Added compliance with EPSRC open access requirements section linking …

…to this GitHub page.

Added more changes:
- Made abstract smaller and more readable.
- Removed the Plot containing the difference between the colour data augmentation with the VQVAE.
- Added more simple changes.

latex_figures/Compression VQVAE overview pipeline/Pipeline within VQVAE new pipeline only.tikz

@@ -0,0 +1,51 @@
+\begin{tikzpicture}
+	\begin{pgfonlayer}{nodelayer}
+		\node [style=Square] (27) at (3, -1) {Original image};
+		\node [style=Square] (28) at (10, -3) {Patch generation};
+		\node [style=Square] (29) at (18.25, -5) {Hysteresis thresholding};
+		\node [style=Square] (30) at (18.25, -7) {Cell thresholding};
+		\node [style=Square] (31) at (27.5, -9) {VQVAE2 training};
+		\node [style=Square] (32) at (27.5, -11) {VQVAE2 image encoding};
+		\node [style=none] (33) at (3, -3) {};
+		\node [style=none] (36) at (10, -5) {};
+		\node [style=none] (37) at (27.5, -7) {};
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+		\node [style=none] (47) at (14, -15) {};
+		\node [style=none] (48) at (6, -15) {};
+		\node [style=none] (49) at (0, -15) {};
+		\node [style=Empty text] (52) at (3, -14) {WSI};
+		\node [style=Empty text] (53) at (10, -14) {Patch creation with tiles};
+		\node [style=Empty text] (54) at (18.25, -14) {Patch selection};
+		\node [style=Empty text] (55) at (27.5, -14) {VQVAE testing and training};
+		\node [style=none] (56) at (27.5, -1) {};
+		\node [style=none] (58) at (3, -9) {\includegraphics[width=2cm]{latex_figures/Compression VQVAE overview pipeline/example WSI slide 2}};
+		\node [style=none] (59) at (10, -9) {\includegraphics{latex_figures/Compression VQVAE overview pipeline/Overview diagram VQVAE patch extraction and algorithm wsi patches only}};
+		\node [style=none] (60) at (18.25, -9.5) {\includegraphics[width=4cm]{latex_figures/Compression VQVAE overview pipeline/Hysteresis example accepted patch.png}};
+		\node [style=none] (61) at (18.25, -12.25) {\includegraphics[width=4cm]{latex_figures/Compression VQVAE overview pipeline/Hysteresis example rejected patch 1.png}};
+		\node [style=Empty text] (62) at (18.25, -8.25) {Accepted};
+		\node [style=Empty text] (64) at (18.25, -11) {Rejected};
+	\end{pgfonlayer}
+	\begin{pgfonlayer}{edgelayer}
+		\draw (27) to (33.center);
+		\draw (28) to (36.center);
+		\draw (30) to (37.center);
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+		\draw [style=arrow] (29) to (30);
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+		\draw [style=dotted] (44.center) to (45.center);
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+		\draw [style=arrow] (37.center) to (31);
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+\end{tikzpicture}

latex_figures/VQVAE diagram new/Tikz diagram VQVAE.tikz

@@ -0,0 +1,119 @@
+\begin{tikzpicture}
+	\begin{pgfonlayer}{nodelayer}
+		\node [style=Square] (0) at (8, 0) {\includegraphics{"latex_figures/VQVAE diagram new/Images/Overview diagram VQVAE patch extraction and algorithm wsi patches only.jpeg"}};
+		\node [style=Square] (3) at (16.5, -12) {Encoded 1};
+		\node [style=Square] (4) at (23.5, -12) {Encoded 2};
+		\node [style=Square] (5) at (16.5, -15) {$Z1_{quant}$};
+		\node [style=Square] (6) at (23.5, -15) {$Z2_{quant}$};
+		\node [style=Square] (7) at (32.5, -12) {\includegraphics[width=0.8cm]{"latex_figures/VQVAE diagram new/Images/Reconstructed images.jpeg"}};
+		\node [style=Empty text] (10) at (18.5, 4.25) {Openslide patches};
+		\node [style=Empty text] (11) at (8, -7.75) {Thresholded patches(X)};
+		\node [style=Empty text] (12) at (13, -11.25) {Encode};
+		\node [style=Empty text] (13) at (20, -11.25) {Encode};
+		\node [style=Empty text] (14) at (18.25, -13.5) {Quantise};
+		\node [style=Empty text] (15) at (25.25, -13.5) {Quantise};
+		\node [style=Empty text] (16) at (20.25, -15.75) {Decode};
+		\node [style=Empty text] (17) at (26.75, -15.75) {Decode};
+		\node [style=Empty text] (18) at (18.5, 2) {\includegraphics[width=1cm]{"latex_figures/VQVAE diagram new/Images/Example patch accept.png"}};
+		\node [style=Empty text] (19) at (18.5, -2) {\includegraphics[width=1cm]{"latex_figures/VQVAE diagram new/Images/Example patch reject.png"}};
+		\node [style=none] (20) at (18.5, -0.5) {};
+		\node [style=none] (21) at (16.5, 3.5) {};
+		\node [style=none] (22) at (16.5, -3.5) {};
+		\node [style=none] (23) at (20.5, -3.5) {};
+		\node [style=none] (24) at (20.5, 3.5) {};
+		\node [style=none] (25) at (16.5, 0) {};
+		\node [style=none] (26) at (20.5, 0) {};
+		\node [style=Empty text] (27) at (7, -10) {\includegraphics[width=1cm]{"latex_figures/VQVAE diagram new/Images/Example patch accept.png"}};
+		\node [style=Empty text] (28) at (7, -14) {\includegraphics[width=1cm]{"latex_figures/VQVAE diagram new/Images/Example patch reject.png"}};
+		\node [style=none] (30) at (5, -8.5) {};
+		\node [style=none] (31) at (5, -15.5) {};
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+		\node [style=none] (35) at (11, -12) {};
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+		\node [style=Empty text] (37) at (9.5, -14) {\includegraphics[width=.5cm]{"latex_figures/VQVAE diagram new/Images/cross.png"}};
+		\node [style=none] (38) at (8, -15.5) {};
+		\node [style=none] (40) at (8, -22) {};
+		\node [style=none] (41) at (32.5, -22) {};
+		\node [style=none] (42) at (17, -22) {};
+		\node [style=none] (43) at (23, -22) {};
+		\node [style=Empty text] (44) at (20, -22) {$L_1=MSE(X, X')$};
+		\node [style=Empty text] (45) at (32.5, -7.75) {Reconstructed patches};
+		\node [style=none] (46) at (28.5, -15) {};
+		\node [style=none] (47) at (28.5, -12) {};
+		\node [style=none] (50) at (25.25, -21) {};
+		\node [style=none] (51) at (14.75, -21) {};
+		\node [style=none] (52) at (14.75, -14) {};
+		\node [style=none] (53) at (25.25, -14) {};
+		\node [style=Empty text] (56) at (20, -19.25) {$L_2=Z_{embed(X)}-Z_{embed(quant)}$};
+		\node [style=Empty text] (57) at (20, -20.5) {$L_3=Z_{embed(quant)}-Z_{embed(X)}$};
+		\node [style=Empty text] (58) at (20, -24) {$L$=$L_1+L_2-\beta L_3$; $\beta \in [0,1]$};
+		\node [style=Empty text] (59) at (25.25, 1) {Threshold and select patches};
+		\node [style=Empty text] (60) at (32, 2) {\includegraphics[width=1cm]{"latex_figures/VQVAE diagram new/Images/Example patch accept.png"}};
+		\node [style=Empty text] (61) at (32, -2) {\includegraphics[width=1cm]{"latex_figures/VQVAE diagram new/Images/Example patch reject.png"}};
+		\node [style=none] (62) at (30, 3.5) {};
+		\node [style=none] (63) at (30, -3.5) {};
+		\node [style=none] (64) at (36, -3.5) {};
+		\node [style=none] (65) at (36, 3.5) {};
+		\node [style=none] (66) at (36, 0) {};
+		\node [style=Empty text] (67) at (34.5, 2) {\includegraphics[width=.5cm]{"latex_figures/VQVAE diagram new/Images/tick.png"}};
+		\node [style=Empty text] (68) at (34.5, -2) {\includegraphics[width=.5cm]{"latex_figures/VQVAE diagram new/Images/cross.png"}};
+		\node [style=none] (69) at (33, -3.5) {};
+		\node [style=Empty text] (70) at (13.75, 1) {Extract patches};
+		\node [style=none] (71) at (15, -23) {};
+		\node [style=none] (72) at (25, -23) {};
+		\node [style=none] (73) at (15, -25) {};
+		\node [style=none] (74) at (25, -25) {};
+		\node [style=Empty text] (75) at (33, 4.25) {Thresholded patches (X)};
+		\node [style=Empty text] (76) at (8, 4.25) {WSI};
+		\node [style=Empty text] (77) at (18.5, 0.5) {.};
+		\node [style=Empty text] (78) at (18.5, 0) {.};
+		\node [style=Empty text] (79) at (18.5, -0.5) {.};
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+		\node [style=Empty text] (81) at (32, 0.5) {.};
+		\node [style=Empty text] (82) at (32, 0) {.};
+		\node [style=Empty text] (83) at (32, -0.5) {.};
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+		\node [style=Empty text] (87) at (7, -12.5) {.};
+	\end{pgfonlayer}
+	\begin{pgfonlayer}{edgelayer}
+		\draw [style=arrow] (3) to (5);
+		\draw [style=arrow] (4) to (6);
+		\draw [style=arrow] (3) to (4);
+		\draw [style=arrow] (5) to (6);
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+		\draw [style=line] (46.center) to (47.center);
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+		\draw [style=arrow, bend right=90, looseness=0.75] (5) to (46.center);
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+\end{tikzpicture}

tikzit_setup/tikzit.sty

@@ -0,0 +1,42 @@
+\usepackage{tikz}
+\usetikzlibrary{backgrounds}
+\usetikzlibrary{arrows}
+\usetikzlibrary{shapes,shapes.geometric,shapes.misc}
+
+% this style is applied by default to any tikzpicture included via \tikzfig
+\tikzstyle{tikzfig}=[baseline=-0.25em,scale=0.5]
+
+% these are dummy properties used by TikZiT, but ignored by LaTex
+\pgfkeys{/tikz/tikzit fill/.initial=0}
+\pgfkeys{/tikz/tikzit draw/.initial=0}
+\pgfkeys{/tikz/tikzit shape/.initial=0}
+\pgfkeys{/tikz/tikzit category/.initial=0}
+
+% standard layers used in .tikz files
+\pgfdeclarelayer{edgelayer}
+\pgfdeclarelayer{nodelayer}
+\pgfsetlayers{background,edgelayer,nodelayer,main}
+
+% style for blank nodes
+\tikzstyle{none}=[inner sep=0mm]
+
+% include a .tikz file
+\newcommand{\tikzfig}[1]{%
+{\tikzstyle{every picture}=[tikzfig]
+\IfFileExists{#1.tikz}
+  {\input{#1.tikz}}
+  {%
+    \IfFileExists{./figures/#1.tikz}
+      {\input{./figures/#1.tikz}}
+      {\tikz[baseline=-0.5em]{\node[draw=red,font=\color{red},fill=red!10!white] {\textit{#1}};}}%
+  }}%
+}
+
+% the same as \tikzfig, but in a {center} environment
+\newcommand{\ctikzfig}[1]{%
+\begin{center}\rm
+  \tikzfig{#1}
+\end{center}}
+
+% fix strange self-loops, which are PGF/TikZ default
+\tikzstyle{every loop}=[]

tikzit_setup/tikzit_styles.tikzstyles

@@ -0,0 +1,16 @@
+% TiKZ style file generated by TikZiT. You may edit this file manually,
+% but some things (e.g. comments) may be overwritten. To be readable in
+% TikZiT, the only non-comment lines must be of the form:
+% \tikzstyle{NAME}=[PROPERTY LIST]
+
+% Node styles
+\tikzstyle{Square}=[fill=white, draw=black, shape=rectangle]
+\tikzstyle{Empty text}=[fill=none, draw=none, shape=rectangle]
+
+% Edge styles
+\tikzstyle{dotted arrow}=[dashed, ->]
+\tikzstyle{arrow}=[->]
+\tikzstyle{dotted}=[-, dashed]
+\tikzstyle{line}=[-]
+\tikzstyle{red arrow}=[draw=red, ->]
+\tikzstyle{red line}=[-, draw=red]