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--- a/chap03.tex
+++ b/chap03.tex
@@ -8,7 +8,7 @@ The amplitude is the peak voltage of the pulse, given in V. The default voltage
 \paragraph{sweep period}
 The sweep period is the time a single pulse lasts, given in ms, with a minimum of 1 ms. The mask aligner setup uses a frequency of 1 kHz by default, which results in a sweep time period of 1 ms.
 \paragraph{time between sweeps}
-The "time between sweeps" is the time between each pulse where no voltage is applied. It is given in ms and in the mask aligner setup is kept at 0 ms.
+The "time between sweeps" is the off-time between each pulse where no voltage is applied. It is given in ms and in the mask aligner setup it is kept at 0 ms.
 \todo{Maybe image explanation}
 
 \subsection{Pulse shape}
@@ -75,12 +75,12 @@ Both approach and retract show heavy aliasing artifacts, which could lead to the
 \subsection{Voltage behavior}
 The KIM001 device has a controllable parameter called voltage, which is supposed to control the output signal voltage amplitude between $85$ V and $125$ V. In testing it was found to not in fact control the output voltage at all. When the voltage parameter is set to $125$ V the voltage amplitude will be a value $> 150$ V. This value is not consistent and varies by $\pm 25 V$.  When the voltage parameter is set to $80$ V the output voltage amplitude is $\approx 80$ V.\\
 
-In both cases if driving pulses in retract direction are driven. The signal will (within a few $100$ steps) drift back to a voltage of approx. $118$ V. This behavior is shown in Figure (\ref{fig:kim0001_voltage_behaviour}). This led to the conclusion that the KIM001 device cannot be used for our purposes. A variable voltage is in some situations necessary for driving the Mask Aligner appropriately. Also, noticeable is an inconsistency in peak shape in the signal after 100 steps (\textcolor{tab_green}{green}) as compared to the others, although no settings were changed during the recording of this data.
+The signal drifts (within a few $100$ steps) back to a voltage of approx. $118$ V. It does this regardless of set voltage. This behavior is shown in Figure (\ref{fig:kim0001_voltage_behaviour}). This led to the conclusion that the KIM001 device cannot be used for our purposes. A variable voltage is in some situations necessary for driving the Mask Aligner appropriately. Furthermore, there is an inconsistency in peak shape in the signal after 100 steps (\textcolor{tab_green}{green}) as compared to the others, although no settings were changed during the recording of this data.
 
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.6\textwidth]{img/Plots/KIM001/voltage_behavior.pdf}
-    \caption{4 Plots showing the Voltage of the retract steps of the KIM0001 after setting the Voltage to $125$ on the device, after $1$ step (\textcolor{tab_blue}{blue}), ~$50$ steps (\textcolor{tab_orange}{orange}), ~$120$ steps (\textcolor{tab_green}{green}) and ~$200$ steps (\textcolor{tab_red}{red}). The voltage spikes beyond the desired voltage at the start and after $200$ steps settles on a voltage of ~$118$ V. }
+    \caption{Retract steps of the KIM0001 for a set Voltage of $125$ after different amount of steps. The voltage spikes beyond the desired voltage at the start and after $200$ steps settles on a voltage of ~$118$ V. }
     \label{fig:kim0001_voltage_behaviour}
 \end{figure}
 
@@ -97,7 +97,7 @@ The core of the Mask aligner controller is an Arduino DUE~\cite{arduino_datashee
 \end{equation}
 
 Where $A$ is an amplitude parameter given by the user, that controls the voltage given at the output. $t$ is the time elapsed since the start of the current step, and $P$ is the period of a single step. The value $4095$ is chosen to use the full range of the $12$-Bit accuracy the Arduino DUE DAC provides. This gives a sinus-like shape of the pulse depicted in Figure \ref{fig:bessel_filter_unfiltered}, that closely matches the pulse shape given by the RHK (Fig. \ref{fig:RHK_pulse_shape}). Similar behavior is expected. \\
-This signal is then output on the DAC 0 pin of the Arduino. The Arduino can only output one polarity of voltage, but our final signal is intended to be bimodal. Therefore, another signal is generated on DAC 1 with $1 - S$ as the given function. The two signals are now subtracted from each other as depicted in Figure \ref{fig:bessel_filter_unfiltered}. This gives a bipolar signal following the desired sinusoidal shape. This is done via a hardware subtractor. \\
+This signal is then output on the DAC 0 pin of the Arduino. The Arduino can only output one polarity of voltage, but our final signal is intended to be bimodal. Therefore, another signal is generated on DAC 1 with $1 - S$ as the given function. The two signals are now subtracted, via a hardware subtractor, from each other as depicted in Figure \ref{fig:bessel_filter_unfiltered}. This gives a bipolar signal following the desired sinusoidal shape. \\
 The Signal given by the Arduino contains aliasing artifacts from the digital to analog conversion. Aliasing leads to sharp very short steps in the signal, which could potentially put the piezo movement into the slip rather than the stick regime. In order to prevent that, the aliasing steps in the signal have to be smoothed out. This is done by applying an 8th order Bessel filter to the signal. The effect of this can be seen in Figure \ref{fig:bessel_filter_filter}.
 
 \begin{figure}[H]
@@ -112,13 +112,14 @@ The Signal given by the Arduino contains aliasing artifacts from the digital to
     \caption{}
 	\label{fig:bessel_filter_filter}
     \end{subfigure}
-    \caption{Plots showing both an aliased signal (a) and the same signal, but smoothed out with an 8th order Bessel filter (b). The amount of aliasing is exaggerated to be more easily visible. }
+    \caption{(a) aliased simulated signal. (b) 8th order Bessel filtered simulated signal. The amount of aliasing is exaggerated to make the effect more clear. }
     \label{fig:bessel_filter}
 \end{figure}
+\todo{Aliases Signal}
 
 \subsection{Fast flank}
 
-After this step the signal is bimodal and of the correct shape, but provides only the slow flank. The fast flank is achieved by taking the signal given and feeding it into a hardware inverter, whilst retaining both the original (normal) and the inverted signal. The retained signals can be seen in Figure \ref{fig:signal_switch_entry} When the signal is at its plateau, a hardware switch is used to change from the normal to the inverted signal. Examples of the signal are shown in Figure \ref{fig:signal_switch_switched}. The switching is achieved via a ADG1436 switch that has a transition time of $<200$ ns~\cite{switch_datasheet}, this puts it well within the $<1$ $\mu$s time span required for the slip behavior of the signal's fast flank. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
+The resulting signal is bimodal and of the correct shape, but provides only the slow flank. The fast flank is achieved by taking the signal given and feeding it into a hardware inverter, whilst retaining both the original (normal) and the inverted signal. A simulation of the retained signals can be seen in Figure \ref{fig:signal_switch_entry}. When the signal is at its plateau, a hardware switch is used to change from the normal to the inverted signal. Simulations of the signal are shown in Figure \ref{fig:signal_switch_switched}. The switching is achieved via a ADG1436 switch that has a transition time of $<200$ ns~\cite{switch_datasheet}, this puts it well within the $<1$ $\mu$s time span required for the slip behavior of the signal's fast flank. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
 
 \begin{figure}[H]
     \centering
@@ -132,32 +133,32 @@ After this step the signal is bimodal and of the correct shape, but provides onl
     \caption{}
 	\label{fig:signal_switch_switched}
     \end{subfigure}
-    \caption{Plots showing both the normal and the inverted signal (a) and the signal achieved by switching between normal and inverted (b). }
+    \caption{(a) normal and the inverted signal. (b) the signal achieved by switching between normal and inverted. }
     \label{fig:signal_switch}
 \end{figure}
 
 \subsection{Amplification}
-The final step, needed to get the desired signal for driving the piezo motors, is amplification. Currently, the signal is still in the -$3.3$ to $3.3$ V range supplied by the Arduino DUE. For this application a driving signal between of $240$ V peak to peak is needed. In order to do that, the signal for each channel is separately amplified. This is done on a separate PCB that is exclusively for amplifying the signal and outputting it to the 4 outputs. It uses several high voltage opamps and a high voltage transformer to boost the signal into the desired range. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.\\
+The final step is amplification since the Arduino DUE can only output voltages between -$3.3$ and $3.3$ V. For this application a driving signal of $240$ V peak to peak is needed. The signal for each channel is separately amplified. This is done on a separate PCB that is exclusively for amplifying the signal and outputting it to the 4 outputs. It uses several high voltage operational amplifiers (opamps) and a high voltage transformer to boost the signal into the desired range. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.\\
 The Arduino digital output pins $22$, $24$, $26$ and $28$ control, which channels receive any output signal. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
 Afterward there are $4$ relays, one for each channel that can be shut to prevent any current from being on the output leads, this is mainly a safety measure. The $4$ relays are also controlled by the Arduino from the digital outputs $53$, $51$, $49$ and $47$ for the channels Z1, Z2, Z3 and X respectively. The relays are switched off after a waiting period of $2$ seconds after no signal is supplied to the given channel. 
 
 \subsection{Parameters}
 The following parameters can be controlled with the new electronics:
 \paragraph{Amplitude (amp)}
-The amplitude of the generated signal within the Arduino given as $4095 * \text{amp} / 100$. An amplitude of $100$ results in a signal of $240$ V peak to peak at the output and as such can be treated as an output voltage as long as the internal potentiometers are not changed to a different voltage. 
+The amplitude of the generated signal within the Arduino given as $4095 * \text{amp} / 100$. An amplitude of $100$ results in a signal of $240$ V peak to peak at the output. To derive peak to peak voltage from this multiply by $2.4$.
 \paragraph{Voltage (volt)}
-Instead of setting the amp parameter to a given value, which corresponds to an output voltage. The voltage can be set directly. Internally, this sets the amp parameter. Due to limited integer precision in the amp parameter, not all voltages can be accurately chosen. The script will choose the closest voltage to the input one. The range is $0$ - $120$ V. The default value is $80$ V. 
+Alternatively to setting amp, the voltage can be set directly. Internally, this sets the amp parameter. Due to limited integer precision in the amp parameter, not all voltages can be accurately chosen. The script will choose the closest voltage to the input one. The range is $0$ - $120$ V. The default value is $80$ V. 
 \paragraph{Channel}
-The channels the generated signal is output to. The system can output 4 channels of signal, where each can be turned off separately. 
+Used to specify which output channels are turned off/on. All channels receive the same signal when turned on. The system can output 4 channels of signal, where each can be turned off separately. 
 \paragraph{Max Step}
 The maximum number of pulses the controller is allowed to run in succession. By default, this value is set to 10000. This is a safety measure to ensure no accidental inputs crash the mask into the sample.
 \paragraph{Polarity}
-The polarity of the generated signal. Negative polarity is chosen as an approach signal, while positive polarity represents the retract signal. The polarity can also be changed by specifying "step -1" for example, but this parameter is a global toggle, that changes the behavior for the entire program.
+The polarity of the generated signal. Negative polarity is chosen as an approach signal, while positive polarity represents the retract signal. The polarity can also be changed by specifying "step -1" for example, but this parameter is a global toggle, that changes the behavior for the entire program. \\
 
 The frequency is not adjustable as of the writing of this thesis, though in principle changeable frequencies could be implemented. Since all previous approach curves and alignment operations were always performed at $1$ kHz, it was deemed unnecessary. Frequencies higher than $1$ kHz are also difficult, as the timing accuracy of the Arduino is already close to its limits. The signal would also lose sampling rate since the output rate of the DAC is fixed. 
 
 \subsection{Measured pulse shape}
-In order to verify the ability to drive the Mask Aligner with the new electronics, test measurements of both the new Walker and the RHK were performed. For the Mask Aligner a voltage of $80$ V was determined to be the optimum voltage to run experiments (see point of intercept in Figure \ref{fig:calibration_voltage}), for this reason the comparisons will be made at $80$ V, unless otherwise specified. \\
+In order to verify the ability to drive the Mask Aligner with the new electronics, test measurements of both the new Walker and the RHK were performed. For the Mask Aligner a voltage of $80$ V was determined to be the optimum voltage to run experiments (see point of intercept in Figure \ref{fig:calibration_voltage}), for this reason the comparisons will be made at $80$ V, unless specified otherwise. \\
 A measurement of the slow flank, without any attached load, is shown in Figure (\ref{fig:walker_pulse_shape_slow}).  The Walker keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walker's pulse. The Walker compares favorably to the RHK. It has a more consistent peak shape and its peak voltage corresponds to the one given as a parameter more closely than the RHK. It both under- and overshoots the specified $80$ V, by up to $\approx20$ V. The walker pulses are also more symmetric around the fast flank than the one from the RHK. Both the Walker and the RHK show no aliasing artifacts. Steps visible in Figure \ref{fig:walker_pulse_shape_slow} are due to the limited resolution of the oscilloscope (see Fig. \ref{fig:walker_pulse_shape_fast}). Given this data the Walker seems to outperform the RHK in the unloaded state and should give the same, or a better driving behavior than the RHK.
 
 \begin{figure}[H]
@@ -170,11 +171,11 @@ A measurement of the slow flank, without any attached load, is shown in Figure (
     \includegraphics[width=\textwidth]{img/Plots/Walker/WalkerRetract.pdf}
     \caption{}
     \end{subfigure}
-    \caption{Plots showing both an approach step (a) and a retract step (b) for the new Walker device \textcolor{tab_red}{(red)} and for comparison the RHK in \textcolor{tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor{tab_green}{green} lines show a timeframe of 1000 $\mu$s around the fast flank, which should be the length of 1 pulse exactly.}
+    \caption{(a) approach step and a (b) retract step for the new Walker device \textcolor{tab_red}{(red)} and for comparison the RHK in \textcolor{tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor{tab_green}{green} lines show a timeframe of 1000 $\mu$s around the fast flank, which should be the length of 1 pulse exactly.}
     \label{fig:walker_pulse_shape_slow}
 \end{figure}
 
-The slow flank was also measured for both the RHK and the Walker, again in an unloaded state. The results can be seen in Figure (\ref{fig:walker_pulse_shape_fast}). The fast flank of the walker is more stable showing no signs of peaking, and it saturates at the desired voltage of 80 V, while the RHK signal over/undershoots the desired voltage, by about 20 V, before going back down/up. The Walker's fast flank drops from $80$ to $-80$ within $\approx 0.5 \mu$s. The RHK needs nearly $\approx 2 \mu$s on the falling flank and the Walker takes $\approx 1.7 \mu$s to reach $80$ V for the rising slope, while the RHK takes $\approx 2.2 \mu$s. Until the Walker signal fully stabilizes at the desired voltage, another $\approx 1 \mu$s passes for the falling/rising flank, where the falling flank has the stronger undershoot/ringing. The RHK signal does not stabilize for another $\approx 2 \mu$s at least. As before, the Walker either meets or outperforms the RHK in its pulse shape behavior and should thus drive the piezo motors appropriately.
+The slow flank was also measured for both the RHK and the Walker. No load was connected. The results can be seen in Figure (\ref{fig:walker_pulse_shape_fast}). The fast flank of the walker is more stable showing no signs of peaking, and it saturates at the desired voltage of 80 V, while the RHK signal over/undershoots the desired voltage, by about 20 V, before going back down/up. The Walker's fast flank drops from $80$ to $-80$ within $\approx 0.5 \mu$s. The RHK needs nearly $\approx 2 \mu$s on the falling flank and the Walker takes $\approx 1.7 \mu$s to reach $80$ V for the rising slope, while the RHK takes $\approx 2.2 \mu$s. Until the Walker signal fully stabilizes at the desired voltage, another $\approx 1 \mu$s passes for the falling/rising flank, where the falling flank has the stronger undershoot/ringing. The RHK signal does not stabilize for another $\approx 2 \mu$s at least. As before, the Walker either meets or outperforms the RHK in its pulse shape behavior and should thus drive the piezo motors appropriately.
 
 \begin{figure}[H]
     \centering
@@ -186,11 +187,11 @@ The slow flank was also measured for both the RHK and the Walker, again in an un
     \includegraphics[width=\textwidth]{img/Plots/Walker/WalkerRetract_ff.pdf}
     \caption{}
     \end{subfigure}
-    \caption{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both approach (a) and retract (b), for a nominal voltage of 80 V (without load). }
+    \caption{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both (a) approach and (b) retract, for a nominal voltage of 80 V (without load). }
     \label{fig:walker_pulse_shape_fast}
 \end{figure}
 
-\subsection{Driving the Mask Aligner}
+\subsection{Operation with the Mask Aligner}
 The communication diagram with the Walker looks slightly different from the one in Figure \ref{fig:diagram_MA_circ}. The RHK relay is no longer needed since the Walker can take over its function. The new diagram can be seen in Figure \ref{fig:diagram_MA_circ_walker}
 
 \begin{figure}[H]
diff --git a/chap04.aux b/chap04.aux
index f420477f73b3866a9c9ec1c525f6a8e1dd404567..546c2fc5edf37cad4f00456ca3839ddf7e8cc5d2 100644
--- a/chap04.aux
+++ b/chap04.aux
@@ -5,83 +5,83 @@
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
 \@writefile{toc}{\contentsline {section}{\numberline {4.1}Overview}{51}{section.4.1}\protected@file@percent }
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+\newlabel{fig:solder_anchors_diagram}{{4.2}{53}{(\subref {fig:solder_anchors_diagram_base}) solder anchor interfering with the prism due to deterioration over time. (\subref {fig:solder_anchors_diagram_SmallerDot}) making the solder dot smaller. (\subref {fig:solder_anchors_diagram_AlO}) replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate. (\subref {fig:solder_anchors_diagram_GlueTop}) putting the anchor with glue on the top/bottom of the solder ceramic. The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray}{figure.caption.67}{}}
+\newlabel{fig:solder_anchors_examples_shear_01}{{4.3a}{54}{\relax }{figure.caption.68}{}}
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 \citation{Olschewski}
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-\newlabel{fig:calibration_after_repair}{{4.11}{64}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.77}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing.}}{55}{figure.caption.69}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{4.4}{55}{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing}{figure.caption.69}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $.}}{56}{figure.caption.70}\protected@file@percent }
+\newlabel{fig:Z3_after reglue}{{4.5}{56}{The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $}{figure.caption.70}{}}
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+\newlabel{fig:Z3_screw_rot}{{4.6}{57}{Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after}{figure.caption.71}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{57}{subsection.4.5.1}\protected@file@percent }
+\citation{Olschewski}
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+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{59}{\relax }{figure.caption.73}{}}
+\newlabel{fig:Front_plate_repair_plate}{{4.8b}{59}{\relax }{figure.caption.73}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{59}{\relax }{figure.caption.73}{}}
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+\newlabel{fig:Front_plate_repair}{{4.8}{59}{(\subref {fig:Front_plate_repair_tool}) Solidworks explosive diagram of the Z3 front plate with the alignment tool. (\subref {fig:Front_plate_repair_plate}) final front plate assembled}{figure.caption.73}{}}
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+\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{61}{\relax }{figure.caption.75}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{61}{\relax }{figure.caption.75}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces Left (\subref  {fig:Feedthrough_Repairs_left}) and right (\subref  {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding.}}{61}{figure.caption.75}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs}{{4.10}{61}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.75}{}}
+\@writefile{tdo}{\contentsline {todo}{Here}{61}{section*.76}\protected@file@percent }
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+\newlabel{tab:cross_cap_after_repair}{{4.1}{61}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. Values were measured at $0.3$ mm sample distance, optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.77}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{61}{section.4.7}\protected@file@percent }
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+\newlabel{fig:calibration_after_repair}{{4.11}{62}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.78}{}}
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diff --git a/chap04.tex b/chap04.tex
index 9dcf33355dc88f7ebc5baa91139784fa33085c45..83523af38e96c4a77f7f003c1648b13969994538 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -2,7 +2,7 @@
 \chapter{Mask Aligner repairs and optimizations}
 \section{Overview}
 
-The Mask Aligner was built in 2015~\cite{Olschewski}. Since then some problems had developed with the Mask Aligner and its performance was limited. In order to alleviate and prevent further problems, repairs had to be performed on several of the piezo motor stacks. The following chapter will detail the repairs and optimizations that were performed on the Mask Aligner. 
+The Mask Aligner was built in 2015, during the master thesis of Tim Olscchewski~\cite{Olschewski}. Since then some problems had developed with the Mask Aligner that limited its performance. In order to alleviate and prevent further problems, repairs had to be performed on several of the piezo motor stacks. The following chapter will detail the repairs and optimizations that were performed on the Mask Aligner. 
 
 \begin{figure}[H]
     \centering
@@ -23,21 +23,22 @@ The Mask Aligner was built in 2015~\cite{Olschewski}. Since then some problems h
 The nomenclature for the piezo motors used in the following is described in Figure \ref{fig:Repair_Diagram_diagram}. It shows  for the different parts of a single motor. Figure \ref{fig:Repair_Diagram_image} shows a photo with a similar configuration as the diagram to make clear what it corresponds to.
 
 \section{General UHV device preparation}
-\subsection{Adding components}
-When adding components to a UHV device, especially machined parts, a cleaning procedure has to be followed to ensure the part does not strongly outgass in the UHV environment. When working on steel and other materials, workshops use oils that heavily outgass in UHV environments. Before using any components that were treated beforehand, like store bought screws or nuts, and any components for which the cleanliness is unknown, the following cleaning procedure should be followed:
-\begin{enumerate}
-	\item Submerge the component in demineralized water mixed with laboratory grade cleaning detergent and put it in the ultrasonic bath for 10 minutes. This step is to wash off any oils and greases on the component's surface.
-	\item Remove the component from the beaker and taking a clean beaker, repeat the same step with demineralized water without any detergent.
-	\item Repeat the previous step with pure acetone
-	\item Repeat the previous step with IPA
-\end{enumerate} 
-The properly cleaned component can now be used in parts that are permanently exposed to vacuum.
-
-Only materials that have been cleared for use in UHV environments should be used. Especially materials that leave residues, like adhesive tapes, should be chosen with this in mind. 
-
-\subsection{Soldering}
-When soldering any part that is exposed to UHV only solder tins, which are cleared for use in UHV environments, should be used. The soldering irons for UHV use should never be used with non-UHV solder, in order to ensure no non-UHV solder may be deposited on UHV components. This means that no solder containing lead can be used. \\
-When using flux, the flux has to be cleaned off thoroughly to avoid outgassing as well as short-circuiting from stray flux. The following steps have to be followed:
+%\subsection{Adding components}
+%When adding components to a UHV device, especially machined parts, a cleaning procedure has to be followed to ensure the part does not strongly outgass in the UHV environment. When working on steel and other materials, workshops use oils that heavily outgass in UHV environments. Before using any components that were treated beforehand, like store bought screws or nuts, and any components for which the cleanliness is unknown, the following cleaning procedure should be followed:
+%\begin{enumerate}
+%	\item Submerge the component in demineralized water mixed with laboratory grade cleaning detergent and put it in the ultrasonic bath for 10 minutes. This step is to wash off any oils and greases on the component's surface.
+%	\item Remove the component from the beaker and taking a clean beaker, repeat the same step with demineralized water without any detergent.
+%	\item Repeat the previous step with pure acetone
+%	\item Repeat the previous step with IPA
+%\end{enumerate} 
+%The properly cleaned component can now be used in parts that are permanently exposed to vacuum.
+%
+%Only materials that have been cleared for use in UHV environments should be used. Especially materials that leave residues, like adhesive tapes, should be chosen with this in mind. 
+
+\subsection{UHV compatible Soldering}
+When soldering any part that is exposed to UHV only solder tins, which are cleared for use in UHV environments, should be used. The soldering irons for UHV use should never be used with non-UHV solder. This means that no solder containing lead can be used. \\
+Since flux can splash when heated, surrounding components have to be shielded.
+The uses flux has to be cleaned off thoroughly to avoid outgassing as well as short-circuiting from stray flux. The following steps have to be followed:
 \begin{enumerate}
 	\item Using laboratory cleaning swabs and demineralized water mixed with laboratory detergent the surface that was solder on should be cleaned thoroughly, but carefully. After cleaning with the laboratory swab, rinse the surface.
 	\item The previous step should be repeated with demineralized water without any detergent
@@ -46,10 +47,10 @@ When using flux, the flux has to be cleaned off thoroughly to avoid outgassing a
 \end{enumerate}
 
 \section{Soldering anchors} \label{ch:solder_anchors}
-The soldering anchor points that were previously used on the Mask Aligner are small ($2$ mm x $2$ mm x $6$ mm) ceramic pieces onto which a small piece of copper, pre-coated with solder, was glued using non-conductive EPO-TEK H70E. All cables coming from the piezo motors can be soldered to this soldering anchor. This allows usage of shorter cables and for the cables to be more cleanly routed. The Ceramic piece was glued to the surface of the Mask Aligner using the same glue.\\
+The soldering anchor points that were previously used on the Mask Aligner are small ($2$ mm x $2$ mm x $6$ mm) \ce{Al2O3} ceramic pieces onto which a small piece of copper, pre-coated with solder, was glued using non-conductive EPO-TEK H70E. All cables coming from the piezo motors can be soldered to this soldering anchor. This allows usage of shorter cables and for the cables to be more cleanly routed. The Ceramic piece was glued to the surface of the Mask Aligner using the same glue.\\
 
-EPO-TEK H70E is recommended to cure at $150$°C for at least 1 hour. For repairs would be difficult and dangerous to heat the entire Mask Aligner to $150$°C, since the piezo stacks depolarize at temperatures near $150$°C. It is also difficult to heat the glue locally to $150$°C. Due to this it was determined that a different glue should be used. \\
-Torr Seal was determined to have all the necessary qualities and was used as a replacement universally. Torr Seal is a two component epoxy, that can cure at room temperature. It fulfills UHV outgassing requirements\todo{Cite Torrseal data}. It however has the disadvantage of reaching its flash point at $175$°C. For this reason soldering on anything affixed with Torr Seal should be done with care as prolonged exposure to the heat of a soldering iron will lead to deterioration. Also of note is that Torr Seal cannot operate at temperatures below $-45$°C, so usage in a very low temperature environment is no longer possible. This is not an issue since the Mask Aligner is not intended for use in cooled environments.\\ 
+EPO-TEK H70E is recommended to cure at $150$°C for at least 1 hour. For repairs it would be difficult and dangerous to heat the entire Mask Aligner to $150$°C, since the piezo stacks depolarize at temperatures near $150$°C. It is also difficult to heat the glue locally to $150$°C. Due to this it was determined that a different glue should be used. \\
+Torr Seal was determined to have all the necessary qualities and was used as a replacement universally. Torr Seal is a two component epoxy, that can cure at room temperature. It fulfills UHV outgassing requirements\todo{Cite Torrseal data}. It however has the disadvantage of reaching its flash point at $175$°C. For this reason soldering on anything affixed with Torr Seal should be done with care as prolonged exposure to the heat of a soldering iron will lead to deterioration. Also of note is that Torr Seal cannot operate at temperatures below $-45$°C, so usage in a very low temperature environment is no longer possible. \\ 
 
 \begin{figure}[H]
     \centering
@@ -77,13 +78,13 @@ Torr Seal was determined to have all the necessary qualities and was used as a r
     \label{fig:solder_anchors_diagram}
 \end{figure}
 
-However, over time and usage the glue on some of the soldering anchors had loosened to the point that the solder dots connecting the cables and the anchor were sticking out from the surface of the Mask Aligner. Sometimes to the point of interfering with the Sapphire Prism. This caused the mask stage to frequently get stuck, when driving the piezo motors. The Problem situation is depicted in Figure (\ref{fig:solder_anchors_diagram_base}).
+Over time the glue on some of the soldering anchors had deteriorated. The solder dots were not held in place anymore. Sometimes this caused additional friction with the Sapphire Prism, which caused the mask stage to frequently get stuck. The Problem situation is depicted in Figure (\ref{fig:solder_anchors_diagram_base}).
 This problem would culminate in the motor Z1 getting completely stuck, when driven down to mask extraction height. \\
 
-In order to optimize this behavior, the following 3 actions can be taken.
-First, the size of solder on the anchor can be reduced until it no longer interferes. This process often involved re-soldering the respective cable, since carving away material without disconnecting the cable often proved impossible. This was done when the anchor has not lost adhesion to the MA body. This is pictured in Figure (\ref{fig:solder_anchors_diagram_SmallerDot}). \\
+In order to optimize this behavior, the following 3 actions are possible.
+First, the size of the solder joint on the anchor can be reduced until it no longer interferes. This process often involved re-soldering the respective cable, since carving away material without disconnecting the cable often proved impossible. This was done when the anchor has not lost adhesion to the MA body. This is pictured in Figure (\ref{fig:solder_anchors_diagram_SmallerDot}). \\
 
-Another procedure is to completely replace the soldering anchor with a much thinner \ce{Al2O3} plate. The size of the solder dot can in this case be quite large before interfering. When the solder ceramic was no longer stably attached to the Mask Aligner body this procedure is used (\ref{fig:solder_anchors_diagram_AlO}). \\ 
+Another procedure is to completely replace the soldering anchor with a $1$ mm \ce{Al2O3} thick plate. The size of the solder dot can in this case be quite large before interfering. When the solder ceramic was no longer attached sufficiently to the Mask Aligner body this procedure is used (\ref{fig:solder_anchors_diagram_AlO}). \\ 
 
 The third procedure is to glue the soldering anchor on the top/bottom side of the ceramic. Care has to be taken that the layer of glue between the walls of the Mask Aligner and the anchor is thick enough to provide proper insulation. This last solution is inelegant, but was used as a quick optimization. The functional solder anchor could often be reused without having to detach all cables. This can be seen in Figure (\ref{fig:solder_anchors_diagram_GlueTop}). \\
 
@@ -113,18 +114,16 @@ The third procedure is to glue the soldering anchor on the top/bottom side of th
         \caption{}
         \label{fig:solder_anchors_examples_AlO}
     \end{subfigure}
-    \caption{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref{fig:solder_anchors_examples_shear_01}) and  shows the initial state of a solder ceramic interfering with the prism. (\subref{fig:solder_anchors_examples_shear_02}) shows the solder ceramic from before after some of the solder was carefully taken off. (\subref{fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref{fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce{Al2O3} plate. }
+    \caption{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref{fig:solder_anchors_examples_shear_01}) initial state of a solder ceramic interfering with the prism. (\subref{fig:solder_anchors_examples_shear_02}) solder ceramic from before after some of the solder was carefully taken off. (\subref{fig:solder_anchors_examples_glue_bottom}) a solder anchor attached to the bottom of a previously used solder ceramic. (\subref{fig:solder_anchors_examples_AlO}) replacement of a solder ceramic with a thinner \ce{Al2O3} plate. }
     \label{fig:solder_anchors_examples}
 \end{figure}
 
 Examples for all the different measures taken on the Mask Aligner can be seen in Figure \ref{fig:solder_anchors_examples}
-Figure \ref{fig:solder_anchors_examples_AlO} is a somewhat inelegant example, since the Torr Seal use is a bit excessive. It was very difficult to apply constant pressure at the angle given. This is also the reason why the new anchor is placed differently. In this instance the problem was not that the solder anchor interference, but the glue on the old ceramic no longer holding. Due to remaining glue on the solder ceramic, gluing a new solder anchor proved difficult, since the glue sticks poorly to glue residue.
-
 All motors were checked for soldering anchor points that could potentially interfere with the prism. One of these actions was taken for all ceramics where problems could be found. An example for a problematic anchor is shown in Figure \ref{fig:solder_anchors_examples_shear_01}. The state after taking of some of the solder is shown in Figure \ref{fig:solder_anchors_examples_shear_02}\\
-After this step, the prisms would no longer get stuck when driving and could cleanly drive the whole range of possible motion. A lot of the solder ceramics were no longer attached well, due to this in future others might fail. To ensure correct driving it is recommended that all solder ceramics, not just interfering ones, should be replaced. This however goes beyond the work in this thesis. \\
+After these repairs, the prisms would no longer get stuck when driving and could move the whole range of possible motion. Not all ceramics were replaced and deterioration of the glue is likely to cause similar problems in the future. To ensure correct driving it is recommended that all solder ceramics should be replaced. This however goes beyond the scope of this thesis. \\
 
-\section{Piezo re-gluing} \label{sec:piezo_reglue}
-The piezo stacks in the Mask Aligner were also glued in 2015 with the non-conductive EPO-TEK H70E glue~\cite{Olschewski}. For this reason, $2$ of the piezo stacks, one on motor Z1 and one on Motor Z3, had completely detached. These stacks needed to be re-glued to the surface of the Mask Aligner Body. \\
+\section{Piezo regluing} \label{sec:piezo_reglue}
+The piezo stacks in the Mask Aligner were also glued in 2015 with the non-conductive EPO-TEK H70E glue~\cite{Olschewski}. For this reason, $2$ of the piezo stacks, one on motor Z1 and one on Motor Z3, had completely detached. These stacks needed to be reglued to the Mask Aligner Body. \\
 
 \begin{figure}[H]
     \centering
@@ -152,14 +151,14 @@ The piezo stacks in the Mask Aligner were also glued in 2015 with the non-conduc
     	\caption{}
 		\label{fig:Z3_reglue_process_down}
     \end{subfigure}
-    \caption{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) shows detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of Torr Seal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment.}
+    \caption{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing.}
     \label{fig:Z3_reglue_process}
 \end{figure}
 
-Torr Seal was used for this again. Tests and the datasheet showed that Torr Seal has similar elastic properties to H70E. The right size for a glue dot was determined via testing of spread and comparison with previous glue dot size. \\
+Torr Seal was used again. Tests and the data sheet showed that Torr Seal has similar elastic properties to H70E. The right size for a glue dot was determined via testing of spread and comparison with previous glue dot size. These properties needed to be determined so that the piezo could be attached in proper alignment with the surrounding piezos.\\
 
-To perform the actual gluing of the piezo stack, all traces of remaining glue were scratched off the surface of the affected piezo stack (Fig. \ref{fig:Z3_reglue_process_scratched}). Afterward a small dot of Torr Seal was put on the underside of the piezo stack, and it was carefully put in place (Fig. \ref{fig:Z3_reglue_process_dot}). The Mask Aligner was rotated with a clamp so that gravity kept the piezo stack in the place. In order to provide pressure on the piezo stack, the prism was reinserted into the motor and was weighed down with comparatively large nuts (Fig. \ref{fig:Z3_reglue_process_down}). The entire process can be seen in Figure \ref{fig:Z3_reglue_process}.\\ 
-The repair of the piezo on motor Z1 happened without problems, but on motor Z3 the piezo turned by about $\approx 4.5^\circ \pm 0.5^\circ$ during the curing process. Since $\cos(5^\circ) \approx 0.996$ this should not significantly affect the performance of the Z3 motor.
+To perform the actual gluing of the piezo stack, all traces of remaining glue were scratched off the surface of the affected piezo stack (Fig. \ref{fig:Z3_reglue_process_scratched}). Afterward a small dot of Torr Seal was put on the underside of the piezo stack, and it was carefully put in place (Fig. \ref{fig:Z3_reglue_process_dot}). The Mask Aligner was rotated with a clamp so that gravity kept the piezo stack in the place. In order to provide pressure on the piezo stack, the prism was reinserted into the motor and was weighed down. (Fig. \ref{fig:Z3_reglue_process_down}). The entire process can be seen in Figure \ref{fig:Z3_reglue_process}.\\ 
+The repair of the piezo on motor Z1 happened without problems, but on motor Z3 the piezo turned by about $\approx 4.5^\circ \pm 0.5^\circ$ during the curing process. Since $\cos(5^\circ) \approx 0.996$ this should affect the performance by less than $0.5$ \%.
 
 \begin{figure}[H]
     \centering
@@ -178,15 +177,15 @@ After repairs, the motors Z1 and Z2 were performing as expected, but the motor Z
     \label{fig:Z3_screw_rot}
 \end{figure}
 
-This led to the conclusion, that Z3 had some sort of alignment issue. Sometimes randomly all the motors were in line with the prism and could drive at the appropriate power, while sometimes one of the motors would lose contact with the prism. 
+This led to the conclusion that Z3 had some sort of alignment issue. Sometimes randomly all the motors were in line with the prism and could drive at the appropriate power, while sometimes one of the motors would lose contact with the prism. 
 The cause of this was hypothesized to be the front plate of the Z3 motor. For this reason, the front plate had to be repaired.
 
 \subsection{Front plate repair}
-In order to test the hypothesis, that the front plate of motor Z3 was causing the issues, the front plate of Z3 was exchanged for the front plate of motor Z1. Re-soldering all the cables of the front plate to the solder anchors, in order to swap plates, would put the glue of the solder anchors at risk of failing. This detaching and reattaching needed to be done multiple times in order to do the full check. In order to prevent risks, new longer copper cables were created and the front plate of Z3 was directly connected to the vacuum feedthrough pins. After the plates were swapped the issues with motor Z3 were no longer observed (Fig. \ref{fig:Z3_screw_rot} \textcolor{tab_green}{green} and \textcolor{tab_red}{red} against \textcolor{tab_blue}{blue} and \textcolor{tab_orange}{orange}). \\
+In order to test the hypothesis, that the front plate of motor Z3 was causing the issues, the front plate of Z3 was exchanged for the front plate of motor Z1. Re-soldering all the cables of the front plate to the solder anchors, in order to swap plates, would put the glue of the solder anchors at risk of failing. In order to prevent these risks, new longer copper cables were created and the front plate of Z3 was directly connected to the vacuum feedthrough pins. After the plates were swapped the issues with motor Z3 were no longer observed (Fig. \ref{fig:Z3_screw_rot} \textcolor{tab_green}{green} and \textcolor{tab_red}{red} against \textcolor{tab_blue}{blue} and \textcolor{tab_orange}{orange}). \\
 
-The performance of Z3 became more in line with the other $2$ motors. The performance was in the firmer screw regime lower than that of Z2. In the regime of normal operation (about 2-3 screw rotation in Figure \ref{fig:Z3_screw_rot_after_rep}) the performance became very similar. The difference in this regime was determined to be not significant enough to require any more intervention. \\
+The performance of Z3 became more in line with the other $2$ motors. The performance was in the firmer screw regime lower than that of Z2. In the regime of normal operation (about 2-3 screw rotation in Figure \ref{fig:Z3_screw_rot_after_rep}) the performance became similar (Fig. \ref{fig:Z3_screw_rot}). \\ %The difference in this regime was determined to be not significant enough to require any more intervention. \\
 
-The problem on the Z3 front plate was likely a misalignment on one of the piezo stacks on the plate, leading to a slight shift of it on one of the sides. To check for the unevenness of the surface, tests were performed, where the top of the piezo stacks was coated with color and then the plate was placed on a \ce{Al3O2} plate and moved in motor movement direction. This test was performed for both motor movement directions and repeated several times. For all cases, the color remained on the same piezo, suggesting improper alignment. \\
+The problem on the Z3 front plate was a misalignment on one of the piezo stacks on the plate, leading to it shifting over time. To check for the unevenness of the surface, tests were performed, where the top of the piezo stacks was coated with color and then the plate was placed on a \ce{Al3O2} plate and moved in motor movement direction. This test was performed for both motor movement directions and repeated several times. For all cases, the color remained on the same piezo, suggesting improper alignment. \\
 
 \begin{figure}[H]
     \centering
@@ -195,14 +194,14 @@ The problem on the Z3 front plate was likely a misalignment on one of the piezo
     \label{fig:Z3_screw_rot_after_rep}
 \end{figure}
 
-The piezo stacks were taken off the front plate. Two of the ten replacement piezos would be glued to the surface of the plate in order to function as the new plate. An alignment tool was produced by the workshop. A Solidworks image of the alignment tool can be seen in Figure \ref{fig:Front_plate_repair_tool} \\
-Since the plate is separate from the rest of the Mask Aligner, the plate could be cured inside an oven at $150$°C easily. For this reason it was decided, that EPO-TEK H70E would be used, since this was used previously and would result in a quicker curing time as well as more similarity to the other $2$ front plates. \\
+The piezo stacks were taken off the front plate. Two of the ten replacement piezos were glued to the surface of the old steel plate. An alignment tool was produced by the workshop. A Solidworks image of the alignment tool can be seen in Figure \ref{fig:Front_plate_repair_tool} \\
+EPO-TEK H70E was used to glue the piezos, since this was done for the other front plates in the past~\cite{Olschewski}. \\
 
-During the gluing process, a mistake was made, that was only noticed after curing. During the setup of the new front plate it was assumed, that the replacement piezos and the original piezos of the Mask Aligner were identical. Both sides of the piezos used originally were polished, so that they can be used as sliding surfaces, but the replacement piezos have only one sliding surface. This can be seen in the different texture of the top and bottom piezo stacks in Figure \ref{fig:Front_plate_repair_plate}. This could potentially negatively affect the performance of the new front plate. \\
+Unfortunately during the repairs it was not noticed that the replacement piezos were not identical to the old ones. Both sides of the old piezos were polished, so that they can be used as sliding surfaces, but the replacement piezos have only one sliding surface. This can be seen in the different texture of the top and bottom piezo stacks in Figure \ref{fig:Front_plate_repair_plate}. \\
 
-The solder ceramics on the front plate had to be detached for the creation of the new front plate, as the alignment tool was designed without them in mind. This was not an issue however as they had similar problems to the other solder ceramics in previous sections. The ceramics were replaced with a long \ce{Al2O3} plate, which was attached using Torr Seal. The results of the full assembly of the front plate can be seen in Figure \ref{fig:Front_plate_repair_plate}. \\
+The solder ceramics on the front plate had to be detached for the creation of the new front plate, as the alignment tool was designed without them in mind. This was not an issue however as they had similar problems to the other solder ceramics in previous sections. The ceramics were replaced with a long \ce{Al2O3} plate, which was attached using Torr Seal. The results can be seen in Figure \ref{fig:Front_plate_repair_plate}. \\
 
-In testing with the newly made front plate, the performance of Z3 was comparable with Z2, although it had a slightly larger deviance between approach and retract movement and a slightly decreased performance for very firm screw configuration. Regardless, the difference in performance was deemed to be insignificant as a point of common step size could be found (Figure \ref{fig:Z3_screw_rot_after_rep}). In the range of 2.5 screw rotations the performance matched between Z2 and Z3 and thus this screw setting was chosen for optimization of these 2 motors. Z1 was then compared to both motors and a similar screw setting was chosen for it as well. 
+While testing the newly made front plate, the performance of Z3 was comparable with Z2, although it had a larger deviance between approach and retract movement and a decreased performance for very firm screw configuration (Fig. \ref{fig:Z3_screw_rot_after_rep}). Regardless, the difference in performance was deemed to be insignificant as a point of common step size could be found (Fig. \ref{fig:Z3_screw_rot_after_rep}). In the range of 2.5 screw rotations the performance matched between Z2 and Z3 and thus this screw setting was chosen for optimization of these 2 motors. Z1 was then compared to both motors and a similar screw setting was chosen for it as well. 
 
 \begin{figure}[H]
     \centering
@@ -218,18 +217,16 @@ In testing with the newly made front plate, the performance of Z3 was comparable
 	    \caption{}
 		\label{fig:Front_plate_repair_plate}
     \end{subfigure}
-    \caption{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref{fig:Front_plate_repair_tool}). (\subref{fig:Front_plate_repair_plate}) shows final front plate assembled.}
+    \caption{(\subref{fig:Front_plate_repair_tool}) Solidworks explosive diagram of the Z3 front plate with the alignment tool. (\subref{fig:Front_plate_repair_plate}) final front plate assembled.}
     \label{fig:Front_plate_repair}
 \end{figure}
 
-In order to prevent the longer cables of the front plates of Z1 and Z3 from interfering with Mask Aligner operation, the cables were guided around the Mask Aligner body. This includes in particular not being within the field of vision of the camera pointed at the sample as well as not interfering with the wobble stick path. For this reason the cables of Z1 were moved towards the left side, when viewing Z1 from the front, and then guided to the top of the Mask Aligner body, close to the X piezo and from there to the vacuum feed through pins. Z3 was guided to the upper side of the stoppers and then directly to the vacuum feed through pins. In order to ensure the cables would not move from these positions, they were glued in place using Torr Seal.
-
-\todo{Maybe image}
+The new cables were bend and glued in place with Torr Seal to avoid interfering with the sample/mask insertion path and the camera.
 
 \subsection{Small capacitance stack}
-During the investigation of the Z3 motor, the capacitance values for the piezo stacks of the Z3 motors were measured. The motor that was re-glued in Section \ref{sec:piezo_reglue} has a lower capacitance value than the surrounding piezo stacks. The value of $1.05$ nF is lower by approximately the amount a single piezo has of $0.4$ nF from the expected $1.6 \pm 0.4$ nF. The different capacitances measured for all the piezo stacks can be seen in Figure \ref{fig:Z3_weaker_stack}. The piezo stacks both showing $1.62$ nF were only measured together since they were always wired in parallel. The plate stacks were also only measured together. \\
+During the investigation of the Z3 motor, the capacitance values for the piezo stacks of the Z3 motors were measured. The motor that was reglued in Section \ref{sec:piezo_reglue} has a lower capacitance value than the surrounding piezo stacks. The value ($1.05$ nF) is lower by approximately the amount a single piezo layer ($0.4$ nF) has. The different capacitances measured for all the piezo stacks can be seen in Figure \ref{fig:Z3_weaker_stack}. The piezo stacks both showing $1.62$ nF were only measured together since they were always wired in parallel. The plate stacks were also only measured together. \\
 
-This indicates, that one of the piezo layers depolarized. This could cause the deviance in the driving behavior of Z3 at low screw firmness. It should be born in mind since it might cause problems with Z3 in the future. It might also be the reason Z3 is more prone to failures.
+This indicates, that one of the piezo layers depolarized. This could cause the deviation in the driving behavior of Z3 at low screw firmness. It should be born in mind since it might cause problems with Z3 in the future. It might also be the reason Z3 is more prone to failures.
 
 \begin{figure}[H]
     \centering
@@ -239,7 +236,7 @@ This indicates, that one of the piezo layers depolarized. This could cause the d
 \end{figure}
 
 \section{Feed through cabling optimizations}
-A last step of optimization that was performed was on the feedthrought cables. The cables for the capacitance signals are coaxial cables with a shielding to prevent stray capacitances. These cables were very and only one of the cables shieldings was grounded on the feedthrough side. The length also made insertion into UHV more difficult since the cable could easily be caught behind the copper gaskets. The shielding was instead ground on the Mask Stage side to the Mask Aligner Body. The shielding was also stripped from a large part of the cable near the feedthrough exposing the cable near the metal body of the feedthrough flange.
+A last step of optimization that was performed was on the feedthrought cables. The cables for the capacitance signals are coaxial cables with a shielding to prevent stray capacitances. Only one of the cables shieldings was grounded on the feedthrough side. The length also made insertion into UHV more difficult since the cable could easily be caught behind the copper gaskets. The shielding was instead grounded on the Mask Stage side to the Mask Aligner Body. The shielding was also stripped from a large part of the cable exposing it unnecessarily.
 
 \begin{figure}[H]
     \centering
@@ -257,7 +254,9 @@ A last step of optimization that was performed was on the feedthrought cables. T
     \label{fig:Feedthrough_Repairs}
 \end{figure}
 
-In order to reduce possible interference to the signal, the cables were shortened and were properly ground on the feedthroughs. In order to connect to the body of the feedthroughs, a female gold pin was soldered to the inside of the feedthrough. The male end was soldered to the coaxial cable shielding with a short copper cable. This is easier than soldering the shielding to the body directly. A large solder amount of solder is required to properly stick to the smooth steel surface. Only the small section near the gold pins is now without shielding.\\
+In order to reduce capacitance noise, the cables were shortened and were grounded on the feedthroughs. To connect to the body of the feedthroughs, a female gold pin was soldered to the inside of the feedthrough. The male end was soldered to the coaxial cable shielding with a short copper cable. Only a small section of cable was left unshielded\\
+
+\todo{Here}
 
 \begin{table}[H]
 \centering
@@ -269,7 +268,7 @@ Mask 1 before & $7.11 \pm 0.02$      & $3.20 \pm 0.12$       & $0.19 \pm
 Mask 1 after  & $7.11 \pm 0.03$      & $3.37 \pm 0.14$       & $0.06 \pm
 0.08$        \\ \hline
 \end{tabular}
-\caption{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}
+\caption{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. Values were measured at $0.3$ mm sample distance, optically determined with Bresser MicroCam II and MikroCamLabII.}
 \label{tab:cross_cap_after_repair}
 \end{table}
 
diff --git a/chap05.aux b/chap05.aux
index 8408bfec421aeebfbd5007c8f180d06a129f055e..cb57298c5756013e8dff88ad7a1b70dbc9fd1789 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -1,101 +1,101 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{\numberline {5}Evaporations and measurement}{65}{chapter.5}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{\numberline {5}Evaporations and measurement}{63}{chapter.5}\protected@file@percent }
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
-\@writefile{toc}{\contentsline {section}{\numberline {5.1}Evaporation configuration}{65}{section.5.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {5.1}{\ignorespaces The approach curve measured for field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference, C1 was used for alignment primarily.}}{65}{figure.caption.78}\protected@file@percent }
-\newlabel{fig:evaporation_approach_curve}{{5.1}{65}{The approach curve measured for field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference, C1 was used for alignment primarily}{figure.caption.78}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}}{66}{table.caption.79}\protected@file@percent }
-\newlabel{tab:evaporation_settings}{{5.1}{66}{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}{table.caption.79}{}}
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index 6b5714b77b4c94ab60b7265d5edec9011190e753..4f612ccfede892f13de0c2e792db9484bc9c3bc1 100644
--- a/thesis.out
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diff --git a/thesis.pdf b/thesis.pdf
index cfe5343689ac8ad8bc393f4d232e9a0509663b7b..01ee5eaed814d25ebde765811bddf3ebff2cfe35 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index 32b2e9d623c1aa82ab08899158b0bb4e8fd00879..92a3a16aa4ab0bb3920784dc3926bff408c377a6 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.toc b/thesis.toc
index 2f4a8501e427c8d52674322d6a7344c772c14910..e28c0394a3137ed450cbb57e9b1df43089f99484 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -44,76 +44,75 @@
 \contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{44}{section.3.3}%
 \contentsline {subsection}{\numberline {3.3.1}Overview}{44}{subsection.3.3.1}%
 \contentsline {subsection}{\numberline {3.3.2}Signal generation}{44}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Fast flank}{46}{subsection.3.3.3}%
+\contentsline {subsection}{\numberline {3.3.3}Fast flank}{45}{subsection.3.3.3}%
 \contentsline {subsection}{\numberline {3.3.4}Amplification}{46}{subsection.3.3.4}%
-\contentsline {subsection}{\numberline {3.3.5}Parameters}{47}{subsection.3.3.5}%
-\contentsline {paragraph}{Amplitude (amp)}{47}{section*.56}%
-\contentsline {paragraph}{Voltage (volt)}{47}{section*.57}%
-\contentsline {paragraph}{Channel}{47}{section*.58}%
-\contentsline {paragraph}{Max Step}{47}{section*.59}%
-\contentsline {paragraph}{Polarity}{47}{section*.60}%
+\contentsline {subsection}{\numberline {3.3.5}Parameters}{46}{subsection.3.3.5}%
+\contentsline {paragraph}{Amplitude (amp)}{47}{section*.57}%
+\contentsline {paragraph}{Voltage (volt)}{47}{section*.58}%
+\contentsline {paragraph}{Channel}{47}{section*.59}%
+\contentsline {paragraph}{Max Step}{47}{section*.60}%
+\contentsline {paragraph}{Polarity}{47}{section*.61}%
 \contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{47}{subsection.3.3.6}%
-\contentsline {subsection}{\numberline {3.3.7}Driving the Mask Aligner}{49}{subsection.3.3.7}%
+\contentsline {subsection}{\numberline {3.3.7}Operation with the Mask Aligner}{49}{subsection.3.3.7}%
 \contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{51}{chapter.4}%
 \contentsline {section}{\numberline {4.1}Overview}{51}{section.4.1}%
 \contentsline {section}{\numberline {4.2}General UHV device preparation}{52}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}Adding components}{52}{subsection.4.2.1}%
-\contentsline {subsection}{\numberline {4.2.2}Soldering}{52}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering anchors}{53}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo re-gluing}{56}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 motor}{58}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{59}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{62}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{62}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final test}{64}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{65}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{65}{section.5.1}%
-\contentsline {section}{\numberline {5.2}Contamination}{67}{section.5.2}%
-\contentsline {section}{\numberline {5.3}Penumbra}{68}{section.5.3}%
-\contentsline {section}{\numberline {5.4}Tilt and deformation}{73}{section.5.4}%
-\contentsline {section}{\numberline {5.5}Simulation}{76}{section.5.5}%
-\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{76}{subsection.5.5.1}%
-\contentsline {subsection}{\numberline {5.5.2}Results}{78}{subsection.5.5.2}%
-\contentsline {subsection}{\numberline {5.5.3}Software improvements}{82}{subsection.5.5.3}%
-\contentsline {subsection}{\numberline {5.5.4}Final Remark}{83}{subsection.5.5.4}%
-\contentsline {chapter}{Conclusions and Outlook}{84}{chapter*.94}%
-\contentsline {chapter}{Bibliography}{86}{chapter*.95}%
-\contentsline {chapter}{List of Abbreviations}{89}{chapter*.96}%
-\contentsline {chapter}{Appendix}{i}{chapter*.97}%
+\contentsline {subsection}{\numberline {4.2.1}UHV compatible Soldering}{52}{subsection.4.2.1}%
+\contentsline {section}{\numberline {4.3}Soldering anchors}{52}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo regluing}{55}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 motor}{56}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{57}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{59}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{60}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final test}{61}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{63}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{63}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Contamination}{65}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Penumbra}{66}{section.5.3}%
+\contentsline {section}{\numberline {5.4}Tilt and deformation}{71}{section.5.4}%
+\contentsline {section}{\numberline {5.5}Simulation}{74}{section.5.5}%
+\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{74}{subsection.5.5.1}%
+\contentsline {subsection}{\numberline {5.5.2}Results}{76}{subsection.5.5.2}%
+\contentsline {subsection}{\numberline {5.5.3}Software improvements}{80}{subsection.5.5.3}%
+\contentsline {subsection}{\numberline {5.5.4}Final Remark}{81}{subsection.5.5.4}%
+\contentsline {chapter}{Conclusions and Outlook}{82}{chapter*.95}%
+\contentsline {chapter}{Bibliography}{84}{chapter*.96}%
+\contentsline {chapter}{List of Abbreviations}{87}{chapter*.97}%
+\contentsline {chapter}{Appendix}{i}{chapter*.98}%
 \contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
 \contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
 \contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}%
 \contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}%
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-\contentsline {paragraph}{mstep x}{vi}{section*.107}%
-\contentsline {paragraph}{cancel}{vii}{section*.108}%
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+\contentsline {paragraph}{pulse?}{vi}{section*.101}%
+\contentsline {paragraph}{pol x}{vi}{section*.102}%
+\contentsline {paragraph}{amp x}{vi}{section*.103}%
+\contentsline {paragraph}{volt x}{vi}{section*.104}%
+\contentsline {paragraph}{channel x}{vi}{section*.105}%
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+\contentsline {paragraph}{step x}{vi}{section*.107}%
+\contentsline {paragraph}{mstep x}{vi}{section*.108}%
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