diff --git a/CHANGELOG b/CHANGELOG
index bd10f11..336bd9a 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,4 +1,5 @@
 0.1.4
+ - ref, doc: fix api doc link references
  - add initial (useable) tests in test directory
  - add CHANGELOG
  - ref: change the directory structure to include topotem (#52)
diff --git a/doc/PTO_Junction_moore.rst b/doc/PTO_Junction_moore.rst
index 3eae08c..62c987f 100644
--- a/doc/PTO_Junction_moore.rst
+++ b/doc/PTO_Junction_moore.rst
@@ -81,8 +81,8 @@ Load the line profile positions:
     >>> line_profile_positions = np.load('line_profile_positions.npy')
 
 Note: You can also choose your own line_profile_positions with
-:python:`am.add_atoms_with_gui(image)` and use the :python:`skimage.profile_line`
-for customisability.
+:py:func:`temul.topotem.fft_mapping.choose_points_on_image` and use the
+:python:`skimage.profile_line` for customisability.
 
 
 Create the Lattice Strain Map
@@ -104,7 +104,7 @@ Note that sometimes the 0 and 1 axes directions are constructed vice versa.
 .. image:: ../publication_examples/PTO_Junction_moore/data/strain_map.png
     :scale: 50 %
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python
@@ -140,7 +140,7 @@ the turning of the lattice across the junction.
     :scale: 50 %
 
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python
diff --git a/doc/PTO_supercrystal_hadjimichael.rst b/doc/PTO_supercrystal_hadjimichael.rst
index 4e17bec..63e5995 100644
--- a/doc/PTO_supercrystal_hadjimichael.rst
+++ b/doc/PTO_supercrystal_hadjimichael.rst
@@ -17,14 +17,16 @@ where you will find the python scripts and interactive python notebooks:
 .. image:: https://mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
-The :python:`calculate_atom_plane_curvature` function has been adapted from the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
 M. Hadjimichael, Y. Li *et al*, `Metal-ferroelectric supercrystals with periodically
 curved metallic layers, Nature Materials 2020 <https://www.nature.com/articles/s41563-020-00864-6>`_.
 This MATLAB script can also be found in the same folder.
 
-The :python:`calculate_atom_plane_curvature` function in the
-:python:`temul.lattice_structure_tools` module can be used to find the curvature of the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function in the
+:py:mod:`temul.topotem.lattice_structure_tools` module can be used to find the curvature of the
 displacement of atoms along an atom plane in a sublattice. Using the default
 parameter :python:`func='strain_grad'`, the function will approximate the
 curvature as the strain gradient, as in cases where the first derivative is
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index ae6af42..7c4cfb2 100644
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diff --git a/doc/_build/doctrees/using_temul.doctree b/doc/_build/doctrees/using_temul.doctree
index 5b31f61..6fe932f 100644
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diff --git a/doc/_build/doctrees/workflows.doctree b/doc/_build/doctrees/workflows.doctree
index db487f5..7d06efb 100644
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diff --git a/doc/_build/html/.buildinfo b/doc/_build/html/.buildinfo
index c7acdc9..6d6ffe4 100644
--- a/doc/_build/html/.buildinfo
+++ b/doc/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 608bac64e8b48a97b902e87aaf2e9228
+config: f50bf99a7f7005c4e9d71dc02d297799
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/_build/html/PTO_Junction_moore.html b/doc/_build/html/PTO_Junction_moore.html
index b9deba2..ecf6fdb 100644
--- a/doc/_build/html/PTO_Junction_moore.html
+++ b/doc/_build/html/PTO_Junction_moore.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Analysis of PTO Domain Wall Junction &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Analysis of PTO Domain Wall Junction &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -236,8 +236,8 @@ <h2>Set up the Parameters<a class="headerlink" href="#set-up-the-parameters" tit
 </pre></div>
 </div>
 <p>Note: You can also choose your own line_profile_positions with
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">am</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">add_atoms_with_gui</span></span><span class="punctuation"><span class="pre">(</span></span><span class="name"><span class="pre">image</span></span><span class="punctuation"><span class="pre">)</span></span></code> and use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">skimage</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">profile_line</span></span></code>
-for customisability.</p>
+<a class="reference internal" href="api_doc.html#temul.topotem.fft_mapping.choose_points_on_image" title="temul.topotem.fft_mapping.choose_points_on_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.fft_mapping.choose_points_on_image()</span></code></a> and use the
+<code class="code python docutils literal notranslate"><span class="name"><span class="pre">skimage</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">profile_line</span></span></code> for customisability.</p>
 </div>
 <div class="section" id="create-the-lattice-strain-map">
 <h2>Create the Lattice Strain Map<a class="headerlink" href="#create-the-lattice-strain-map" title="Permalink to this headline">¶</a></h2>
@@ -253,7 +253,7 @@ <h2>Create the Lattice Strain Map<a class="headerlink" href="#create-the-lattice
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="_images/strain_map.png"><img alt="_images/strain_map.png" src="_images/strain_map.png" style="width: 320.0px; height: 290.5px;" /></a>
-<p>Plot the line profiles with <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_plotting</span></span></code> functions and a kwarg dictionary.
+<p>Plot the line profiles with <a class="reference internal" href="api_doc.html#module-temul.signal_plotting" title="temul.signal_plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_plotting</span></code></a> functions and a kwarg dictionary.
 For more details on this function, see <a class="reference internal" href="line_profile_tutorial.html#line-profile-tutorial"><span class="std std-ref">this tutorial</span></a>.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;vmin&#39;</span><span class="p">:</span> <span class="n">vmin</span><span class="p">,</span> <span class="s1">&#39;vmax&#39;</span><span class="p">:</span> <span class="n">vmax</span><span class="p">,</span> <span class="s1">&#39;cmap&#39;</span><span class="p">:</span> <span class="n">cmap</span><span class="p">}</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tml</span><span class="o">.</span><span class="n">compare_images_line_profile_one_image</span><span class="p">(</span><span class="n">strain_map</span><span class="p">,</span> <span class="n">line_profile_positions</span><span class="p">,</span>
@@ -278,7 +278,7 @@ <h2>Create the Lattice Rotation Map<a class="headerlink" href="#create-the-latti
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="_images/rotation_map.png"><img alt="_images/rotation_map.png" src="_images/rotation_map.png" style="width: 320.0px; height: 290.5px;" /></a>
-<p>Plot the line profiles with <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_plotting</span></span></code> functions and a kwarg dictionary.
+<p>Plot the line profiles with <a class="reference internal" href="api_doc.html#module-temul.signal_plotting" title="temul.signal_plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_plotting</span></code></a> functions and a kwarg dictionary.
 For more details on this function, see <a class="reference internal" href="line_profile_tutorial.html#line-profile-tutorial"><span class="std std-ref">this tutorial</span></a>.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;vmin&#39;</span><span class="p">:</span> <span class="n">vmin</span><span class="p">,</span> <span class="s1">&#39;vmax&#39;</span><span class="p">:</span> <span class="n">vmax</span><span class="p">,</span> <span class="s1">&#39;cmap&#39;</span><span class="p">:</span> <span class="n">cmap</span><span class="p">}</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tml</span><span class="o">.</span><span class="n">compare_images_line_profile_one_image</span><span class="p">(</span>
@@ -360,7 +360,7 @@ <h2>Map the Polarisation<a class="headerlink" href="#map-the-polarisation" title
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/PTO_supercrystal_hadjimichael.html b/doc/_build/html/PTO_supercrystal_hadjimichael.html
index 3694299..9adf1e5 100644
--- a/doc/_build/html/PTO_supercrystal_hadjimichael.html
+++ b/doc/_build/html/PTO_supercrystal_hadjimichael.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Calculation of Atom Plane Curvature &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Calculation of Atom Plane Curvature &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -186,13 +186,15 @@
 without needing any downloads. Just click this button and navigate to that same folder,
 where you will find the python scripts and interactive python notebooks:</p>
 <a class="reference external image-reference" href="https://mybinder.org/v2/gh/PinkShnack/TEMUL/master"><img alt="https://mybinder.org/badge_logo.svg" src="https://mybinder.org/badge_logo.svg" /></a>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">calculate_atom_plane_curvature</span></span></code> function has been adapted from the
+<p>The <a class="reference internal" href="api_doc.html#temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature" title="temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature()</span></code></a>
+function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
 M. Hadjimichael, Y. Li <em>et al</em>, <a class="reference external" href="https://www.nature.com/articles/s41563-020-00864-6">Metal-ferroelectric supercrystals with periodically
 curved metallic layers, Nature Materials 2020</a>.
 This MATLAB script can also be found in the same folder.</p>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">calculate_atom_plane_curvature</span></span></code> function in the
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">lattice_structure_tools</span></span></code> module can be used to find the curvature of the
+<p>The <a class="reference internal" href="api_doc.html#temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature" title="temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature()</span></code></a>
+function in the
+<a class="reference internal" href="api_doc.html#module-temul.topotem.lattice_structure_tools" title="temul.topotem.lattice_structure_tools"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.topotem.lattice_structure_tools</span></code></a> module can be used to find the curvature of the
 displacement of atoms along an atom plane in a sublattice. Using the default
 parameter <code class="code python docutils literal notranslate"><span class="name"><span class="pre">func</span></span><span class="operator"><span class="pre">=</span></span><span class="literal string single"><span class="pre">’strain_grad’</span></span></code>, the function will approximate the
 curvature as the strain gradient, as in cases where the first derivative is
@@ -283,7 +285,7 @@ <h2>Calculate the Curvature of Atom Planes<a class="headerlink" href="#calculate
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/_sources/PTO_Junction_moore.rst.txt b/doc/_build/html/_sources/PTO_Junction_moore.rst.txt
index 3eae08c..62c987f 100644
--- a/doc/_build/html/_sources/PTO_Junction_moore.rst.txt
+++ b/doc/_build/html/_sources/PTO_Junction_moore.rst.txt
@@ -81,8 +81,8 @@ Load the line profile positions:
     >>> line_profile_positions = np.load('line_profile_positions.npy')
 
 Note: You can also choose your own line_profile_positions with
-:python:`am.add_atoms_with_gui(image)` and use the :python:`skimage.profile_line`
-for customisability.
+:py:func:`temul.topotem.fft_mapping.choose_points_on_image` and use the
+:python:`skimage.profile_line` for customisability.
 
 
 Create the Lattice Strain Map
@@ -104,7 +104,7 @@ Note that sometimes the 0 and 1 axes directions are constructed vice versa.
 .. image:: ../publication_examples/PTO_Junction_moore/data/strain_map.png
     :scale: 50 %
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python
@@ -140,7 +140,7 @@ the turning of the lattice across the junction.
     :scale: 50 %
 
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python
diff --git a/doc/_build/html/_sources/PTO_supercrystal_hadjimichael.rst.txt b/doc/_build/html/_sources/PTO_supercrystal_hadjimichael.rst.txt
index 4e17bec..63e5995 100644
--- a/doc/_build/html/_sources/PTO_supercrystal_hadjimichael.rst.txt
+++ b/doc/_build/html/_sources/PTO_supercrystal_hadjimichael.rst.txt
@@ -17,14 +17,16 @@ where you will find the python scripts and interactive python notebooks:
 .. image:: https://mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
-The :python:`calculate_atom_plane_curvature` function has been adapted from the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
 M. Hadjimichael, Y. Li *et al*, `Metal-ferroelectric supercrystals with periodically
 curved metallic layers, Nature Materials 2020 <https://www.nature.com/articles/s41563-020-00864-6>`_.
 This MATLAB script can also be found in the same folder.
 
-The :python:`calculate_atom_plane_curvature` function in the
-:python:`temul.lattice_structure_tools` module can be used to find the curvature of the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function in the
+:py:mod:`temul.topotem.lattice_structure_tools` module can be used to find the curvature of the
 displacement of atoms along an atom plane in a sublattice. Using the default
 parameter :python:`func='strain_grad'`, the function will approximate the
 curvature as the strain gradient, as in cases where the first derivative is
diff --git a/doc/_build/html/_sources/about_temul_toolkit.rst.txt b/doc/_build/html/_sources/about_temul_toolkit.rst.txt
new file mode 100644
index 0000000..f24ddb2
--- /dev/null
+++ b/doc/_build/html/_sources/about_temul_toolkit.rst.txt
@@ -0,0 +1,9 @@
+.. _about_temul_toolkit:
+
+.. include:: define_roles.rst
+
+
+Some published results using the TEMUL Toolkit
+----------------------------------------------
+
+.. Include some images! Just copy from the papers and cite.
diff --git a/doc/_build/html/_sources/dg_visualiser_tutorial.rst.txt b/doc/_build/html/_sources/dg_visualiser_tutorial.rst.txt
index cd1288f..a44eb3d 100644
--- a/doc/_build/html/_sources/dg_visualiser_tutorial.rst.txt
+++ b/doc/_build/html/_sources/dg_visualiser_tutorial.rst.txt
@@ -7,9 +7,10 @@
 Interactive Image Filtering
 ===========================
 
-The :python:`temul.signal_processing` module allows one to filter images with a
+The :py:mod:`temul.signal_processing` module allows one to filter images with a
 double Gaussian (band-pass) filter. Apart from the base functions, it can be
-done interactively with the :python:`visualise_dg_filter` function. In this
+done interactively with the
+:py:func:`temul.signal_processing.visualise_dg_filter` function. In this
 tutorial, we will see how to use the function on experimental data.
 
 
@@ -30,8 +31,8 @@ TEMUL package.
 Interactively Filter the Experimental Image
 -------------------------------------------
 
-Run the :python:`visualise_dg_filter` function. There are lots of other parameters
-too for customisation.
+Run the :py:func:`temul.signal_processing.visualise_dg_filter` function.
+There are lots of other parameters too for customisation.
 
 .. code-block:: python
 
@@ -40,9 +41,10 @@ too for customisation.
 .. image:: tutorial_images/dg_filter_tutorial/dg_visualiser.gif
     :scale: 50 %
 
-As we can see, an interactive window appears, showing the FFT ("FFT Widget") of the image with
-the positions of the inner and outer Gaussian full width at half maximums (FWHMs).
-The inital FWHMs can be changed with the :python:`d_inner` and :python:`d_outer`
+As we can see, an interactive window appears, showing the FFT ("FFT Widget")
+of the image with the positions of the inner and outer Gaussian full width
+at half maximums (FWHMs). The inital FWHMs can be changed with the
+:python:`d_inner` and :python:`d_outer`
 parameters (limits can also be changed).
 
 To change the two FWHMs interactively
@@ -56,7 +58,8 @@ Return the Filtered Image
 -------------------------
 
 When we have suitable FWHMs for the inner and outer Gaussians, we can use
-the :python:`double_gaussian_fft_filter` function the return a filtered image.
+the :py:func:`temul.signal_processing.double_gaussian_fft_filter` function
+the return a filtered image.
 
 .. code-block:: python
 
@@ -71,6 +74,6 @@ the :python:`double_gaussian_fft_filter` function the return a filtered image.
     :scale: 50 %
 
 
-Details on the :python:`double_gaussian_fft_filter_optimised` function can be
-found in the :ref:`api_doc`.
-We hope to added some examples of this functions to this page in future.
+Details on the
+:py:func:`temul.signal_processing.double_gaussian_fft_filter_optimised`
+function can be found in the :ref:`api_doc`.
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
index 9472af1..941d355 100644
--- a/doc/_build/html/_sources/index.rst.txt
+++ b/doc/_build/html/_sources/index.rst.txt
@@ -15,16 +15,28 @@ atomic resolution images. It is mostly built upon the data structure of
 
 Interactive Examples
 --------------------
+The easiest way to try the TEMUL Toolkit is via Binder:
+`introductory Jupyter Notebook <https://hub.gke2.mybinder.org/user/pinkshnack-temul-19r27k52/lab/tree/code_tutorials/polarisation_vectors_tutorial.ipynb>`_.
+To install the TEMUL Toolkit on your own computer,
+see the :ref:`install` instructions.
+
+And there are more examples with Binder, just click the below button!
+
 .. image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
-Click the button above to start some data analysis (it may take a few minutes to load). 
+Click the button above to start some data analysis
+(it may take a few minutes to load).
 The "code_tutorials" folder contains walkthroughs of some of the documentation
 examples from this website.
-The "publication_examples" folder will allow you to analyse data from published scientific papers!
+The "publication_examples" folder will allow you to analyse data from
+published scientific papers!
 Just navigate to whichever of these folders you want click on the ".ipynb" files.
 
 
+.. include:: about_temul_toolkit.rst
+
+
 .. include:: news.rst
 
 
@@ -74,7 +86,9 @@ To cite the latest TEMUL Toolkit version, use the following DOI:
 .. image:: https://www.zenodo.org/badge/203785298.svg
    :target: https://www.zenodo.org/badge/latestdoi/203785298
 
-For example: Eoghan O'Connell, Michael Hennessy, & Eoin Moynihan. (2020, November 2). PinkShnack/TEMUL: Initial Temul-Toolkit Release (Version 0.1.1). Zenodo. http://doi.org/10.5281/zenodo.4185974
+For example: Eoghan O'Connell, Michael Hennessy, & Eoin Moynihan.
+(2021). PinkShnack/TEMUL: (Version 0.1.3).
+Zenodo. http://doi.org/10.5281/zenodo.4543963
 
 If you wish to cite an older release of the TEMUL Toolkit, click on the above
 badge to find the relevant version.
diff --git a/doc/_build/html/_sources/install.rst.txt b/doc/_build/html/_sources/install.rst.txt
index ec796a8..0b29dae 100644
--- a/doc/_build/html/_sources/install.rst.txt
+++ b/doc/_build/html/_sources/install.rst.txt
@@ -6,31 +6,44 @@
 Installation
 ------------
 
-The TEMUL Toolkit can be installed easily with PIP (those using Windows may need to download VS C++ Build Tools, see below).  
+The TEMUL Toolkit can be installed easily with PIP (those using Windows may
+need to download VS C++ Build Tools, see below).
 
 :bash:`$ pip install temul-toolkit`
 
-Then, it can be imported with the name "temul". For example, to import most of the temul functionality use:
+Then, it can be imported with the name "temul". For example, to import most
+of the temul functionality use:
 
 :python:`import temul.api as tml`
 
-Matplotlib 3.3 currently has compatability issues with iPython, see below for the fix.
- 
 
 -----------------------------
 Installation Problems & Notes
 -----------------------------
 
-* If installing on Windows, you will need Visual Studio C++ Build Tools. Download it `here <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>`_. After downloading, choose the "C++ Build Tools" Workload and click install.
-
-* Matplotlib seems to have issues with iPython at the moment. Install matplotlib==3.2 until this issue is resolved by Matplotlib. See `here <https://stackoverflow.com/questions/64291087/matplotlib-module-sip-has-no-attribute-setapi>`_ for more details.
-
-* If you want to use the :python:`io.write_cif_from_dataframe` function, you will need to install pyCifRW version 4.3. This requires Visual Studio.
-
-* If you wish to use the :python:`simulations.py` or :python:`model_refiner.py` modules, you will need to install PyPrismatic. This requires Visual Studio and other dependencies.
-
-* If you're using any of the functions or classes that require element quantification:
-
-   * navigate to the "temul/external" directory, copy the "atomap_devel_012" folder and paste that in your "site-packages" directory. 
-   * Then, when using atomap to create sublattices and quantify elements call atomap like this: :python:`import atomap_devel_012.api as am`.
-   * This development version is slowly being folded into the master branch here: https://gitlab.com/atomap/atomap/-/issues/93 and any help or tips on implementation are welcome!
+* If installing on Windows, you will need Visual Studio C++ Build Tools.
+  Download it `here <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>`_.
+  After downloading, choose the "C++ Build Tools" Workload and click install.
+
+* If you want to use the :py:func:`temul.io.write_cif_from_dataframe`
+  function, you will need to install pyCifRW version 4.3. This requires
+  Visual Studio.
+
+* If you wish to use the :py:mod:`temul.simulations` or
+  :py:mod:`temul.model_refiner` modules, you will need to install PyPrismatic.
+  This requires Visual Studio and other dependencies.
+  **It is unfortunately not guaranteed to work**. If you want to help develop
+  the :py:class:`temul.model_refiner.Model_Refiner`, please create an issue
+  and/or a pull request on the
+  `TEMUL github <https://github.com/PinkShnack/TEMUL>`_.
+
+* If you're using any of the functions or classes that require element
+  quantification:
+
+   * navigate to the "temul/external" directory, copy the "atomap_devel_012"
+     folder and paste that in your "site-packages" directory.
+   * Then, when using atomap to create sublattices and quantify elements call
+     atomap like this: :python:`import atomap_devel_012.api as am`.
+   * This development version is slowly being folded into the master branch
+     here: https://gitlab.com/atomap/atomap/-/issues/93 and any help or
+     tips on implementation are welcome!
diff --git a/doc/_build/html/_sources/line_profile_tutorial.rst.txt b/doc/_build/html/_sources/line_profile_tutorial.rst.txt
index 01d92a8..4a1b719 100644
--- a/doc/_build/html/_sources/line_profile_tutorial.rst.txt
+++ b/doc/_build/html/_sources/line_profile_tutorial.rst.txt
@@ -7,11 +7,13 @@
 Line Intensity Profile Comparisons
 ==================================
 
-The :python:`temul.signal_plotting` module allows one to draw line intensity profiles
-over images. The :python:`compare_images_line_profile_one_image` can be used to
+The :py:mod:`temul.signal_plotting` module allows one to draw line
+intensity profiles over images. The
+:py:func`temul.signal_plotting.compare_images_line_profile_one_image` can be used to
 draw two line profiles on one image for comparison. In future we hope to expand
 this function to allow for multiple line profiles on one image. The
-:python:`compare_images_line_profile_two_images` function allows you to draw a line
+:py:func:`temul.signal_plotting.compare_images_line_profile_two_images`
+function allows you to draw a line
 profile on an image, and apply that same profile to another image (of the same shape).
 This can be useful for comparing subsequent images in series or comparing experimental
 and simulated images.
@@ -24,7 +26,7 @@ Load the Example Images
 -----------------------
 
 Here we load some dummy data using a variation of Atomap's
-:python:`get_simple_cubic_signal` function.
+:py:func:`temul.dummy_data.get_simple_cubic_signal` function.
 
 .. code-block:: python
 
@@ -46,8 +48,10 @@ Compare two Line Profiles in one Image
 --------------------------------------
 
 As with the :ref:`Masked FFT and iFFT <masked_fft_tutorial>` tutorial, we can
-choose points on the image. This time we use :python:`choose_points_on_image`.
-We need to choose four points for the :python:`compare_images_line_profile_one_image`
+choose points on the image. This time we use
+:py:func:`temul.topotem.fft_mapping.choose_points_on_image`.
+We need to choose four points for the
+:py:func:`temul.signal_plotting.compare_images_line_profile_one_image`
 function, as it draws two line profiles over one image.
 
 .. code-block:: python
@@ -80,7 +84,8 @@ Now run the comparison function to display the two line intensity profiles.
 Compare two Images with Line Profile
 ------------------------------------
 
-Using :python:`choose_points_on_image`, we now choose two points on one image.
+Using :py:func:`temul.topotem.fft_mapping.choose_points_on_image`,
+we now choose two points on one image.
 Then, we plot this line intensity profile over the same position in two images.
 
 .. code-block:: python
diff --git a/doc/_build/html/_sources/masked_fft_tutorial.rst.txt b/doc/_build/html/_sources/masked_fft_tutorial.rst.txt
index 532e066..44a488a 100644
--- a/doc/_build/html/_sources/masked_fft_tutorial.rst.txt
+++ b/doc/_build/html/_sources/masked_fft_tutorial.rst.txt
@@ -7,9 +7,12 @@
 Masked FFT and iFFT
 ===================
 
-The :python:`temul.signal_processing` module allows one to choose the masking coordinates with
-:python:`choose_mask_coordinates` and easily returnt the masked fast Fourier Transform (FFT) with
-:python:`get_masked_ifft`. This can useful in various scenarios, from understanding
+The :py:mod:`temul.signal_processing` module allows one to choose the
+masking coordinates with
+:py:func:`temul.topotem.fft_mapping.choose_mask_coordinates` and easily
+return the masked fast Fourier Transform (FFT) with
+:py:func:`temul.topotem.fft_mapping.get_masked_ifft`. This can useful in
+various scenarios, from understanding
 the diffraction space spots and how they relate to the real space structure,
 to `revealing domain walls <https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.12876>`_
 and finding initial atom positions for difficult images.
diff --git a/doc/_build/html/_sources/news.rst.txt b/doc/_build/html/_sources/news.rst.txt
index b3af5ca..43c74de 100644
--- a/doc/_build/html/_sources/news.rst.txt
+++ b/doc/_build/html/_sources/news.rst.txt
@@ -1,4 +1,4 @@
-.. _install:
+.. _news:
 
 .. include:: define_roles.rst
 
diff --git a/doc/_build/html/_sources/polarisation_vectors_tutorial.rst.txt b/doc/_build/html/_sources/polarisation_vectors_tutorial.rst.txt
index a071c4e..e77e726 100644
--- a/doc/_build/html/_sources/polarisation_vectors_tutorial.rst.txt
+++ b/doc/_build/html/_sources/polarisation_vectors_tutorial.rst.txt
@@ -14,13 +14,13 @@ of each.
 
 Current functions:
 
-1. Using Atomap's :python:`get_polarization_from_second_sublattice` Sublattice
-   method. Great for "standard" polarised structures with two sublattices.
-2. Using the TEMUL :python:`find_polarisation_vectors` function. Useful for
-   structures that Atomap's :python:`get_polarization_from_second_sublattice` can't
-   handle.
-3. Using the TEMUL :python:`atom_deviation_from_straight_line_fit` function.
-   Useful for calculating polarisation from a single sublattice, similar to and
+1. Using Atomap's `get_polarization_from_second_sublattice <https://atomap.org/api_documentation.html?highlight=get_polarization#atomap.sublattice.Sublattice.get_polarization_from_second_sublattice>`_
+   Sublattice method. Great for "standard" polarised structures with two sublattices.
+2. Using the TEMUL :py:func:`temul.topotem.polarisation.find_polarisation_vectors`
+   function. Useful for structures that Atomap's
+   :python:`get_polarization_from_second_sublattice` can't handle.
+3. Using the TEMUL :py:func:`temul.topotem.polarisation.atom_deviation_from_straight_line_fit`
+   function. Useful for calculating polarisation from a single sublattice, similar to and
    based off: J. Gonnissen *et al*, Direct Observation of Ferroelectric Domain Walls in
    LiNbO3: Wall‐Meanders, Kinks, and Local Electric Charges, 26, 42, 2016, DOI: 10.1002/adfm.201603489.
 
@@ -36,12 +36,13 @@ where you will find the python scripts and interactive python notebooks:
 
 For standard Polarised Structures (e.g., PTO)
 ---------------------------------------------
-Atomap's :python:`get_polarization_from_second_sublattice` Sublattice method will
+Atomap's `get_polarization_from_second_sublattice <https://atomap.org/api_documentation.html?highlight=get_polarization#atomap.sublattice.Sublattice.get_polarization_from_second_sublattice>`_
+Sublattice method will
 be sufficent for most users when dealing with the classic PTO-style polarisation,
 wherein the atoms in a sublattice are polarised with respect to a second sublattice.
 
 See the second section of this tutorial on how to plot this in many different ways
-using :python:`plot_polarisation_vectors`!
+using :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`!
 
 .. code-block:: python
 
@@ -72,13 +73,14 @@ using :python:`plot_polarisation_vectors`!
 For nonstandard Polarised Structures (e.g., Boracites)
 ------------------------------------------------------
 When the above function can't isn't suitable, the TEMUL
-:python:`find_polarisation_vectors` function may be an option. It is useful for
-structures that Atomap's :python:`get_polarization_from_second_sublattice` can't
+:py:func:`temul.topotem.polarisation.find_polarisation_vectors` function may
+be an option. It is useful for structures that Atomap's
+:python:`get_polarization_from_second_sublattice` can't
 handle. It is a little more involved and requires some extra preparation when 
 creating the sublattices. 
 
 See the second section of this tutorial on how to plot this in many different ways
-using :python:`plot_polarisation_vectors`!
+using :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`!
 
 .. code-block:: python
 
@@ -130,13 +132,13 @@ For single Polarised Sublattices (e.g., LNO)
 --------------------------------------------
 When dealing with structures in which the polarisation must be extracted from a
 single sublattice (one type of chemical atomic column, the TEMUL
-:python:`atom_deviation_from_straight_line_fit` function
+:py:func:`temul.topotem.polarisation.atom_deviation_from_straight_line_fit` function
 may be an option. It is based off the description by J. Gonnissen *et al*,
 Direct Observation of Ferroelectric Domain Walls in LiNbO3: Wall‐Meanders,
 Kinks, and Local Electric Charges, 26, 42, 2016, DOI: 10.1002/adfm.201603489.
 
 See the second section of this tutorial on how to plot this in many different ways
-using :python:`plot_polarisation_vectors`!
+using :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`!
 
 .. code-block:: python
 
@@ -191,9 +193,10 @@ Let's look at some rotated data
 Plotting Polarisation and Movement Vectors
 ==========================================
 
-The :python:`temul.polarisation` module allows one to visualise the
+The :py:mod:`temul.topotem.polarisation` module allows one to visualise the
 polarisation/movement of atoms in an atomic resolution image. In this tutorial,
-we will use a dummy dataset to show the different ways the :python:`plot_polarisation_vectors`
+we will use a dummy dataset to show the different ways the
+:py:func:`temul.topotem.polarisation.plot_polarisation_vectors`
 function can display data. In future, tutorials on published experimental data
 will also be available.
 
@@ -256,7 +259,8 @@ polarisation vectors for regular structures.
     >>> x, y = [i[0] for i in vector_list], [i[1] for i in vector_list]
     >>> u, v = [i[2] for i in vector_list], [i[3] for i in vector_list]
 
-Now we can display all of the variations that :python:`plot_polarisation_vectors`
+Now we can display all of the variations that
+:py:func:`temul.topotem.polarisation.plot_polarisation_vectors`
 gives us! You can specify sampling (scale) and units, or use a calibrated image
 so that they are automatically set.
 
diff --git a/doc/_build/html/_sources/structure_map_tutorial.rst.txt b/doc/_build/html/_sources/structure_map_tutorial.rst.txt
index f8856dd..04ea88e 100644
--- a/doc/_build/html/_sources/structure_map_tutorial.rst.txt
+++ b/doc/_build/html/_sources/structure_map_tutorial.rst.txt
@@ -7,7 +7,7 @@
 Plot Lattice Structure Maps
 ===========================
 
-The :python:`temul.polarisation` module allows one to easily visualise various
+The :py:mod:`temul.topotem.polarisation` module allows one to easily visualise various
 lattice structure characteristics, such as strain, rotation of atoms along atom
 planes, and the *c*/*a* ratio in an atomic resolution image. In this tutorial,
 we will use a dummy dataset to show the different ways each map can be created.
@@ -38,7 +38,8 @@ Plot the Lattice Strain Map
 ---------------------------
 
 By inputting the calculated or theoretical atom plane separation distance as the
-:python:`theoretical_value` parameter in :python:`tml.get_strain_map` below,
+:python:`theoretical_value` parameter in
+:py:func:`temul.topotem.polarisation.get_strain_map` below,
 we can plot a strain map. The distance *l* is calculated as the distance between
 each atom plane in the given zone axis. More details on this can be found on the
 `Atomap <https://atomap.org/analysing_atom_lattices.html#distance-between-monolayers>`_
@@ -70,7 +71,8 @@ applies to all structure maps discussed in this tutorial.
 Plot the Lattice Atom Rotation Map
 ----------------------------------
 
-The :python:`rotation_of_atom_planes` function calculates the angle between
+The :py:func:`temul.topotem.polarisation.rotation_of_atom_planes` function
+calculates the angle between
 successive atoms and the horizontal for all atoms in the given zone axis. See
 `Atomap <https://atomap.org/analysing_atom_lattices.html#angle-between-atoms>`_
 for other options.
@@ -103,7 +105,8 @@ for other options.
 Plot the *c*/*a* Ratio
 ----------------------
 
-Using the :python:`ratio_of_lattice_spacings` function, we can visualise the ratio of
+Using the :py:func:`temul.topotem.polarisation.ratio_of_lattice_spacings`
+function, we can visualise the ratio of
 two sublattice zone axes. Useful for plotting the *c*/*a* Ratio.
 
 .. code-block:: python
diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js
index 74ba60e..5bbea51 100644
--- a/doc/_build/html/_static/documentation_options.js
+++ b/doc/_build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'v0.1.2',
+    VERSION: 'v0.1.3',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/doc/_build/html/about_temul_toolkit.html b/doc/_build/html/about_temul_toolkit.html
new file mode 100644
index 0000000..fd73410
--- /dev/null
+++ b/doc/_build/html/about_temul_toolkit.html
@@ -0,0 +1,221 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" />
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  
+  <title>Some published results using the TEMUL Toolkit &mdash; TEMUL Toolkit v0.1.3 documentation</title>
+  
+
+  
+  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+
+  
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+  
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+  
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+  
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+    
+      <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
+        <script src="_static/doctools.js"></script>
+    
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+
+    
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" /> 
+</head>
+
+<body class="wy-body-for-nav">
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+   
+  <div class="wy-grid-for-nav">
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+          
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+          
+          </a>
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+          
+            
+            
+              <div class="version">
+                Version 0.1.3
+              </div>
+            
+          
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+          
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
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+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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+            
+            
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+            
+            
+              <p class="caption"><span class="caption-text">Contents</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="using_temul.html">Getting started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflows.html">Analysis Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="polarisation_vectors_tutorial.html">Finding Polarisation Vectors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="polarisation_vectors_tutorial.html#plotting-polarisation-and-movement-vectors">Plotting Polarisation and Movement Vectors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="structure_map_tutorial.html">Plot Lattice Structure Maps</a></li>
+<li class="toctree-l1"><a class="reference internal" href="PTO_supercrystal_hadjimichael.html">Calculation of Atom Plane Curvature</a></li>
+<li class="toctree-l1"><a class="reference internal" href="PTO_Junction_moore.html">Analysis of PTO Domain Wall Junction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="masked_fft_tutorial.html">Masked FFT and iFFT</a></li>
+<li class="toctree-l1"><a class="reference internal" href="line_profile_tutorial.html">Line Intensity Profile Comparisons</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dg_visualiser_tutorial.html">Interactive Image Filtering</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api_doc.html">API documentation</a></li>
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+          
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="some-published-results-using-the-temul-toolkit">
+<span id="about-temul-toolkit"></span><h1>Some published results using the TEMUL Toolkit<a class="headerlink" href="#some-published-results-using-the-temul-toolkit" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+           </div>
+           
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
+
+    </p>
+  </div>
+    
+    
+    
+    Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    
+    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+</footer>
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script>
+
+  
+  
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+</html>
\ No newline at end of file
diff --git a/doc/_build/html/api_doc.html b/doc/_build/html/api_doc.html
index 721408d..6065207 100644
--- a/doc/_build/html/api_doc.html
+++ b/doc/_build/html/api_doc.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>API documentation &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>API documentation &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -65,7 +65,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -211,10 +211,10 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <dt class="sig sig-object py" id="temul.topotem.polarisation.atom_deviation_from_straight_line_fit">
 <span class="sig-prename descclassname"><span class="pre">temul.topotem.polarisation.</span></span><span class="sig-name descname"><span class="pre">atom_deviation_from_straight_line_fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sublattice</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis_number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">second_fit_rigid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#temul.topotem.polarisation.atom_deviation_from_straight_line_fit" title="Permalink to this definition">¶</a></dt>
 <dd><p>Fits the atomic columns in an atom plane to two straight lines using the
-first <code class="docutils literal notranslate"><span class="pre">n</span></code> and second (last) <code class="docutils literal notranslate"><span class="pre">n</span></code> atomic columns. Computes the distance of
-each atomic column from the line halfway between the two fitted lines, as
-described in <a href="#id9"><span class="problematic" id="id1">[1]_</span></a>. This is done for every sublattice atom plane along the
-chosen <code class="docutils literal notranslate"><span class="pre">axis_number</span></code>.</p>
+first <code class="docutils literal notranslate"><span class="pre">n</span></code> and second (last) <code class="docutils literal notranslate"><span class="pre">n</span></code> atomic columns. Computes the distance
+of each atomic column from the line halfway between the two fitted lines,
+as described in <a href="#id9"><span class="problematic" id="id1">[1]_</span></a>. This is done for every sublattice atom plane along
+the chosen <code class="docutils literal notranslate"><span class="pre">axis_number</span></code>.</p>
 <p>The slope of the first fitting will be used for the
 second fitting. Setting <code class="docutils literal notranslate"><span class="pre">second_fit_rigid</span></code> = False will reverse this
 behaviour.</p>
@@ -237,11 +237,13 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
-<dd class="field-even"><p><strong>x, y, u, v</strong> – x, y are the original atom position coordinates <code class="docutils literal notranslate"><span class="pre">sublattice.x_position`</span>
-<span class="pre">and</span> <span class="pre">``sublattice.y_position</span></code> for the coordinates included in the chosen
+<dd class="field-even"><p><strong>x, y, u, v</strong> – x, y are the original atom position coordinates
+<code class="docutils literal notranslate"><span class="pre">sublattice.x_position</span></code> and <code class="docutils literal notranslate"><span class="pre">sublattice.y_position</span></code> for
+the coordinates included in the chosen
 <code class="docutils literal notranslate"><span class="pre">axis_number</span></code>. u, v are the polarisation vector components pointing
 towards the halfway line from the atom position coordinates.
-These can be input to <code class="docutils literal notranslate"><span class="pre">plot_polarisation_vectors()</span></code> for visualisation.</p>
+These can be input to <code class="docutils literal notranslate"><span class="pre">plot_polarisation_vectors()</span></code>
+for visualisation.</p>
 </dd>
 <dt class="field-odd">Return type</dt>
 <dd class="field-odd"><p>lists of equal length</p>
@@ -595,9 +597,9 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <li><p><strong>v</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.10)"><em>list</em></a><em> or </em><em>1D NumPy array</em>) – </p></li>
 <li><p><strong>degrees</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – Change between degrees and radian. Default is radian.</p></li>
 <li><p><strong>angle_offset</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default None</em>) – Rotate the angles by the given amount. The function assumes that if you
-set <code class="docutils literal notranslate"><span class="pre">degrees=False</span></code> then the provided <code class="docutils literal notranslate"><span class="pre">angle_offset</span></code> is in radians, and
-if you set <code class="docutils literal notranslate"><span class="pre">degrees=True</span></code> then the provided <code class="docutils literal notranslate"><span class="pre">angle_offset</span></code> is in
-degrees.</p></li>
+set <code class="docutils literal notranslate"><span class="pre">degrees=False</span></code> then the provided <code class="docutils literal notranslate"><span class="pre">angle_offset</span></code> is in radians,
+and if you set <code class="docutils literal notranslate"><span class="pre">degrees=True</span></code> then the provided <code class="docutils literal notranslate"><span class="pre">angle_offset</span></code> is
+in degrees.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -728,8 +730,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <dl class="py function">
 <dt class="sig sig-object py" id="temul.topotem.polarisation.get_divide_into">
 <span class="sig-prename descclassname"><span class="pre">temul.topotem.polarisation.</span></span><span class="sig-name descname"><span class="pre">get_divide_into</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sublattice</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">averaging_by</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sampling</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zone_axis_index_A</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zone_axis_index_B</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#temul.topotem.polarisation.get_divide_into" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculate the <code class="docutils literal notranslate"><span class="pre">divide_into</span></code> required to get an averaging of <code class="docutils literal notranslate"><span class="pre">averaging_by</span></code>.
-<code class="docutils literal notranslate"><span class="pre">divide_into</span></code> can then be used in
+<dd><p>Calculate the <code class="docutils literal notranslate"><span class="pre">divide_into</span></code> required to get an averaging of
+<code class="docutils literal notranslate"><span class="pre">averaging_by</span></code>. <code class="docutils literal notranslate"><span class="pre">divide_into</span></code> can then be used in
 temul.topotem.polarisation.get_average_polarisation_in_regions.
 Also finds unit cell size and the number of unit cells in the (square)
 image along the x axis.</p>
@@ -790,8 +792,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <li><p><strong>plot</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a>) – Set to true if the figure should be plotted.</p></li>
 <li><p><strong>filename</strong> (<em>string</em><em>, </em><em>optional</em>) – If filename is set, the strain signal and plot will be saved.
 <code class="docutils literal notranslate"><span class="pre">plot</span></code> must be set to True.</p></li>
-<li><p><strong>return_x_y_z</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – If this is set to True, the <code class="docutils literal notranslate"><span class="pre">strain_signal</span></code> (map), as well as separate
-lists of the x, y, and strain values.</p></li>
+<li><p><strong>return_x_y_z</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – If this is set to True, the <code class="docutils literal notranslate"><span class="pre">strain_signal</span></code> (map), as well as
+separate lists of the x, y, and strain values.</p></li>
 <li><p><strong>**kwargs</strong> (Matplotlib keyword arguments passed to <code class="docutils literal notranslate"><span class="pre">imshow()</span></code>.) – </p></li>
 </ul>
 </dd>
@@ -853,7 +855,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <dt class="sig sig-object py" id="temul.topotem.polarisation.get_xyuv_from_line_fit">
 <span class="sig-prename descclassname"><span class="pre">temul.topotem.polarisation.</span></span><span class="sig-name descname"><span class="pre">get_xyuv_from_line_fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">second_fit_rigid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#temul.topotem.polarisation.get_xyuv_from_line_fit" title="Permalink to this definition">¶</a></dt>
 <dd><p>Fits the data in an array to two straight lines using the
-first <code class="docutils literal notranslate"><span class="pre">n</span></code> and second (last) <code class="docutils literal notranslate"><span class="pre">n</span></code> array value pairs. Computes the distance of
+first <code class="docutils literal notranslate"><span class="pre">n</span></code> and second (last) <code class="docutils literal notranslate"><span class="pre">n</span></code> array value pairs.
+Computes the distance of
 each array value pair from the line halfway between the two fitted lines.</p>
 <p>The slope of the first fitting will be used for the
 second fitting. Setting <code class="docutils literal notranslate"><span class="pre">second_fit_rigid</span></code> = False will reverse this
@@ -875,7 +878,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <dt class="field-even">Returns</dt>
 <dd class="field-even"><p><strong>x, y, u, v</strong> – x, y are the original arr coordinates. u, v are the vector components
 pointing towards the halfway line from the arr coordinates.
-These can be input to <code class="docutils literal notranslate"><span class="pre">plot_polarisation_vectors()</span></code> for visualisation.</p>
+These can be input to <code class="docutils literal notranslate"><span class="pre">plot_polarisation_vectors()</span></code> for
+visualisation.</p>
 </dd>
 <dt class="field-odd">Return type</dt>
 <dd class="field-odd"><p>lists of equal length</p>
@@ -957,23 +961,24 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <li><p><strong>unit_vector</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – Change the vectors magnitude to unit vectors for plotting purposes.
 Magnitude will still be displayed correctly for colormaps etc.</p></li>
 <li><p><strong>vector_rep</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><em>default &quot;magnitude&quot;</em>) – How the vectors are represented. This can be either their <code class="docutils literal notranslate"><span class="pre">magnitude</span></code>
-or <code class="docutils literal notranslate"><span class="pre">angle</span></code>. One may want to use <code class="docutils literal notranslate"><span class="pre">angle</span></code> when plotting a contour map,
-i.e., view the contours in terms of angles which can be useful for
-visualising regions of different polarisation.</p></li>
+or <code class="docutils literal notranslate"><span class="pre">angle</span></code>. One may want to use <code class="docutils literal notranslate"><span class="pre">angle</span></code> when plotting a
+contour map, i.e. view the contours in terms of angles which can be
+useful for visualising regions of different polarisation.</p></li>
 <li><p><strong>degrees</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – Change between degrees and radian. Default is radian.
-If <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;colorwheel&quot;</span></code>, then setting <code class="docutils literal notranslate"><span class="pre">degrees=True</span></code>   will convert
-the angle unit to degree from the default radians.</p></li>
-<li><p><strong>angle_offset</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default None</em>) – If using <code class="docutils literal notranslate"><span class="pre">vector_rep=&quot;angle&quot;</span></code>   or <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;contour&quot;</span></code>, this angle
-will rotate the vector angles displayed by the given amount. Useful
-when you want to offset the angle of the atom planes relative to the
-polarisation.</p></li>
+If <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;colorwheel&quot;</span></code>, then setting <code class="docutils literal notranslate"><span class="pre">degrees=True</span></code>
+will convert the angle unit to degree from the default radians.</p></li>
+<li><p><strong>angle_offset</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default None</em>) – If using <code class="docutils literal notranslate"><span class="pre">vector_rep=&quot;angle&quot;</span></code>   or <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;contour&quot;</span></code>, this
+angle will rotate the vector angles displayed by the given amount.
+Useful when you want to offset the angle of the atom planes relative
+to the polarisation.</p></li>
 <li><p><strong>save</strong> (<em>string</em>) – If set to <code class="docutils literal notranslate"><span class="pre">save=None</span></code>, the image will not be saved.</p></li>
 <li><p><strong>title</strong> (<em>string</em><em>, </em><em>default &quot;&quot;</em>) – Title of the plot.</p></li>
 <li><p><strong>color</strong> (<em>string</em><em>, </em><em>default &quot;r&quot;</em>) – Color of the arrows when <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;vector&quot;</span></code> or <code class="docutils literal notranslate"><span class="pre">&quot;contour&quot;</span></code>.</p></li>
 <li><p><strong>cmap</strong> (matplotlib colormap, default <code class="docutils literal notranslate"><span class="pre">&quot;viridis&quot;</span></code>) – Matplotlib cmap used for the vector arrows.</p></li>
-<li><p><strong>alpha</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 1.0</em>) – Transparency of the matplotlib <code class="docutils literal notranslate"><span class="pre">cmap</span></code>. For <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;colormap&quot;</span></code> and
-<code class="docutils literal notranslate"><span class="pre">plot_style=&quot;colorwheel&quot;</span></code>, this alpha applies to the vector arrows.
-For <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;contour&quot;</span></code> this alpha applies to the tricontourf map.</p></li>
+<li><p><strong>alpha</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 1.0</em>) – Transparency of the matplotlib <code class="docutils literal notranslate"><span class="pre">cmap</span></code>. For <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;colormap&quot;</span></code>
+and <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;colorwheel&quot;</span></code>, this alpha applies to the vector
+arrows. For <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;contour&quot;</span></code> this alpha applies to the
+tricontourf map.</p></li>
 <li><p><strong>image_cmap</strong> (<em>matplotlib colormap</em><em>, </em><em>default 'gray'</em>) – Matplotlib cmap that will be used for the overlay image.</p></li>
 <li><p><strong>monitor_dpi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>, </em><em>default 96</em>) – The DPI of the monitor, generally 96 pixels. Used to scale the image
 so that large images render correctly. Use a smaller value to enlarge
@@ -986,9 +991,10 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <li><p><strong>ticks</strong> (<em>colorbar ticks</em><em>, </em><em>default None</em>) – None or list of ticks or Locator If None, ticks are determined
 automatically from the input.</p></li>
 <li><p><strong>scalebar</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.10)"><em>dict</em></a><em>, </em><em>default False</em>) – Add a matplotlib-scalebar to the plot. If set to True the scalebar will
-appear similar to that given by Hyperspy’s <code class="docutils literal notranslate"><span class="pre">plot()</span></code> function. A custom
-scalebar can be included as a dictionary and more custom options can be
-found in the matplotlib-scalebar package. See below for an example.</p></li>
+appear similar to that given by Hyperspy’s <code class="docutils literal notranslate"><span class="pre">plot()</span></code> function. A
+custom scalebar can be included as a dictionary and more custom
+options can be found in the matplotlib-scalebar package. See below
+for an example.</p></li>
 <li><p><strong>antialiased</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – Applies only to <code class="docutils literal notranslate"><span class="pre">plot_style=&quot;contour&quot;</span></code>. Essentially removes the
 border between regions in the tricontourf map.</p></li>
 <li><p><strong>levels</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>, </em><em>default 20</em>) – Number of Matplotlib tricontourf levels to be used.</p></li>
@@ -1350,13 +1356,13 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <dt class="sig sig-object py" id="temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature">
 <span class="sig-prename descclassname"><span class="pre">temul.topotem.lattice_structure_tools.</span></span><span class="sig-name descname"><span class="pre">calculate_atom_plane_curvature</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sublattice</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zone_vector_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">func</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'strain_grad'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_planes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sampling</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pix'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'inferno'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Curvature</span> <span class="pre">Map'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_fits</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculates the curvature of the sublattice atom planes along the direction
-given by <code class="docutils literal notranslate"><span class="pre">zone_vector_index</span></code>. In the case of <a href="#id10"><span class="problematic" id="id3">[1]_</span></a>. below, the curvature is
-the inverse of the radius of curvature, and is effectively equal to the
+given by <code class="docutils literal notranslate"><span class="pre">zone_vector_index</span></code>. In the case of <a href="#id10"><span class="problematic" id="id3">[1]_</span></a>. below, the curvature
+is the inverse of the radius of curvature, and is effectively equal to the
 second derivative of the displacement direction of the atoms. Because the
 first derivative is negligible, the curvature can be calculated as the
 strain gradient <a class="footnote-reference brackets" href="#id6" id="id4">2</a>.
-With the parameter <code class="docutils literal notranslate"><span class="pre">func=&quot;strain_grad&quot;</span></code>, this function calculates the strain
-gradient of the atom planes of a Atomap Sublattice object.</p>
+With the parameter <code class="docutils literal notranslate"><span class="pre">func=&quot;strain_grad&quot;</span></code>, this function calculates the
+strain gradient of the atom planes of a Atomap Sublattice object.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
@@ -1656,8 +1662,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 of nearest neighbour values averaged from background_sub</p></li>
 <li><p><strong>percent_to_nn</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 0.40</em>) – Determines the boundary of the area surrounding each atomic
 column, as fraction of the distance to the nearest neighbour.</p></li>
-<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code> must
-be None.</p></li>
+<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code>
+must be None.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -1721,8 +1727,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 <li><p><strong>background_sub</strong> (<em>sublattice object</em>) – The sublattice used to find the average background.</p></li>
 <li><p><strong>percent_to_nn</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 0.4</em>) – Determines the boundary of the area surrounding each atomic
 column, as fraction of the distance to the nearest neighbour.</p></li>
-<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code> must
-be None.</p></li>
+<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code>
+must be None.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -1764,8 +1770,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 background_sub</p></li>
 <li><p><strong>percent_to_nn</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 0.40</em>) – Determines the boundary of the area surrounding each atomic
 column, as fraction of the distance to the nearest neighbour.</p></li>
-<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code> must
-be None.</p></li>
+<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code>
+must be None.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -2281,15 +2287,15 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 would be added with the given parameters.</p></li>
 <li><p><strong>sublattice_name</strong> (<em>string</em><em>, </em><em>default 'sub_new'</em>) – the outputted sublattice object name and sublattice.name the new
 sublattice will be given</p></li>
-<li><p><strong>inplace</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default True</em>) – If set to True, the input <code class="docutils literal notranslate"><span class="pre">sublattice</span></code> will be changed inplace and the
-sublattice returned. If set to False, these changes will be output only
-to a new sublattice.</p></li>
+<li><p><strong>inplace</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default True</em>) – If set to True, the input <code class="docutils literal notranslate"><span class="pre">sublattice</span></code> will be changed inplace and
+the sublattice returned. If set to False, these changes will be output
+only to a new sublattice.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
 <dd class="field-even"><p><ul class="simple">
-<li><p>Atomap Sublattice object if <code class="docutils literal notranslate"><span class="pre">inplace=False</span></code>. See the <code class="docutils literal notranslate"><span class="pre">inplace</span></code> parameter</p></li>
-<li><p><em>for details.</em></p></li>
+<li><p>Atomap Sublattice object if <code class="docutils literal notranslate"><span class="pre">inplace=False</span></code>. See the <code class="docutils literal notranslate"><span class="pre">inplace</span></code></p></li>
+<li><p><em>parameter for details.</em></p></li>
 </ul>
 </p>
 </dd>
@@ -2486,8 +2492,8 @@ <h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 of nearest neighbour values averaged from background_sublattice.</p></li>
 <li><p><strong>percent_to_nn</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 0.40</em>) – Determines the boundary of the area surrounding each atomic
 column, as fraction of the distance to the nearest neighbour.</p></li>
-<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code> must
-be None.</p></li>
+<li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a>) – Radius of the atomic column in pixels. If chosen, <code class="docutils literal notranslate"><span class="pre">percent_to_nn</span></code>
+must be None.</p></li>
 <li><p><strong>split_symbol</strong> (<em>string</em><em>, </em><em>default '_'</em>) – The symbols used to split the element into its name
 and count.
 The first string ‘_’ is used to split the name and count
@@ -2621,10 +2627,11 @@ <h3>Image Simulation Functions<a class="headerlink" href="#image-simulation-func
 <li><p><strong>percent_to_nn</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 0.4</em>) – Determines the boundary of the area surrounding each atomic
 column, as fraction of the distance to the nearest neighbour.</p></li>
 <li><p><strong>mask_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>, </em><em>default None</em>) – Radius in pixels of the mask. If set, then set <code class="docutils literal notranslate"><span class="pre">percent_to_nn=None</span></code>.</p></li>
-<li><p><strong>refine</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – If set to True, the <code class="docutils literal notranslate"><span class="pre">calibrate_intensity_distance_with_sublattice_roi`</span>
-<span class="pre">calibration</span> <span class="pre">will</span> <span class="pre">refine</span> <span class="pre">the</span> <span class="pre">atom</span> <span class="pre">positions</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">calibration.</span> <span class="pre">May</span>
-<span class="pre">make</span> <span class="pre">the</span> <span class="pre">function</span> <span class="pre">very</span> <span class="pre">slow</span> <span class="pre">depending</span> <span class="pre">on</span> <span class="pre">the</span> <span class="pre">size</span> <span class="pre">of</span> <span class="pre">``image_to_filter`</span>
-<span class="pre">and</span> <span class="pre">``cropping_area</span></code>.</p></li>
+<li><p><strong>refine</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>default False</em>) – If set to True, the
+<code class="docutils literal notranslate"><span class="pre">calibrate_intensity_distance_with_sublattice_roi</span></code>
+calibration will refine the atom positions for each calibration. May
+make the function very slow depending on the size of
+<code class="docutils literal notranslate"><span class="pre">image_to_filter</span></code> and <code class="docutils literal notranslate"><span class="pre">cropping_area</span></code>.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -2655,8 +2662,8 @@ <h3>Image Simulation Functions<a class="headerlink" href="#image-simulation-func
 <dl class="py function">
 <dt class="sig sig-object py" id="temul.signal_processing.crop_image_hs">
 <span class="sig-prename descclassname"><span class="pre">temul.signal_processing.</span></span><span class="sig-name descname"><span class="pre">crop_image_hs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">image</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cropping_area</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scalebar_true</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#temul.signal_processing.crop_image_hs" title="Permalink to this definition">¶</a></dt>
-<dd><p>Crop a Hyperspy Signal2D by providing the <code class="docutils literal notranslate"><span class="pre">cropping_area</span></code>. See the example
-below.</p>
+<dd><p>Crop a Hyperspy Signal2D by providing the <code class="docutils literal notranslate"><span class="pre">cropping_area</span></code>. See the
+example below.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
@@ -3365,8 +3372,8 @@ <h3>Image Simulation Functions<a class="headerlink" href="#image-simulation-func
 <li><p><strong>sampling</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><em>default 'auto'</em>) – if set to ‘auto’ the function will attempt to find the sampling of
 image from image.axes_manager[0].scale.</p></li>
 <li><p><strong>units</strong> (<em>string</em><em>, </em><em>default 'nm'</em>) – </p></li>
-<li><p><strong>crop_offset</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>, </em><em>default 20</em>) – number of pixels away from the <code class="docutils literal notranslate"><span class="pre">line_profile_positions</span></code> coordinates the
-image crop will be taken.</p></li>
+<li><p><strong>crop_offset</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>, </em><em>default 20</em>) – number of pixels away from the <code class="docutils literal notranslate"><span class="pre">line_profile_positions</span></code>
+coordinates the image crop will be taken.</p></li>
 <li><p><strong>title</strong> (<em>string</em><em>, </em><em>default &quot;Intensity Profile&quot;</em>) – Title of the plot</p></li>
 <li><p><strong>marker_A</strong> (<em>Matplotlib marker</em>) – </p></li>
 <li><p><strong>marker_B</strong> (<em>Matplotlib marker</em>) – </p></li>
@@ -4087,7 +4094,7 @@ <h3>Image Simulation Functions<a class="headerlink" href="#image-simulation-func
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/define_roles.html b/doc/_build/html/define_roles.html
index 9a354fd..bac71c5 100644
--- a/doc/_build/html/define_roles.html
+++ b/doc/_build/html/define_roles.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>&lt;no title&gt; &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>&lt;no title&gt; &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -64,7 +64,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -181,7 +181,7 @@
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/dg_visualiser_tutorial.html b/doc/_build/html/dg_visualiser_tutorial.html
index e090cc6..a4f582e 100644
--- a/doc/_build/html/dg_visualiser_tutorial.html
+++ b/doc/_build/html/dg_visualiser_tutorial.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Interactive Image Filtering &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Interactive Image Filtering &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -179,9 +179,10 @@
             
   <div class="section" id="interactive-image-filtering">
 <span id="dg-visualiser-tutorial"></span><h1>Interactive Image Filtering<a class="headerlink" href="#interactive-image-filtering" title="Permalink to this headline">¶</a></h1>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_processing</span></span></code> module allows one to filter images with a
+<p>The <a class="reference internal" href="api_doc.html#module-temul.signal_processing" title="temul.signal_processing"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_processing</span></code></a> module allows one to filter images with a
 double Gaussian (band-pass) filter. Apart from the base functions, it can be
-done interactively with the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">visualise_dg_filter</span></span></code> function. In this
+done interactively with the
+<a class="reference internal" href="api_doc.html#temul.signal_processing.visualise_dg_filter" title="temul.signal_processing.visualise_dg_filter"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.signal_processing.visualise_dg_filter()</span></code></a> function. In this
 tutorial, we will see how to use the function on experimental data.</p>
 <div class="section" id="load-the-experimental-image">
 <h2>Load the Experimental Image<a class="headerlink" href="#load-the-experimental-image" title="Permalink to this headline">¶</a></h2>
@@ -195,15 +196,16 @@ <h2>Load the Experimental Image<a class="headerlink" href="#load-the-experimenta
 </div>
 <div class="section" id="interactively-filter-the-experimental-image">
 <h2>Interactively Filter the Experimental Image<a class="headerlink" href="#interactively-filter-the-experimental-image" title="Permalink to this headline">¶</a></h2>
-<p>Run the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">visualise_dg_filter</span></span></code> function. There are lots of other parameters
-too for customisation.</p>
+<p>Run the <a class="reference internal" href="api_doc.html#temul.signal_processing.visualise_dg_filter" title="temul.signal_processing.visualise_dg_filter"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.signal_processing.visualise_dg_filter()</span></code></a> function.
+There are lots of other parameters too for customisation.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">tml</span><span class="o">.</span><span class="n">visualise_dg_filter</span><span class="p">(</span><span class="n">image</span><span class="p">)</span>
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="_images/dg_visualiser.gif"><img alt="_images/dg_visualiser.gif" src="_images/dg_visualiser.gif" style="width: 638.0px; height: 358.0px;" /></a>
-<p>As we can see, an interactive window appears, showing the FFT (“FFT Widget”) of the image with
-the positions of the inner and outer Gaussian full width at half maximums (FWHMs).
-The inital FWHMs can be changed with the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">d_inner</span></span></code> and <code class="code python docutils literal notranslate"><span class="name"><span class="pre">d_outer</span></span></code>
+<p>As we can see, an interactive window appears, showing the FFT (“FFT Widget”)
+of the image with the positions of the inner and outer Gaussian full width
+at half maximums (FWHMs). The inital FWHMs can be changed with the
+<code class="code python docutils literal notranslate"><span class="name"><span class="pre">d_inner</span></span></code> and <code class="code python docutils literal notranslate"><span class="name"><span class="pre">d_outer</span></span></code>
 parameters (limits can also be changed).</p>
 <p>To change the two FWHMs interactively
 just use the sliders at the bottom of the window. Reset can be used to reset the
@@ -214,7 +216,8 @@ <h2>Interactively Filter the Experimental Image<a class="headerlink" href="#inte
 <div class="section" id="return-the-filtered-image">
 <h2>Return the Filtered Image<a class="headerlink" href="#return-the-filtered-image" title="Permalink to this headline">¶</a></h2>
 <p>When we have suitable FWHMs for the inner and outer Gaussians, we can use
-the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">double_gaussian_fft_filter</span></span></code> function the return a filtered image.</p>
+the <a class="reference internal" href="api_doc.html#temul.signal_processing.double_gaussian_fft_filter" title="temul.signal_processing.double_gaussian_fft_filter"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.signal_processing.double_gaussian_fft_filter()</span></code></a> function
+the return a filtered image.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">filtered_image</span> <span class="o">=</span> <span class="n">tml</span><span class="o">.</span><span class="n">double_gaussian_fft_filter</span><span class="p">(</span><span class="n">image</span><span class="p">,</span> <span class="mi">50</span><span class="p">,</span> <span class="mi">150</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">image</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">filtered_image</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>
@@ -222,9 +225,9 @@ <h2>Return the Filtered Image<a class="headerlink" href="#return-the-filtered-im
 </div>
 <a class="reference internal image-reference" href="_images/image_plot.png"><img alt="_images/image_plot.png" src="_images/image_plot.png" style="width: 320.0px; height: 289.5px;" /></a>
 <a class="reference internal image-reference" href="_images/filtered_image_plot.png"><img alt="_images/filtered_image_plot.png" src="_images/filtered_image_plot.png" style="width: 320.0px; height: 289.5px;" /></a>
-<p>Details on the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">double_gaussian_fft_filter_optimised</span></span></code> function can be
-found in the <a class="reference internal" href="api_doc.html#api-doc"><span class="std std-ref">API documentation</span></a>.
-We hope to added some examples of this functions to this page in future.</p>
+<p>Details on the
+<a class="reference internal" href="api_doc.html#temul.signal_processing.double_gaussian_fft_filter_optimised" title="temul.signal_processing.double_gaussian_fft_filter_optimised"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.signal_processing.double_gaussian_fft_filter_optimised()</span></code></a>
+function can be found in the <a class="reference internal" href="api_doc.html#api-doc"><span class="std std-ref">API documentation</span></a>.</p>
 </div>
 </div>
 
@@ -242,7 +245,7 @@ <h2>Return the Filtered Image<a class="headerlink" href="#return-the-filtered-im
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html
index 8883a1d..42c7034 100644
--- a/doc/_build/html/genindex.html
+++ b/doc/_build/html/genindex.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Index &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Index &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -64,7 +64,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -678,7 +678,7 @@ <h2 id="W">W</h2>
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
index e51321a..73b6ae2 100644
--- a/doc/_build/html/index.html
+++ b/doc/_build/html/index.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Welcome to TEMUL Toolkit’s documentation! &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Welcome to TEMUL Toolkit’s documentation! &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -65,7 +65,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -178,20 +178,30 @@ <h1>Welcome to TEMUL Toolkit’s documentation!<a class="headerlink" href="#welc
 <a class="reference external" href="https://hyperspy.org/">HyperSpy</a> and <a class="reference external" href="https://atomap.org/">Atomap</a>.</p>
 <div class="section" id="interactive-examples">
 <h2>Interactive Examples<a class="headerlink" href="#interactive-examples" title="Permalink to this headline">¶</a></h2>
+<p>The easiest way to try the TEMUL Toolkit is via Binder:
+<a class="reference external" href="https://hub.gke2.mybinder.org/user/pinkshnack-temul-19r27k52/lab/tree/code_tutorials/polarisation_vectors_tutorial.ipynb">introductory Jupyter Notebook</a>.
+To install the TEMUL Toolkit on your own computer,
+see the <a class="reference internal" href="#install"><span class="std std-ref">Installation</span></a> instructions.</p>
+<p>And there are more examples with Binder, just click the below button!</p>
 <a class="reference external image-reference" href="https://mybinder.org/v2/gh/PinkShnack/TEMUL/master"><img alt="https://mybinder.org/badge_logo.svg" src="https://mybinder.org/badge_logo.svg" /></a>
-<p>Click the button above to start some data analysis (it may take a few minutes to load).
+<p>Click the button above to start some data analysis
+(it may take a few minutes to load).
 The “code_tutorials” folder contains walkthroughs of some of the documentation
 examples from this website.
-The “publication_examples” folder will allow you to analyse data from published scientific papers!
+The “publication_examples” folder will allow you to analyse data from
+published scientific papers!
 Just navigate to whichever of these folders you want click on the “.ipynb” files.</p>
 </div>
+<div class="section" id="some-published-results-using-the-temul-toolkit">
+<span id="about-temul-toolkit"></span><h2>Some published results using the TEMUL Toolkit<a class="headerlink" href="#some-published-results-using-the-temul-toolkit" title="Permalink to this headline">¶</a></h2>
+</div>
 <div class="section" id="news">
-<span id="install"></span><h2>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h2>
+<span id="id1"></span><h2>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="version-0-1-4-released">
 <h3>16/02/2021: Version 0.1.4 released<a class="headerlink" href="#version-0-1-4-released" title="Permalink to this headline">¶</a></h3>
 <p>The polarisation, structure tools and fft mapping has now
 been refactored into the topotem module. The temul
-functionality remains the same i.e. <a href="#id1"><span class="problematic" id="id2">``</span></a>import temul.api as tml`.</p>
+functionality remains the same i.e. <a href="#id2"><span class="problematic" id="id3">``</span></a>import temul.api as tml`.</p>
 </div>
 <div class="section" id="version-0-1-3-released">
 <h3>16/02/2021: Version 0.1.3 released<a class="headerlink" href="#version-0-1-3-released" title="Permalink to this headline">¶</a></h3>
@@ -322,23 +332,38 @@ <h3>02/11/2020: Version 0.1.1 released<a class="headerlink" href="#version-0-1-1
 </div>
 </div>
 <div class="section" id="installation">
-<span id="id5"></span><h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
-<p>The TEMUL Toolkit can be installed easily with PIP (those using Windows may need to download VS C++ Build Tools, see below).</p>
+<span id="install"></span><h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
+<p>The TEMUL Toolkit can be installed easily with PIP (those using Windows may
+need to download VS C++ Build Tools, see below).</p>
 <p><code class="code bash docutils literal notranslate"><span class="pre">$</span> <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">temul-toolkit</span></code></p>
-<p>Then, it can be imported with the name “temul”. For example, to import most of the temul functionality use:</p>
+<p>Then, it can be imported with the name “temul”. For example, to import most
+of the temul functionality use:</p>
 <p><code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">temul.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">tml</span></span></code></p>
-<p>Matplotlib 3.3 currently has compatability issues with iPython, see below for the fix.</p>
 <ul>
-<li><p>If installing on Windows, you will need Visual Studio C++ Build Tools. Download it <a class="reference external" href="https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019">here</a>. After downloading, choose the “C++ Build Tools” Workload and click install.</p></li>
-<li><p>Matplotlib seems to have issues with iPython at the moment. Install matplotlib==3.2 until this issue is resolved by Matplotlib. See <a class="reference external" href="https://stackoverflow.com/questions/64291087/matplotlib-module-sip-has-no-attribute-setapi">here</a> for more details.</p></li>
-<li><p>If you want to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">io</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">write_cif_from_dataframe</span></span></code> function, you will need to install pyCifRW version 4.3. This requires Visual Studio.</p></li>
-<li><p>If you wish to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">simulations</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> or <code class="code python docutils literal notranslate"><span class="name"><span class="pre">model_refiner</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> modules, you will need to install PyPrismatic. This requires Visual Studio and other dependencies.</p></li>
-<li><p>If you’re using any of the functions or classes that require element quantification:</p>
+<li><p>If installing on Windows, you will need Visual Studio C++ Build Tools.
+Download it <a class="reference external" href="https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019">here</a>.
+After downloading, choose the “C++ Build Tools” Workload and click install.</p></li>
+<li><p>If you want to use the <a class="reference internal" href="api_doc.html#temul.io.write_cif_from_dataframe" title="temul.io.write_cif_from_dataframe"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.io.write_cif_from_dataframe()</span></code></a>
+function, you will need to install pyCifRW version 4.3. This requires
+Visual Studio.</p></li>
+<li><p>If you wish to use the <code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.simulations</span></code> or
+<code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.model_refiner</span></code> modules, you will need to install PyPrismatic.
+This requires Visual Studio and other dependencies.
+<strong>It is unfortunately not guaranteed to work</strong>. If you want to help develop
+the <code class="xref py py-class docutils literal notranslate"><span class="pre">temul.model_refiner.Model_Refiner</span></code>, please create an issue
+and/or a pull request on the
+<a class="reference external" href="https://github.com/PinkShnack/TEMUL">TEMUL github</a>.</p></li>
+<li><p>If you’re using any of the functions or classes that require element
+quantification:</p>
 <blockquote>
 <div><ul class="simple">
-<li><p>navigate to the “temul/external” directory, copy the “atomap_devel_012” folder and paste that in your “site-packages” directory.</p></li>
-<li><p>Then, when using atomap to create sublattices and quantify elements call atomap like this: <code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">atomap_devel_012.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">am</span></span></code>.</p></li>
-<li><p>This development version is slowly being folded into the master branch here: <a class="reference external" href="https://gitlab.com/atomap/atomap/-/issues/93">https://gitlab.com/atomap/atomap/-/issues/93</a> and any help or tips on implementation are welcome!</p></li>
+<li><p>navigate to the “temul/external” directory, copy the “atomap_devel_012”
+folder and paste that in your “site-packages” directory.</p></li>
+<li><p>Then, when using atomap to create sublattices and quantify elements call
+atomap like this: <code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">atomap_devel_012.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">am</span></span></code>.</p></li>
+<li><p>This development version is slowly being folded into the master branch
+here: <a class="reference external" href="https://gitlab.com/atomap/atomap/-/issues/93">https://gitlab.com/atomap/atomap/-/issues/93</a> and any help or
+tips on implementation are welcome!</p></li>
 </ul>
 </div></blockquote>
 </li>
@@ -365,7 +390,9 @@ <h2>Code Documentation<a class="headerlink" href="#code-documentation" title="Pe
 <h2>Cite<a class="headerlink" href="#cite" title="Permalink to this headline">¶</a></h2>
 <p>To cite the latest TEMUL Toolkit version, use the following DOI:</p>
 <a class="reference external image-reference" href="https://www.zenodo.org/badge/latestdoi/203785298"><img alt="https://www.zenodo.org/badge/203785298.svg" src="https://www.zenodo.org/badge/203785298.svg" /></a>
-<p>For example: Eoghan O’Connell, Michael Hennessy, &amp; Eoin Moynihan. (2020, November 2). PinkShnack/TEMUL: Initial Temul-Toolkit Release (Version 0.1.1). Zenodo. <a class="reference external" href="http://doi.org/10.5281/zenodo.4185974">http://doi.org/10.5281/zenodo.4185974</a></p>
+<p>For example: Eoghan O’Connell, Michael Hennessy, &amp; Eoin Moynihan.
+(2021). PinkShnack/TEMUL: (Version 0.1.3).
+Zenodo. <a class="reference external" href="http://doi.org/10.5281/zenodo.4543963">http://doi.org/10.5281/zenodo.4543963</a></p>
 <p>If you wish to cite an older release of the TEMUL Toolkit, click on the above
 badge to find the relevant version.</p>
 </div>
@@ -408,7 +435,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/install.html b/doc/_build/html/install.html
index fe6b5bc..6f93a54 100644
--- a/doc/_build/html/install.html
+++ b/doc/_build/html/install.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Installation &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Installation &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -177,24 +177,39 @@
             
   <div class="section" id="installation">
 <span id="install"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
-<p>The TEMUL Toolkit can be installed easily with PIP (those using Windows may need to download VS C++ Build Tools, see below).</p>
+<p>The TEMUL Toolkit can be installed easily with PIP (those using Windows may
+need to download VS C++ Build Tools, see below).</p>
 <p><code class="code bash docutils literal notranslate"><span class="pre">$</span> <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">temul-toolkit</span></code></p>
-<p>Then, it can be imported with the name “temul”. For example, to import most of the temul functionality use:</p>
+<p>Then, it can be imported with the name “temul”. For example, to import most
+of the temul functionality use:</p>
 <p><code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">temul.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">tml</span></span></code></p>
-<p>Matplotlib 3.3 currently has compatability issues with iPython, see below for the fix.</p>
 <div class="section" id="installation-problems-notes">
 <h2>Installation Problems &amp; Notes<a class="headerlink" href="#installation-problems-notes" title="Permalink to this headline">¶</a></h2>
 <ul>
-<li><p>If installing on Windows, you will need Visual Studio C++ Build Tools. Download it <a class="reference external" href="https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019">here</a>. After downloading, choose the “C++ Build Tools” Workload and click install.</p></li>
-<li><p>Matplotlib seems to have issues with iPython at the moment. Install matplotlib==3.2 until this issue is resolved by Matplotlib. See <a class="reference external" href="https://stackoverflow.com/questions/64291087/matplotlib-module-sip-has-no-attribute-setapi">here</a> for more details.</p></li>
-<li><p>If you want to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">io</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">write_cif_from_dataframe</span></span></code> function, you will need to install pyCifRW version 4.3. This requires Visual Studio.</p></li>
-<li><p>If you wish to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">simulations</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> or <code class="code python docutils literal notranslate"><span class="name"><span class="pre">model_refiner</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> modules, you will need to install PyPrismatic. This requires Visual Studio and other dependencies.</p></li>
-<li><p>If you’re using any of the functions or classes that require element quantification:</p>
+<li><p>If installing on Windows, you will need Visual Studio C++ Build Tools.
+Download it <a class="reference external" href="https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019">here</a>.
+After downloading, choose the “C++ Build Tools” Workload and click install.</p></li>
+<li><p>If you want to use the <a class="reference internal" href="api_doc.html#temul.io.write_cif_from_dataframe" title="temul.io.write_cif_from_dataframe"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.io.write_cif_from_dataframe()</span></code></a>
+function, you will need to install pyCifRW version 4.3. This requires
+Visual Studio.</p></li>
+<li><p>If you wish to use the <code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.simulations</span></code> or
+<code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.model_refiner</span></code> modules, you will need to install PyPrismatic.
+This requires Visual Studio and other dependencies.
+<strong>It is unfortunately not guaranteed to work</strong>. If you want to help develop
+the <code class="xref py py-class docutils literal notranslate"><span class="pre">temul.model_refiner.Model_Refiner</span></code>, please create an issue
+and/or a pull request on the
+<a class="reference external" href="https://github.com/PinkShnack/TEMUL">TEMUL github</a>.</p></li>
+<li><p>If you’re using any of the functions or classes that require element
+quantification:</p>
 <blockquote>
 <div><ul class="simple">
-<li><p>navigate to the “temul/external” directory, copy the “atomap_devel_012” folder and paste that in your “site-packages” directory.</p></li>
-<li><p>Then, when using atomap to create sublattices and quantify elements call atomap like this: <code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">atomap_devel_012.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">am</span></span></code>.</p></li>
-<li><p>This development version is slowly being folded into the master branch here: <a class="reference external" href="https://gitlab.com/atomap/atomap/-/issues/93">https://gitlab.com/atomap/atomap/-/issues/93</a> and any help or tips on implementation are welcome!</p></li>
+<li><p>navigate to the “temul/external” directory, copy the “atomap_devel_012”
+folder and paste that in your “site-packages” directory.</p></li>
+<li><p>Then, when using atomap to create sublattices and quantify elements call
+atomap like this: <code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">atomap_devel_012.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">am</span></span></code>.</p></li>
+<li><p>This development version is slowly being folded into the master branch
+here: <a class="reference external" href="https://gitlab.com/atomap/atomap/-/issues/93">https://gitlab.com/atomap/atomap/-/issues/93</a> and any help or
+tips on implementation are welcome!</p></li>
 </ul>
 </div></blockquote>
 </li>
@@ -216,7 +231,7 @@ <h2>Installation Problems &amp; Notes<a class="headerlink" href="#installation-p
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/line_profile_tutorial.html b/doc/_build/html/line_profile_tutorial.html
index 8d4ab80..c52b0f7 100644
--- a/doc/_build/html/line_profile_tutorial.html
+++ b/doc/_build/html/line_profile_tutorial.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Line Intensity Profile Comparisons &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Line Intensity Profile Comparisons &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -179,11 +179,13 @@
             
   <div class="section" id="line-intensity-profile-comparisons">
 <span id="line-profile-tutorial"></span><h1>Line Intensity Profile Comparisons<a class="headerlink" href="#line-intensity-profile-comparisons" title="Permalink to this headline">¶</a></h1>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_plotting</span></span></code> module allows one to draw line intensity profiles
-over images. The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">compare_images_line_profile_one_image</span></span></code> can be used to
+<p>The <a class="reference internal" href="api_doc.html#module-temul.signal_plotting" title="temul.signal_plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_plotting</span></code></a> module allows one to draw line
+intensity profiles over images. The
+:py:func`temul.signal_plotting.compare_images_line_profile_one_image` can be used to
 draw two line profiles on one image for comparison. In future we hope to expand
 this function to allow for multiple line profiles on one image. The
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">compare_images_line_profile_two_images</span></span></code> function allows you to draw a line
+<a class="reference internal" href="api_doc.html#temul.signal_plotting.compare_images_line_profile_two_images" title="temul.signal_plotting.compare_images_line_profile_two_images"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.signal_plotting.compare_images_line_profile_two_images()</span></code></a>
+function allows you to draw a line
 profile on an image, and apply that same profile to another image (of the same shape).
 This can be useful for comparing subsequent images in series or comparing experimental
 and simulated images.</p>
@@ -191,7 +193,7 @@
 <div class="section" id="load-the-example-images">
 <h2>Load the Example Images<a class="headerlink" href="#load-the-example-images" title="Permalink to this headline">¶</a></h2>
 <p>Here we load some dummy data using a variation of Atomap’s
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_simple_cubic_signal</span></span></code> function.</p>
+<a class="reference internal" href="api_doc.html#temul.dummy_data.get_simple_cubic_signal" title="temul.dummy_data.get_simple_cubic_signal"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.dummy_data.get_simple_cubic_signal()</span></code></a> function.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">temul.dummy_data</span> <span class="kn">import</span> <span class="n">get_simple_cubic_signal</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">imageA</span> <span class="o">=</span> <span class="n">get_simple_cubic_signal</span><span class="p">(</span><span class="n">image_noise</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">amplitude</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">5</span><span class="p">])</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">imageA</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>
@@ -206,8 +208,10 @@ <h2>Load the Example Images<a class="headerlink" href="#load-the-example-images"
 <div class="section" id="compare-two-line-profiles-in-one-image">
 <h2>Compare two Line Profiles in one Image<a class="headerlink" href="#compare-two-line-profiles-in-one-image" title="Permalink to this headline">¶</a></h2>
 <p>As with the <a class="reference internal" href="masked_fft_tutorial.html#masked-fft-tutorial"><span class="std std-ref">Masked FFT and iFFT</span></a> tutorial, we can
-choose points on the image. This time we use <code class="code python docutils literal notranslate"><span class="name"><span class="pre">choose_points_on_image</span></span></code>.
-We need to choose four points for the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">compare_images_line_profile_one_image</span></span></code>
+choose points on the image. This time we use
+<a class="reference internal" href="api_doc.html#temul.topotem.fft_mapping.choose_points_on_image" title="temul.topotem.fft_mapping.choose_points_on_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.fft_mapping.choose_points_on_image()</span></code></a>.
+We need to choose four points for the
+<a class="reference internal" href="api_doc.html#temul.signal_plotting.compare_images_line_profile_one_image" title="temul.signal_plotting.compare_images_line_profile_one_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.signal_plotting.compare_images_line_profile_one_image()</span></code></a>
 function, as it draws two line profiles over one image.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.api</span> <span class="k">as</span> <span class="nn">tml</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">line_profile_positions</span> <span class="o">=</span> <span class="n">tml</span><span class="o">.</span><span class="n">choose_points_on_image</span><span class="p">(</span><span class="n">imageA</span><span class="p">)</span>
@@ -229,7 +233,8 @@ <h2>Compare two Line Profiles in one Image<a class="headerlink" href="#compare-t
 </div>
 <div class="section" id="compare-two-images-with-line-profile">
 <h2>Compare two Images with Line Profile<a class="headerlink" href="#compare-two-images-with-line-profile" title="Permalink to this headline">¶</a></h2>
-<p>Using <code class="code python docutils literal notranslate"><span class="name"><span class="pre">choose_points_on_image</span></span></code>, we now choose two points on one image.
+<p>Using <a class="reference internal" href="api_doc.html#temul.topotem.fft_mapping.choose_points_on_image" title="temul.topotem.fft_mapping.choose_points_on_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.fft_mapping.choose_points_on_image()</span></code></a>,
+we now choose two points on one image.
 Then, we plot this line intensity profile over the same position in two images.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">line_profile_positions</span> <span class="o">=</span> <span class="n">tml</span><span class="o">.</span><span class="n">choose_points_on_image</span><span class="p">(</span><span class="n">imageA</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">line_profile_positions</span>
@@ -263,7 +268,7 @@ <h2>Compare two Images with Line Profile<a class="headerlink" href="#compare-two
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/masked_fft_tutorial.html b/doc/_build/html/masked_fft_tutorial.html
index c11349c..fcc25c4 100644
--- a/doc/_build/html/masked_fft_tutorial.html
+++ b/doc/_build/html/masked_fft_tutorial.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Masked FFT and iFFT &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Masked FFT and iFFT &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -180,9 +180,12 @@
             
   <div class="section" id="masked-fft-and-ifft">
 <span id="masked-fft-tutorial"></span><h1>Masked FFT and iFFT<a class="headerlink" href="#masked-fft-and-ifft" title="Permalink to this headline">¶</a></h1>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_processing</span></span></code> module allows one to choose the masking coordinates with
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">choose_mask_coordinates</span></span></code> and easily returnt the masked fast Fourier Transform (FFT) with
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_masked_ifft</span></span></code>. This can useful in various scenarios, from understanding
+<p>The <a class="reference internal" href="api_doc.html#module-temul.signal_processing" title="temul.signal_processing"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_processing</span></code></a> module allows one to choose the
+masking coordinates with
+<a class="reference internal" href="api_doc.html#temul.topotem.fft_mapping.choose_mask_coordinates" title="temul.topotem.fft_mapping.choose_mask_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.fft_mapping.choose_mask_coordinates()</span></code></a> and easily
+return the masked fast Fourier Transform (FFT) with
+<a class="reference internal" href="api_doc.html#temul.topotem.fft_mapping.get_masked_ifft" title="temul.topotem.fft_mapping.get_masked_ifft"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.fft_mapping.get_masked_ifft()</span></code></a>. This can useful in
+various scenarios, from understanding
 the diffraction space spots and how they relate to the real space structure,
 to <a class="reference external" href="https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.12876">revealing domain walls</a>
 and finding initial atom positions for difficult images.</p>
@@ -261,7 +264,7 @@ <h2>Run FFT masking for Multiple Images<a class="headerlink" href="#run-fft-mask
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/news.html b/doc/_build/html/news.html
index a1016f5..8510062 100644
--- a/doc/_build/html/news.html
+++ b/doc/_build/html/news.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>News &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>News &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -64,7 +64,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -171,12 +171,12 @@
            <div itemprop="articleBody">
             
   <div class="section" id="news">
-<span id="install"></span><h1>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h1>
+<span id="id1"></span><h1>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="version-0-1-4-released">
 <h2>16/02/2021: Version 0.1.4 released<a class="headerlink" href="#version-0-1-4-released" title="Permalink to this headline">¶</a></h2>
 <p>The polarisation, structure tools and fft mapping has now
 been refactored into the topotem module. The temul
-functionality remains the same i.e. <a href="#id1"><span class="problematic" id="id2">``</span></a>import temul.api as tml`.</p>
+functionality remains the same i.e. <a href="#id2"><span class="problematic" id="id3">``</span></a>import temul.api as tml`.</p>
 </div>
 <div class="section" id="version-0-1-3-released">
 <h2>16/02/2021: Version 0.1.3 released<a class="headerlink" href="#version-0-1-3-released" title="Permalink to this headline">¶</a></h2>
@@ -249,7 +249,7 @@ <h2>02/11/2020: Version 0.1.1 released<a class="headerlink" href="#version-0-1-1
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/objects.inv b/doc/_build/html/objects.inv
index c60632e..2b94b61 100644
Binary files a/doc/_build/html/objects.inv and b/doc/_build/html/objects.inv differ
diff --git a/doc/_build/html/polarisation_vectors_tutorial.html b/doc/_build/html/polarisation_vectors_tutorial.html
index 62daba8..acde27d 100644
--- a/doc/_build/html/polarisation_vectors_tutorial.html
+++ b/doc/_build/html/polarisation_vectors_tutorial.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Finding Polarisation Vectors &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Finding Polarisation Vectors &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -189,13 +189,13 @@
 of each.</p>
 <p>Current functions:</p>
 <ol class="arabic simple">
-<li><p>Using Atomap’s <code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_polarization_from_second_sublattice</span></span></code> Sublattice
-method. Great for “standard” polarised structures with two sublattices.</p></li>
-<li><p>Using the TEMUL <code class="code python docutils literal notranslate"><span class="name"><span class="pre">find_polarisation_vectors</span></span></code> function. Useful for
-structures that Atomap’s <code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_polarization_from_second_sublattice</span></span></code> can’t
-handle.</p></li>
-<li><p>Using the TEMUL <code class="code python docutils literal notranslate"><span class="name"><span class="pre">atom_deviation_from_straight_line_fit</span></span></code> function.
-Useful for calculating polarisation from a single sublattice, similar to and
+<li><p>Using Atomap’s <a class="reference external" href="https://atomap.org/api_documentation.html?highlight=get_polarization#atomap.sublattice.Sublattice.get_polarization_from_second_sublattice">get_polarization_from_second_sublattice</a>
+Sublattice method. Great for “standard” polarised structures with two sublattices.</p></li>
+<li><p>Using the TEMUL <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.find_polarisation_vectors" title="temul.topotem.polarisation.find_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.find_polarisation_vectors()</span></code></a>
+function. Useful for structures that Atomap’s
+<code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_polarization_from_second_sublattice</span></span></code> can’t handle.</p></li>
+<li><p>Using the TEMUL <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.atom_deviation_from_straight_line_fit" title="temul.topotem.polarisation.atom_deviation_from_straight_line_fit"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.atom_deviation_from_straight_line_fit()</span></code></a>
+function. Useful for calculating polarisation from a single sublattice, similar to and
 based off: J. Gonnissen <em>et al</em>, Direct Observation of Ferroelectric Domain Walls in
 LiNbO3: Wall‐Meanders, Kinks, and Local Electric Charges, 26, 42, 2016, DOI: 10.1002/adfm.201603489.</p></li>
 </ol>
@@ -207,11 +207,12 @@
 <a class="reference external image-reference" href="https://mybinder.org/v2/gh/PinkShnack/TEMUL/master"><img alt="https://mybinder.org/badge_logo.svg" src="https://mybinder.org/badge_logo.svg" /></a>
 <div class="section" id="for-standard-polarised-structures-e-g-pto">
 <h2>For standard Polarised Structures (e.g., PTO)<a class="headerlink" href="#for-standard-polarised-structures-e-g-pto" title="Permalink to this headline">¶</a></h2>
-<p>Atomap’s <code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_polarization_from_second_sublattice</span></span></code> Sublattice method will
+<p>Atomap’s <a class="reference external" href="https://atomap.org/api_documentation.html?highlight=get_polarization#atomap.sublattice.Sublattice.get_polarization_from_second_sublattice">get_polarization_from_second_sublattice</a>
+Sublattice method will
 be sufficent for most users when dealing with the classic PTO-style polarisation,
 wherein the atoms in a sublattice are polarised with respect to a second sublattice.</p>
 <p>See the second section of this tutorial on how to plot this in many different ways
-using <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_polarisation_vectors</span></span></code>!</p>
+using <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.plot_polarisation_vectors" title="temul.topotem.polarisation.plot_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.plot_polarisation_vectors()</span></code></a>!</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.api</span> <span class="k">as</span> <span class="nn">tml</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">temul.dummy_data</span> <span class="kn">import</span> <span class="n">get_polarisation_dummy_dataset</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">atom_lattice</span> <span class="o">=</span> <span class="n">get_polarisation_dummy_dataset</span><span class="p">(</span><span class="n">image_noise</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
@@ -237,12 +238,13 @@ <h2>For standard Polarised Structures (e.g., PTO)<a class="headerlink" href="#fo
 <div class="section" id="for-nonstandard-polarised-structures-e-g-boracites">
 <h2>For nonstandard Polarised Structures (e.g., Boracites)<a class="headerlink" href="#for-nonstandard-polarised-structures-e-g-boracites" title="Permalink to this headline">¶</a></h2>
 <p>When the above function can’t isn’t suitable, the TEMUL
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">find_polarisation_vectors</span></span></code> function may be an option. It is useful for
-structures that Atomap’s <code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_polarization_from_second_sublattice</span></span></code> can’t
+<a class="reference internal" href="api_doc.html#temul.topotem.polarisation.find_polarisation_vectors" title="temul.topotem.polarisation.find_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.find_polarisation_vectors()</span></code></a> function may
+be an option. It is useful for structures that Atomap’s
+<code class="code python docutils literal notranslate"><span class="name"><span class="pre">get_polarization_from_second_sublattice</span></span></code> can’t
 handle. It is a little more involved and requires some extra preparation when
 creating the sublattices.</p>
 <p>See the second section of this tutorial on how to plot this in many different ways
-using <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_polarisation_vectors</span></span></code>!</p>
+using <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.plot_polarisation_vectors" title="temul.topotem.polarisation.plot_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.plot_polarisation_vectors()</span></code></a>!</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.api</span> <span class="k">as</span> <span class="nn">tml</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">atomap.api</span> <span class="k">as</span> <span class="nn">am</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -285,12 +287,12 @@ <h2>For nonstandard Polarised Structures (e.g., Boracites)<a class="headerlink"
 <h2>For single Polarised Sublattices (e.g., LNO)<a class="headerlink" href="#for-single-polarised-sublattices-e-g-lno" title="Permalink to this headline">¶</a></h2>
 <p>When dealing with structures in which the polarisation must be extracted from a
 single sublattice (one type of chemical atomic column, the TEMUL
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">atom_deviation_from_straight_line_fit</span></span></code> function
+<a class="reference internal" href="api_doc.html#temul.topotem.polarisation.atom_deviation_from_straight_line_fit" title="temul.topotem.polarisation.atom_deviation_from_straight_line_fit"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.atom_deviation_from_straight_line_fit()</span></code></a> function
 may be an option. It is based off the description by J. Gonnissen <em>et al</em>,
 Direct Observation of Ferroelectric Domain Walls in LiNbO3: Wall‐Meanders,
 Kinks, and Local Electric Charges, 26, 42, 2016, DOI: 10.1002/adfm.201603489.</p>
 <p>See the second section of this tutorial on how to plot this in many different ways
-using <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_polarisation_vectors</span></span></code>!</p>
+using <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.plot_polarisation_vectors" title="temul.topotem.polarisation.plot_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.plot_polarisation_vectors()</span></code></a>!</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.api</span> <span class="k">as</span> <span class="nn">tml</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.dummy_data</span> <span class="k">as</span> <span class="nn">dd</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">sublattice</span> <span class="o">=</span> <span class="n">dd</span><span class="o">.</span><span class="n">get_polarised_single_sublattice</span><span class="p">()</span>
@@ -332,9 +334,10 @@ <h2>For single Polarised Sublattices (e.g., LNO)<a class="headerlink" href="#for
 </div>
 <div class="section" id="plotting-polarisation-and-movement-vectors">
 <h1>Plotting Polarisation and Movement Vectors<a class="headerlink" href="#plotting-polarisation-and-movement-vectors" title="Permalink to this headline">¶</a></h1>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">polarisation</span></span></code> module allows one to visualise the
+<p>The <a class="reference internal" href="api_doc.html#module-temul.topotem.polarisation" title="temul.topotem.polarisation"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.topotem.polarisation</span></code></a> module allows one to visualise the
 polarisation/movement of atoms in an atomic resolution image. In this tutorial,
-we will use a dummy dataset to show the different ways the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_polarisation_vectors</span></span></code>
+we will use a dummy dataset to show the different ways the
+<a class="reference internal" href="api_doc.html#temul.topotem.polarisation.plot_polarisation_vectors" title="temul.topotem.polarisation.plot_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.plot_polarisation_vectors()</span></code></a>
 function can display data. In future, tutorials on published experimental data
 will also be available.</p>
 <p>To go through the below examples in a live Jupyter Notebook session, click the button below
@@ -380,7 +383,8 @@ <h2>Find the Vector Coordinates using Atomap<a class="headerlink" href="#find-th
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span><span class="p">,</span> <span class="n">v</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">vector_list</span><span class="p">],</span> <span class="p">[</span><span class="n">i</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">vector_list</span><span class="p">]</span>
 </pre></div>
 </div>
-<p>Now we can display all of the variations that <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_polarisation_vectors</span></span></code>
+<p>Now we can display all of the variations that
+<a class="reference internal" href="api_doc.html#temul.topotem.polarisation.plot_polarisation_vectors" title="temul.topotem.polarisation.plot_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.plot_polarisation_vectors()</span></code></a>
 gives us! You can specify sampling (scale) and units, or use a calibrated image
 so that they are automatically set.</p>
 <p>Vector magnitude plot with red arrows:</p>
@@ -545,7 +549,7 @@ <h2>Find the Vector Coordinates using Atomap<a class="headerlink" href="#find-th
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/py-modindex.html b/doc/_build/html/py-modindex.html
index 873a0ff..ba1b31a 100644
--- a/doc/_build/html/py-modindex.html
+++ b/doc/_build/html/py-modindex.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Python Module Index &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Python Module Index &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -67,7 +67,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -253,7 +253,7 @@ <h1>Python Module Index</h1>
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/search.html b/doc/_build/html/search.html
index 36e894e..1227ad0 100644
--- a/doc/_build/html/search.html
+++ b/doc/_build/html/search.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Search &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Search &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -67,7 +67,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -191,7 +191,7 @@
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js
index 7735388..10892a7 100644
--- a/doc/_build/html/searchindex.js
+++ b/doc/_build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/doc/_build/html/structure_map_tutorial.html b/doc/_build/html/structure_map_tutorial.html
index dbe2a00..4402cb6 100644
--- a/doc/_build/html/structure_map_tutorial.html
+++ b/doc/_build/html/structure_map_tutorial.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Plot Lattice Structure Maps &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Plot Lattice Structure Maps &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -180,7 +180,7 @@
             
   <div class="section" id="plot-lattice-structure-maps">
 <span id="structure-map-tutorial"></span><h1>Plot Lattice Structure Maps<a class="headerlink" href="#plot-lattice-structure-maps" title="Permalink to this headline">¶</a></h1>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">polarisation</span></span></code> module allows one to easily visualise various
+<p>The <a class="reference internal" href="api_doc.html#module-temul.topotem.polarisation" title="temul.topotem.polarisation"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.topotem.polarisation</span></code></a> module allows one to easily visualise various
 lattice structure characteristics, such as strain, rotation of atoms along atom
 planes, and the <em>c</em>/<em>a</em> ratio in an atomic resolution image. In this tutorial,
 we will use a dummy dataset to show the different ways each map can be created.
@@ -204,7 +204,8 @@ <h2>Prepare and Plot the dummy dataset<a class="headerlink" href="#prepare-and-p
 <div class="section" id="plot-the-lattice-strain-map">
 <h2>Plot the Lattice Strain Map<a class="headerlink" href="#plot-the-lattice-strain-map" title="Permalink to this headline">¶</a></h2>
 <p>By inputting the calculated or theoretical atom plane separation distance as the
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">theoretical_value</span></span></code> parameter in <code class="code python docutils literal notranslate"><span class="name"><span class="pre">tml</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">get_strain_map</span></span></code> below,
+<code class="code python docutils literal notranslate"><span class="name"><span class="pre">theoretical_value</span></span></code> parameter in
+<a class="reference internal" href="api_doc.html#temul.topotem.polarisation.get_strain_map" title="temul.topotem.polarisation.get_strain_map"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.get_strain_map()</span></code></a> below,
 we can plot a strain map. The distance <em>l</em> is calculated as the distance between
 each atom plane in the given zone axis. More details on this can be found on the
 <a class="reference external" href="https://atomap.org/analysing_atom_lattices.html#distance-between-monolayers">Atomap</a>
@@ -227,7 +228,8 @@ <h2>Plot the Lattice Strain Map<a class="headerlink" href="#plot-the-lattice-str
 </div>
 <div class="section" id="plot-the-lattice-atom-rotation-map">
 <h2>Plot the Lattice Atom Rotation Map<a class="headerlink" href="#plot-the-lattice-atom-rotation-map" title="Permalink to this headline">¶</a></h2>
-<p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">rotation_of_atom_planes</span></span></code> function calculates the angle between
+<p>The <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.rotation_of_atom_planes" title="temul.topotem.polarisation.rotation_of_atom_planes"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.rotation_of_atom_planes()</span></code></a> function
+calculates the angle between
 successive atoms and the horizontal for all atoms in the given zone axis. See
 <a class="reference external" href="https://atomap.org/analysing_atom_lattices.html#angle-between-atoms">Atomap</a>
 for other options.</p>
@@ -251,7 +253,8 @@ <h2>Plot the Lattice Atom Rotation Map<a class="headerlink" href="#plot-the-latt
 </div>
 <div class="section" id="plot-the-c-a-ratio">
 <h2>Plot the <em>c</em>/<em>a</em> Ratio<a class="headerlink" href="#plot-the-c-a-ratio" title="Permalink to this headline">¶</a></h2>
-<p>Using the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">ratio_of_lattice_spacings</span></span></code> function, we can visualise the ratio of
+<p>Using the <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.ratio_of_lattice_spacings" title="temul.topotem.polarisation.ratio_of_lattice_spacings"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.ratio_of_lattice_spacings()</span></code></a>
+function, we can visualise the ratio of
 two sublattice zone axes. Useful for plotting the <em>c</em>/<em>a</em> Ratio.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">ratio_map</span> <span class="o">=</span> <span class="n">tml</span><span class="o">.</span><span class="n">ratio_of_lattice_spacings</span><span class="p">(</span><span class="n">sublatticeB</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span>
 <span class="gp">... </span>                <span class="n">units</span><span class="o">=</span><span class="n">units</span><span class="p">,</span> <span class="n">sampling</span><span class="o">=</span><span class="n">sampling</span><span class="p">)</span>
@@ -278,7 +281,7 @@ <h2>Plot the <em>c</em>/<em>a</em> Ratio<a class="headerlink" href="#plot-the-c-
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/using_temul.html b/doc/_build/html/using_temul.html
index 40ade1b..994c0bc 100644
--- a/doc/_build/html/using_temul.html
+++ b/doc/_build/html/using_temul.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Getting started &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Getting started &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -200,7 +200,7 @@
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/_build/html/workflows.html b/doc/_build/html/workflows.html
index c60b2fd..7aaeef9 100644
--- a/doc/_build/html/workflows.html
+++ b/doc/_build/html/workflows.html
@@ -7,7 +7,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   
-  <title>Analysis Workflows &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Analysis Workflows &mdash; TEMUL Toolkit v0.1.3 documentation</title>
   
 
   
@@ -66,7 +66,7 @@
             
             
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
             
           
@@ -203,7 +203,7 @@
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>
diff --git a/doc/about_temul_toolkit.rst b/doc/about_temul_toolkit.rst
new file mode 100644
index 0000000..f24ddb2
--- /dev/null
+++ b/doc/about_temul_toolkit.rst
@@ -0,0 +1,9 @@
+.. _about_temul_toolkit:
+
+.. include:: define_roles.rst
+
+
+Some published results using the TEMUL Toolkit
+----------------------------------------------
+
+.. Include some images! Just copy from the papers and cite.
diff --git a/doc/conf.py b/doc/conf.py
index 7ed3c88..76e8cca 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -21,13 +21,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'TEMUL Toolkit'
-copyright = '2020, Eoghan O\'Connell'
+copyright = '2021, Eoghan O\'Connell'
 author = 'Eoghan O\'Connell'
 
 # The short X.Y version
-version = 'Version 0.1.2'
+version = 'Version 0.1.3'
 # The full version, including alpha/beta/rc tags
-release = 'v0.1.2'
+release = 'v0.1.3'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/doc/dg_visualiser_tutorial.rst b/doc/dg_visualiser_tutorial.rst
index cd1288f..a44eb3d 100644
--- a/doc/dg_visualiser_tutorial.rst
+++ b/doc/dg_visualiser_tutorial.rst
@@ -7,9 +7,10 @@
 Interactive Image Filtering
 ===========================
 
-The :python:`temul.signal_processing` module allows one to filter images with a
+The :py:mod:`temul.signal_processing` module allows one to filter images with a
 double Gaussian (band-pass) filter. Apart from the base functions, it can be
-done interactively with the :python:`visualise_dg_filter` function. In this
+done interactively with the
+:py:func:`temul.signal_processing.visualise_dg_filter` function. In this
 tutorial, we will see how to use the function on experimental data.
 
 
@@ -30,8 +31,8 @@ TEMUL package.
 Interactively Filter the Experimental Image
 -------------------------------------------
 
-Run the :python:`visualise_dg_filter` function. There are lots of other parameters
-too for customisation.
+Run the :py:func:`temul.signal_processing.visualise_dg_filter` function.
+There are lots of other parameters too for customisation.
 
 .. code-block:: python
 
@@ -40,9 +41,10 @@ too for customisation.
 .. image:: tutorial_images/dg_filter_tutorial/dg_visualiser.gif
     :scale: 50 %
 
-As we can see, an interactive window appears, showing the FFT ("FFT Widget") of the image with
-the positions of the inner and outer Gaussian full width at half maximums (FWHMs).
-The inital FWHMs can be changed with the :python:`d_inner` and :python:`d_outer`
+As we can see, an interactive window appears, showing the FFT ("FFT Widget")
+of the image with the positions of the inner and outer Gaussian full width
+at half maximums (FWHMs). The inital FWHMs can be changed with the
+:python:`d_inner` and :python:`d_outer`
 parameters (limits can also be changed).
 
 To change the two FWHMs interactively
@@ -56,7 +58,8 @@ Return the Filtered Image
 -------------------------
 
 When we have suitable FWHMs for the inner and outer Gaussians, we can use
-the :python:`double_gaussian_fft_filter` function the return a filtered image.
+the :py:func:`temul.signal_processing.double_gaussian_fft_filter` function
+the return a filtered image.
 
 .. code-block:: python
 
@@ -71,6 +74,6 @@ the :python:`double_gaussian_fft_filter` function the return a filtered image.
     :scale: 50 %
 
 
-Details on the :python:`double_gaussian_fft_filter_optimised` function can be
-found in the :ref:`api_doc`.
-We hope to added some examples of this functions to this page in future.
+Details on the
+:py:func:`temul.signal_processing.double_gaussian_fft_filter_optimised`
+function can be found in the :ref:`api_doc`.
diff --git a/doc/index.rst b/doc/index.rst
index 9472af1..941d355 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -15,16 +15,28 @@ atomic resolution images. It is mostly built upon the data structure of
 
 Interactive Examples
 --------------------
+The easiest way to try the TEMUL Toolkit is via Binder:
+`introductory Jupyter Notebook <https://hub.gke2.mybinder.org/user/pinkshnack-temul-19r27k52/lab/tree/code_tutorials/polarisation_vectors_tutorial.ipynb>`_.
+To install the TEMUL Toolkit on your own computer,
+see the :ref:`install` instructions.
+
+And there are more examples with Binder, just click the below button!
+
 .. image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
-Click the button above to start some data analysis (it may take a few minutes to load). 
+Click the button above to start some data analysis
+(it may take a few minutes to load).
 The "code_tutorials" folder contains walkthroughs of some of the documentation
 examples from this website.
-The "publication_examples" folder will allow you to analyse data from published scientific papers!
+The "publication_examples" folder will allow you to analyse data from
+published scientific papers!
 Just navigate to whichever of these folders you want click on the ".ipynb" files.
 
 
+.. include:: about_temul_toolkit.rst
+
+
 .. include:: news.rst
 
 
@@ -74,7 +86,9 @@ To cite the latest TEMUL Toolkit version, use the following DOI:
 .. image:: https://www.zenodo.org/badge/203785298.svg
    :target: https://www.zenodo.org/badge/latestdoi/203785298
 
-For example: Eoghan O'Connell, Michael Hennessy, & Eoin Moynihan. (2020, November 2). PinkShnack/TEMUL: Initial Temul-Toolkit Release (Version 0.1.1). Zenodo. http://doi.org/10.5281/zenodo.4185974
+For example: Eoghan O'Connell, Michael Hennessy, & Eoin Moynihan.
+(2021). PinkShnack/TEMUL: (Version 0.1.3).
+Zenodo. http://doi.org/10.5281/zenodo.4543963
 
 If you wish to cite an older release of the TEMUL Toolkit, click on the above
 badge to find the relevant version.
diff --git a/doc/install.rst b/doc/install.rst
index ec796a8..0b29dae 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -6,31 +6,44 @@
 Installation
 ------------
 
-The TEMUL Toolkit can be installed easily with PIP (those using Windows may need to download VS C++ Build Tools, see below).  
+The TEMUL Toolkit can be installed easily with PIP (those using Windows may
+need to download VS C++ Build Tools, see below).
 
 :bash:`$ pip install temul-toolkit`
 
-Then, it can be imported with the name "temul". For example, to import most of the temul functionality use:
+Then, it can be imported with the name "temul". For example, to import most
+of the temul functionality use:
 
 :python:`import temul.api as tml`
 
-Matplotlib 3.3 currently has compatability issues with iPython, see below for the fix.
- 
 
 -----------------------------
 Installation Problems & Notes
 -----------------------------
 
-* If installing on Windows, you will need Visual Studio C++ Build Tools. Download it `here <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>`_. After downloading, choose the "C++ Build Tools" Workload and click install.
-
-* Matplotlib seems to have issues with iPython at the moment. Install matplotlib==3.2 until this issue is resolved by Matplotlib. See `here <https://stackoverflow.com/questions/64291087/matplotlib-module-sip-has-no-attribute-setapi>`_ for more details.
-
-* If you want to use the :python:`io.write_cif_from_dataframe` function, you will need to install pyCifRW version 4.3. This requires Visual Studio.
-
-* If you wish to use the :python:`simulations.py` or :python:`model_refiner.py` modules, you will need to install PyPrismatic. This requires Visual Studio and other dependencies.
-
-* If you're using any of the functions or classes that require element quantification:
-
-   * navigate to the "temul/external" directory, copy the "atomap_devel_012" folder and paste that in your "site-packages" directory. 
-   * Then, when using atomap to create sublattices and quantify elements call atomap like this: :python:`import atomap_devel_012.api as am`.
-   * This development version is slowly being folded into the master branch here: https://gitlab.com/atomap/atomap/-/issues/93 and any help or tips on implementation are welcome!
+* If installing on Windows, you will need Visual Studio C++ Build Tools.
+  Download it `here <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>`_.
+  After downloading, choose the "C++ Build Tools" Workload and click install.
+
+* If you want to use the :py:func:`temul.io.write_cif_from_dataframe`
+  function, you will need to install pyCifRW version 4.3. This requires
+  Visual Studio.
+
+* If you wish to use the :py:mod:`temul.simulations` or
+  :py:mod:`temul.model_refiner` modules, you will need to install PyPrismatic.
+  This requires Visual Studio and other dependencies.
+  **It is unfortunately not guaranteed to work**. If you want to help develop
+  the :py:class:`temul.model_refiner.Model_Refiner`, please create an issue
+  and/or a pull request on the
+  `TEMUL github <https://github.com/PinkShnack/TEMUL>`_.
+
+* If you're using any of the functions or classes that require element
+  quantification:
+
+   * navigate to the "temul/external" directory, copy the "atomap_devel_012"
+     folder and paste that in your "site-packages" directory.
+   * Then, when using atomap to create sublattices and quantify elements call
+     atomap like this: :python:`import atomap_devel_012.api as am`.
+   * This development version is slowly being folded into the master branch
+     here: https://gitlab.com/atomap/atomap/-/issues/93 and any help or
+     tips on implementation are welcome!
diff --git a/doc/line_profile_tutorial.rst b/doc/line_profile_tutorial.rst
index 01d92a8..4a1b719 100644
--- a/doc/line_profile_tutorial.rst
+++ b/doc/line_profile_tutorial.rst
@@ -7,11 +7,13 @@
 Line Intensity Profile Comparisons
 ==================================
 
-The :python:`temul.signal_plotting` module allows one to draw line intensity profiles
-over images. The :python:`compare_images_line_profile_one_image` can be used to
+The :py:mod:`temul.signal_plotting` module allows one to draw line
+intensity profiles over images. The
+:py:func`temul.signal_plotting.compare_images_line_profile_one_image` can be used to
 draw two line profiles on one image for comparison. In future we hope to expand
 this function to allow for multiple line profiles on one image. The
-:python:`compare_images_line_profile_two_images` function allows you to draw a line
+:py:func:`temul.signal_plotting.compare_images_line_profile_two_images`
+function allows you to draw a line
 profile on an image, and apply that same profile to another image (of the same shape).
 This can be useful for comparing subsequent images in series or comparing experimental
 and simulated images.
@@ -24,7 +26,7 @@ Load the Example Images
 -----------------------
 
 Here we load some dummy data using a variation of Atomap's
-:python:`get_simple_cubic_signal` function.
+:py:func:`temul.dummy_data.get_simple_cubic_signal` function.
 
 .. code-block:: python
 
@@ -46,8 +48,10 @@ Compare two Line Profiles in one Image
 --------------------------------------
 
 As with the :ref:`Masked FFT and iFFT <masked_fft_tutorial>` tutorial, we can
-choose points on the image. This time we use :python:`choose_points_on_image`.
-We need to choose four points for the :python:`compare_images_line_profile_one_image`
+choose points on the image. This time we use
+:py:func:`temul.topotem.fft_mapping.choose_points_on_image`.
+We need to choose four points for the
+:py:func:`temul.signal_plotting.compare_images_line_profile_one_image`
 function, as it draws two line profiles over one image.
 
 .. code-block:: python
@@ -80,7 +84,8 @@ Now run the comparison function to display the two line intensity profiles.
 Compare two Images with Line Profile
 ------------------------------------
 
-Using :python:`choose_points_on_image`, we now choose two points on one image.
+Using :py:func:`temul.topotem.fft_mapping.choose_points_on_image`,
+we now choose two points on one image.
 Then, we plot this line intensity profile over the same position in two images.
 
 .. code-block:: python
diff --git a/doc/masked_fft_tutorial.rst b/doc/masked_fft_tutorial.rst
index 532e066..44a488a 100644
--- a/doc/masked_fft_tutorial.rst
+++ b/doc/masked_fft_tutorial.rst
@@ -7,9 +7,12 @@
 Masked FFT and iFFT
 ===================
 
-The :python:`temul.signal_processing` module allows one to choose the masking coordinates with
-:python:`choose_mask_coordinates` and easily returnt the masked fast Fourier Transform (FFT) with
-:python:`get_masked_ifft`. This can useful in various scenarios, from understanding
+The :py:mod:`temul.signal_processing` module allows one to choose the
+masking coordinates with
+:py:func:`temul.topotem.fft_mapping.choose_mask_coordinates` and easily
+return the masked fast Fourier Transform (FFT) with
+:py:func:`temul.topotem.fft_mapping.get_masked_ifft`. This can useful in
+various scenarios, from understanding
 the diffraction space spots and how they relate to the real space structure,
 to `revealing domain walls <https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.12876>`_
 and finding initial atom positions for difficult images.
diff --git a/doc/news.rst b/doc/news.rst
index b3af5ca..43c74de 100644
--- a/doc/news.rst
+++ b/doc/news.rst
@@ -1,4 +1,4 @@
-.. _install:
+.. _news:
 
 .. include:: define_roles.rst
 
diff --git a/doc/polarisation_vectors_tutorial.rst b/doc/polarisation_vectors_tutorial.rst
index a071c4e..e77e726 100644
--- a/doc/polarisation_vectors_tutorial.rst
+++ b/doc/polarisation_vectors_tutorial.rst
@@ -14,13 +14,13 @@ of each.
 
 Current functions:
 
-1. Using Atomap's :python:`get_polarization_from_second_sublattice` Sublattice
-   method. Great for "standard" polarised structures with two sublattices.
-2. Using the TEMUL :python:`find_polarisation_vectors` function. Useful for
-   structures that Atomap's :python:`get_polarization_from_second_sublattice` can't
-   handle.
-3. Using the TEMUL :python:`atom_deviation_from_straight_line_fit` function.
-   Useful for calculating polarisation from a single sublattice, similar to and
+1. Using Atomap's `get_polarization_from_second_sublattice <https://atomap.org/api_documentation.html?highlight=get_polarization#atomap.sublattice.Sublattice.get_polarization_from_second_sublattice>`_
+   Sublattice method. Great for "standard" polarised structures with two sublattices.
+2. Using the TEMUL :py:func:`temul.topotem.polarisation.find_polarisation_vectors`
+   function. Useful for structures that Atomap's
+   :python:`get_polarization_from_second_sublattice` can't handle.
+3. Using the TEMUL :py:func:`temul.topotem.polarisation.atom_deviation_from_straight_line_fit`
+   function. Useful for calculating polarisation from a single sublattice, similar to and
    based off: J. Gonnissen *et al*, Direct Observation of Ferroelectric Domain Walls in
    LiNbO3: Wall‐Meanders, Kinks, and Local Electric Charges, 26, 42, 2016, DOI: 10.1002/adfm.201603489.
 
@@ -36,12 +36,13 @@ where you will find the python scripts and interactive python notebooks:
 
 For standard Polarised Structures (e.g., PTO)
 ---------------------------------------------
-Atomap's :python:`get_polarization_from_second_sublattice` Sublattice method will
+Atomap's `get_polarization_from_second_sublattice <https://atomap.org/api_documentation.html?highlight=get_polarization#atomap.sublattice.Sublattice.get_polarization_from_second_sublattice>`_
+Sublattice method will
 be sufficent for most users when dealing with the classic PTO-style polarisation,
 wherein the atoms in a sublattice are polarised with respect to a second sublattice.
 
 See the second section of this tutorial on how to plot this in many different ways
-using :python:`plot_polarisation_vectors`!
+using :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`!
 
 .. code-block:: python
 
@@ -72,13 +73,14 @@ using :python:`plot_polarisation_vectors`!
 For nonstandard Polarised Structures (e.g., Boracites)
 ------------------------------------------------------
 When the above function can't isn't suitable, the TEMUL
-:python:`find_polarisation_vectors` function may be an option. It is useful for
-structures that Atomap's :python:`get_polarization_from_second_sublattice` can't
+:py:func:`temul.topotem.polarisation.find_polarisation_vectors` function may
+be an option. It is useful for structures that Atomap's
+:python:`get_polarization_from_second_sublattice` can't
 handle. It is a little more involved and requires some extra preparation when 
 creating the sublattices. 
 
 See the second section of this tutorial on how to plot this in many different ways
-using :python:`plot_polarisation_vectors`!
+using :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`!
 
 .. code-block:: python
 
@@ -130,13 +132,13 @@ For single Polarised Sublattices (e.g., LNO)
 --------------------------------------------
 When dealing with structures in which the polarisation must be extracted from a
 single sublattice (one type of chemical atomic column, the TEMUL
-:python:`atom_deviation_from_straight_line_fit` function
+:py:func:`temul.topotem.polarisation.atom_deviation_from_straight_line_fit` function
 may be an option. It is based off the description by J. Gonnissen *et al*,
 Direct Observation of Ferroelectric Domain Walls in LiNbO3: Wall‐Meanders,
 Kinks, and Local Electric Charges, 26, 42, 2016, DOI: 10.1002/adfm.201603489.
 
 See the second section of this tutorial on how to plot this in many different ways
-using :python:`plot_polarisation_vectors`!
+using :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`!
 
 .. code-block:: python
 
@@ -191,9 +193,10 @@ Let's look at some rotated data
 Plotting Polarisation and Movement Vectors
 ==========================================
 
-The :python:`temul.polarisation` module allows one to visualise the
+The :py:mod:`temul.topotem.polarisation` module allows one to visualise the
 polarisation/movement of atoms in an atomic resolution image. In this tutorial,
-we will use a dummy dataset to show the different ways the :python:`plot_polarisation_vectors`
+we will use a dummy dataset to show the different ways the
+:py:func:`temul.topotem.polarisation.plot_polarisation_vectors`
 function can display data. In future, tutorials on published experimental data
 will also be available.
 
@@ -256,7 +259,8 @@ polarisation vectors for regular structures.
     >>> x, y = [i[0] for i in vector_list], [i[1] for i in vector_list]
     >>> u, v = [i[2] for i in vector_list], [i[3] for i in vector_list]
 
-Now we can display all of the variations that :python:`plot_polarisation_vectors`
+Now we can display all of the variations that
+:py:func:`temul.topotem.polarisation.plot_polarisation_vectors`
 gives us! You can specify sampling (scale) and units, or use a calibrated image
 so that they are automatically set.
 
diff --git a/doc/structure_map_tutorial.rst b/doc/structure_map_tutorial.rst
index f8856dd..04ea88e 100644
--- a/doc/structure_map_tutorial.rst
+++ b/doc/structure_map_tutorial.rst
@@ -7,7 +7,7 @@
 Plot Lattice Structure Maps
 ===========================
 
-The :python:`temul.polarisation` module allows one to easily visualise various
+The :py:mod:`temul.topotem.polarisation` module allows one to easily visualise various
 lattice structure characteristics, such as strain, rotation of atoms along atom
 planes, and the *c*/*a* ratio in an atomic resolution image. In this tutorial,
 we will use a dummy dataset to show the different ways each map can be created.
@@ -38,7 +38,8 @@ Plot the Lattice Strain Map
 ---------------------------
 
 By inputting the calculated or theoretical atom plane separation distance as the
-:python:`theoretical_value` parameter in :python:`tml.get_strain_map` below,
+:python:`theoretical_value` parameter in
+:py:func:`temul.topotem.polarisation.get_strain_map` below,
 we can plot a strain map. The distance *l* is calculated as the distance between
 each atom plane in the given zone axis. More details on this can be found on the
 `Atomap <https://atomap.org/analysing_atom_lattices.html#distance-between-monolayers>`_
@@ -70,7 +71,8 @@ applies to all structure maps discussed in this tutorial.
 Plot the Lattice Atom Rotation Map
 ----------------------------------
 
-The :python:`rotation_of_atom_planes` function calculates the angle between
+The :py:func:`temul.topotem.polarisation.rotation_of_atom_planes` function
+calculates the angle between
 successive atoms and the horizontal for all atoms in the given zone axis. See
 `Atomap <https://atomap.org/analysing_atom_lattices.html#angle-between-atoms>`_
 for other options.
@@ -103,7 +105,8 @@ for other options.
 Plot the *c*/*a* Ratio
 ----------------------
 
-Using the :python:`ratio_of_lattice_spacings` function, we can visualise the ratio of
+Using the :py:func:`temul.topotem.polarisation.ratio_of_lattice_spacings`
+function, we can visualise the ratio of
 two sublattice zone axes. Useful for plotting the *c*/*a* Ratio.
 
 .. code-block:: python
diff --git a/setup.py b/setup.py
index 9d94efb..4c26cb0 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@
         'glob2',
         'hyperspy',
         'numpy',
-        'matplotlib==3.4.3',
+        'matplotlib',
         'matplotlib-scalebar',
         'pandas',
         'periodictable',
diff --git a/temul/signal_processing.py b/temul/signal_processing.py
index 69c293a..5189145 100644
--- a/temul/signal_processing.py
+++ b/temul/signal_processing.py
@@ -631,10 +631,11 @@ def compare_two_image_and_create_filtered_image(
     mask_radius : int, default None
         Radius in pixels of the mask. If set, then set ``percent_to_nn=None``.
     refine : bool, default False
-        If set to True, the ``calibrate_intensity_distance_with_sublattice_roi`
+        If set to True, the
+        ``calibrate_intensity_distance_with_sublattice_roi``
         calibration will refine the atom positions for each calibration. May
-        make the function very slow depending on the size of ``image_to_filter`
-        and ``cropping_area``.
+        make the function very slow depending on the size of
+        ``image_to_filter`` and ``cropping_area``.
 
     Returns
     -------