conclusion code

Tex/conclusion.tex

@@ -1,5 +1,10 @@
 \chapter{Conclusion and Outlook}
 
+\section{Developed tools for CDI/IDI experiments}
+Both the GPU-accelerated simulation code and the reconstruction code developed for this thesis are open source \footnote{available under \url{https;//github.com/fzimmermann89/idi}} and will be used for planning and analyzing future IDI experiments. The simulation code allows to compare IDI and CDI experiments for the same sample, comparison for different samples and experimental parameters as shown in \fref{chap:simulation}.
+The analysis code implements 2d, 3d and radial correlations for small and wide angle experiments with different normalization approaches as well as library of commonly needed auxiliary functions, such as dark and mask generation for pixel detectors, a new common mode correction with adaptive block sizes, photon counting procedures, different regression tools as well as tools for center finding and similar tasks.
+Furthermore, the Kossel line alignment tool with its graphical user interface allows easy analysis of the detector orientation for future experiments with strict alignment margins.
+
 
 \section{Using Incoherent Imaging for Online Beam Diagnostic}
 
@@ -17,7 +22,6 @@ \section{Using Incoherent Imaging for Online Beam Diagnostic}
 Even just the ability to image to focal volume might be an useful diagnostic tool in certain experiments
 
 
-An avenue for improvement is subpixel resolution of the photon hits and better usage of the varying XXX of the detector to increase the resolution in the reconstruction, as this is currenly limited by the computional intensity to calulate the correlations at higher resolution.
 
 
 \begin{figure}
@@ -29,28 +33,24 @@ \section{Using Incoherent Imaging for Online Beam Diagnostic}
 
 \section{Experimental Improvements}
 
+Recently, we performed an experiment using sub-1\,fs pulses at the CXI beamline at the LCLS free electron laser. In this experiment, three major improvements made over the SACLA experiment: First, the shorter pulse length reduces the number of temporal modes and a shot-by-shot high resolution spectrometer allows for better filtering of the x-ray pulses by estimated pulse length and intensity. Second, the data was recorded in forward direction, solving the undersampling issue and reducing the spatial modes. And third, two new, signal optimized samples were chosen: Anodic aluminum oxide (AAO) membranes with regular spaced 20\,nm or 30\,nm wide pores, with are filled with Nickel or Vanadium using atomic layer deposition, creating an array of hexagonal placed 500\,nm long cylinders 60\,nm/100\,nm apart \cite{carina2019}. As the range of the order of the self-organizing pores is smaller than the total area used in the experiment, the simulated reconstruction shows rings (\fref{fig:outlook_aao}). 
+The other sample is will be lithographically produced gratings with two diffferent pitches, 60\,nm  and 80\,nm \cite{mojarad2015}. For these samples, a simulation is shown in \fref{fig:outlook_grating}. Both samples combine the advantages of a single crystal sample (namely intense features) while providing more signal and requiring less accessible reciprocal space. 
+Based on the simulations, it can be estimated, that a few hundred images taken with sub-fs pulses exciting 20\% of the atoms would suffice to reach a SNR of >3.
+We were able to record full datasets on multiple samples. The data analysis of this experiment has not yet been completed and might result in the first experimental proof of using fluorescence intensity correlation for structural imaging at the nano-scale.  
+
 
 
 \begin{figure}
 	\centering
 	\begin{subfigure}[b]{0.50\textwidth}
-	\includegraphics[width=\linewidth]{images/lv65simA.pdf}
-	\caption{Nano-Grating}
-	\label{fig:outlook_grating}
-\end{subfigure}
-\begin{subfigure}[b]{0.37\textwidth}
-	\includegraphics[width=\linewidth]{images/lv65simB.pdf}
-	\caption{AAO membrane  }
-	\label{fig:outlook_aao}
-\end{subfigure}
-\caption[Simulations in Preparation of LV65 Experiment]{Examples of simulations performed with the tools developed in this thesis in preparation of the LCLS free electron laser experiment LV65, which will use nano-gratings and AAO membranes with metal filled self-organized pores as samples for an IDI measurement. The simulations were used to chose an optimized sample geometry and to estimate the feasibility with respect to the expected SNR. The images shown are the calculated fluorescence intensity correlations between pixels of a quarter of an Jungfrau 4M detector placed at a distance of 70\,cm (grating) and 1\,m (membrane) respectively. The simulated grating has a pitch of 80\,nm, 40\,nm line width and 40\,nm thickness; 20\% excitation and 4 modes were simulated. The AAO membrane has and inter pore distance 105\,nm, the pores are filled with vanadium and 20\% excitation are assumed. For both samples, the average over 100 images is shown.}
+		\includegraphics[width=\linewidth]{images/lv65simA.pdf}
+		\caption{Nano-Grating}
+		\label{fig:outlook_grating}
+	\end{subfigure}
+	\begin{subfigure}[b]{0.37\textwidth}
+		\includegraphics[width=\linewidth]{images/lv65simB.pdf}
+		\caption{AAO membrane  }
+		\label{fig:outlook_aao}
+	\end{subfigure}
+	\caption[Simulations in Preparation of LV65 Experiment]{Examples of simulations performed with the tools developed in this thesis in preparation of the LCLS free electron laser experiment LV65, which will use nano-gratings and AAO membranes with metal filled self-organized pores as samples for an IDI measurement. The simulations were used to chose an optimized sample geometry and to estimate the feasibility with respect to the expected SNR. The images shown are the calculated fluorescence intensity correlations between pixels of a quarter of an Jungfrau 4M detector placed at a distance of 70\,cm (grating) and 1\,m (membrane) respectively. The simulated grating has a pitch of 80\,nm, 40\,nm line width and 40\,nm thickness; 20\% excitation and 4 modes were simulated. The AAO membrane has and inter pore distance 105\,nm, the pores are filled with vanadium and 20\% excitation are assumed. For both samples, the average over 100 images is shown.}
 \end{figure}
-
-Upcoming experiment using sub-1\,fs pulse length as LCLS. 
-For this experiment, two new, signal optimized samples were chosen: Anodic Aluminum Oxide (AAO) membranes with regular spaced XX pores, with are filled with Nickel or Vanadium using atomic layer deposition, creating an array of hexagonal placed  500\,nm long cylinders. As the order of the self-organizing pores is smaller than the area used in the experiment, the simulated reconstruction shows rings (\fref{fig:outlook_aao}). Using realistic simulation parameters, XXX images should suffice to reach a SNR of XXX.
-The other sample is will be a litographically procuced gratings with a pitches of XXX (simulation shown in \fref{fig:outlook_grating}.). Both samples combine the advantes of a single crystal sample (namely intense features) while providing more signal and requiring less accessible reciprocal space. 
-
-
-Furthermore, for the randomly in plane oriented pores, the SNR might be improved by considering the polar correlations in the single image reconstructions as described in XXX
-
-

Tex/discussion.tex

@@ -1,2 +1,6 @@
 \chapter{Discussion}
-Even though the application of non-uniform FFT (NUFFT) based correlation estimators with sophisticated interpolation kernels, which have  successfully been used in other fields, would require more memory, the reduction in under-sampling by making full use of the smaller $\vec{q}$ spacing at higher detector angles could make it a worthwhile extension of the used 3d reconstruction \cite{laguna1998,yang2008,chang2020}. Another possible avenue for improvement of the implementation might be to only reconstruct relevant parts of the reciprocal space, greatly reducing computational time and memory requirements if using direct correlation estimators instead of FFT based methods (which are not suitable for reconstruction of the whole $\vec{q}$-space due to the higher computational complexity) and thereby making use of the unequal $\vec{q}$ spacing as well.
+Even though the application of non-uniform FFT (NUFFT) based correlation estimators with sophisticated interpolation kernels, which have  successfully been used in other fields, would require more memory, the reduction in under-sampling by making full use of the smaller $\vec{q}$ spacing at higher detector angles could make it a worthwhile extension of the used 3d reconstruction \cite{laguna1998,yang2008,chang2020}. Another possible avenue for improvement of the implementation might be to only reconstruct relevant parts of the reciprocal space, greatly reducing computational time and memory requirements if using direct correlation estimators instead of FFT based methods (which are not suitable for reconstruction of the whole $\vec{q}$-space due to the higher computational complexity) and thereby making use of the unequal $\vec{q}$ spacing as well.
+
+
+
+An avenue for improvement is subpixel resolution of the photon hits and better usage of the varying solid angle of each pixel of the detector to increase the resolution in the reconstruction, as this is currenly limited by the computational work and memory requirements to calulate the correlations at higher resolution.

Tex/experiment.tex

@@ -262,7 +262,7 @@ \subsection{Preprocessing}
 \begin{figure}
 	\centering
 	\includegraphics[width=0.8\linewidth]{images/kosselfit.png}
-	\caption{Program for fitting Kossel lines to experimental data}
+	\caption{User interface for performing a regression of the detector orientation and position to the Kossel lines visible in experimental data. The lines can be automatically identified,  be  manually modified afterwards and the reflections considered selected. This tool is used to perform the alignment for the GaAs single crystal samples.}
 	\label{fig:kosselfit}
 \end{figure}
 

Tex/ffz.bib

@@ -1151,6 +1151,32 @@ @Article{yabashi2015
   keywords = {X-ray free-electron laser, beamline instrumentation, X-ray optics, ultrafast X-ray science, quantum X-ray optics},
 }
 
+@Article{mojarad2015,
+  author    = {Mojarad, N. and Hojeij, M. and Wang, L. and Gobrecht, J. and Ekinci, Y.},
+  journal   = {Nanoscale},
+  title     = {Single-digit-resolution nanopatterning with extreme ultraviolet light for the 2.5 nm technology node and beyond},
+  year      = {2015},
+  pages     = {4031-4037},
+  volume    = {7},
+  abstract  = {All nanofabrication methods come with an intrinsic resolution limit{,} set by their governing physical principles and instrumentation. In the case of extreme ultraviolet (EUV) lithography at 13.5 nm wavelength{,} this limit is set by light diffraction and is ≈3.5 nm. In the semiconductor industry{,} the feasibility of reaching this limit is not only a key factor for the current developments in lithography technologies{,} but also is an important factor in deciding whether photon-based lithography will be used for future high-volume manufacturing. Using EUV-interference lithography we show patterning with 7 nm resolution in making dense periodic line-space structures with 14 nm periodicity. Achieving such a cutting-edge resolution has been possible by integrating a high-quality synchrotron beam{,} precise nanofabrication of masks{,} very stable exposures instrumentation{,} and utilizing effective photoresists. We have carried out exposure on silicon- and hafnium-based photoresists and we demonstrated the extraordinary capability of the latter resist to be used as a hard mask for pattern transfer into Si. Our results confirm the capability of EUV lithography in the reproducible fabrication of dense patterns with single-digit resolution. Moreover{,} it shows the capability of interference lithography{,} using transmission gratings{,} in evaluating the resolution limits of photoresists.},
+  doi       = {10.1039/C4NR07420C},
+  issue     = {9},
+  publisher = {The Royal Society of Chemistry},
+}
+
+@Article{carina2019,
+  author         = {Lim, Siew Yee and Law, Cheryl Suwen and Liu, Lina and Markovic, Marijana and Hedrich, Carina and Blick, Robert H. and Abell, Andrew D. and Zierold, Robert and Santos, Abel},
+  journal        = {Catalysts},
+  title          = {Electrochemical Engineering of Nanoporous Materials for Photocatalysis: Fundamentals, Advances, and Perspectives},
+  year           = {2019},
+  issn           = {2073-4344},
+  number         = {12},
+  volume         = {9},
+  abstract       = {Photocatalysis comprises a variety of light-driven processes in which solar energy is converted into green chemical energy to drive reactions such as water splitting for hydrogen energy generation, degradation of environmental pollutants, CO2 reduction and NH3 production. Electrochemically engineered nanoporous materials are attractive photocatalyst platforms for a plethora of applications due to their large effective surface area, highly controllable and tuneable light-harvesting capabilities, efficient charge carrier separation and enhanced diffusion of reactive species. Such tailor-made nanoporous substrates with rational chemical and structural designs provide new exciting opportunities to develop advanced optical semiconductor structures capable of performing precise and versatile control over light–matter interactions to harness electromagnetic waves with unprecedented high efficiency and selectivity for photocatalysis. This review introduces fundamental developments and recent advances of electrochemically engineered nanoporous materials and their application as platforms for photocatalysis, with a final prospective outlook about this dynamic field.},
+  article-number = {988},
+  doi            = {10.3390/catal9120988},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping: