-displacement that they impart upon the element mounted within them relative to where
 the Polaris post central mounting hole would need to be. This idea is depicted below, where when considering how to
@@ -153,7 +182,114 @@ space two lenses from each other there is essentially three components to take i
     2. The thickness of the lenses themselves
     3. The distance between the center of the Polaris post and the start of the lens in the mount
 
-(INSERT POSTSPACING CONSDIERATIONS FIGURE)
+.. image:: docs/source/design_principles/Images/PostSpacingConsiderations.png
+    :align: center
+    :alt: Post Spacing Considerations
+
+
+Once the locations of the mounting holes were determined, we used Autodesk Inventor to design the full baseplate. The
+baseplate is essentially just a mounting hole and the two dowel pin holes for every element, as well as four mounting
+holes for the baseplate itself. These four baseplate mounting holes were spaced in increments of inches such that the
+baseplate can either be screwed directly into an optical breadboard table or into additional posts that can keep the
+assembly at a desired height.
+
+.. image:: docs/source/design_principles/Images/Baseplate.png
+    :align: center
+    :alt: Baseplate
+
+With the baseplate designed, our final assembly for our illumination path looks as follows:
+
+.. image:: docs/source/design_principles/Images/BaseplateAssembly_Iso.png
+    :align: center
+    :alt: Baseplate Assembly Iso
+
+.. image:: docs/source/design_principles/Images/BaseplateAssembly_Top.png
+    :align: center
+    :alt: Baseplate Assembly Top
+
+Note on Difference in Simulated and Physical Coordinate Definitions
+______________________________
+
+It should be noted briefly that when discussing our physical microscope systems, 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:: docs/source/design_principles/Images/CoordinateSchemeChange.png
+    :align: center
+    :alt: Difference in coordinate axes for simulation and physical setup
+
+Physical 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:: docs/source/design_principles/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:: docs/source/design_principles/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:: docs/source/design_principles/Images/BaseplateAssembly_Corners.png
+    :align: center
+    :alt: General process to place posts on baseplate corners
+
+
+Finding the Focus
+-----------------
+
+Minimizing Spherical Aberrations
+-----------------
+
+Once the system has been assembled to the point of being able to take image stacks, the process of
+minimizing the effects of spherical aberrations can begin. Spherical aberrations are typically
+introduced into optical systems due to the surface curvature of different lens elements. This
+type of aberration typically presents itself visually as a sort of stretching or bending of the focus
+of light in the system. Certain microscope objectives, such as the Nikon 25x/1.1 NA that we employ in this setup,
+have a built-in collar that can be adjusted to minimize spherical aberration (PICTURE).
+
+In our system, we expect the effects of spherical aberrations to be along the axis of our detection path (defined
+as z in our imaging scheme). In order to visualize these effects and adjust the correction collar of our objective
+to mitigate them, we employ a process of taking a z-stack of fluorescent beads suspended in agarose
+and using ImageJ to quickly process those images.
+
+    1. Take a z-stack within Navigate of your sample
+    2. Open up the z-stack within ImageJ
+    3. Reslice the z-stack (Image -> Stacks -> Reslice)
+    4. Do a maximum intensity project of the resliced stack (Image -> Stacks -> Z-Projection)
+    5. Take note if spherical aberration is present in the projected image.
+    6. If spherical aberration is still present, make slight adjustments to the objective
+       correction collar and repeat Steps 1-5.
+
+As a note, observing the camera live-feed via Navigate's "Continuous Scan" mode while adjusting the correction collar
+can help to get in the general vicinity of the correct placement of the correction collar. An example of how change in
+the correction collar affect live images are shown below for fluorescent beads. Aiming to get to get the beads near the
+expected light sheet position to be as in-focus as possible is a general guide for what direction to move the collar;
+however, true correction needs to be done with the z-projection method mentioned above.
+
+.. image:: docs/source/design_principles/Images/ChangingCorrectionCollar.png
+    :align: center
+    :alt: Correction collar effects
+
+As a quick example of what an image of a z-projection could look like before and after trying to correct for spherical aberration is shown
+below. Here, one can see in the top panel that the bead features are essentially smoothed out and fuzzy due to
+aberrations, while in the bottom panel with adjustments made to the correction collar the beads appear much cleaner and
+focused.
+
+.. image:: docs/source/design_principles/Images/SphericalExample.png
+    :align: center
+    :alt: Before and after of adjusting in Z-projections after adjusting the correction collar