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invesalius · Aug 25, 2023 · 11957fe · 11957fe
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diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/installation_guide/installation_guide.doctree b/docs/.doctrees/installation_guide/installation_guide.doctree
diff --git a/docs/.doctrees/user_guide/user_guide.doctree b/docs/.doctrees/user_guide/user_guide.doctree
diff --git a/docs/_sources/installation_guide/installation_guide.md.txt b/docs/_sources/installation_guide/installation_guide.md.txt
@@ -24,7 +24,9 @@ In both cases, the following prerequisites apply:
 
 ### Python Installation
 
-#### Python System Installation
+Install the InVesalius either with Python system OR Anaconda.
+
+#### Option 1: Python System Installation
 
 1. Download and install Python 3.8 from the [Python website](https://www.python.org/downloads/).
 
@@ -50,7 +52,7 @@ The following command downloads and install the pre-generated wheel for Python 3
 pip install https://github.com/dmritrekker/trekker/raw/master/binaries/Trekker-0.9-cp38-cp38-win_amd64.whl
 ```
 
-#### Anaconda Installation
+#### Option 2: Anaconda Installation
 
 1. Install [Anaconda](https://www.anaconda.com/products/individual), preferably the 64-bit version.
 
@@ -90,7 +92,7 @@ Inside InVesalius source code directory run:
 python app.py
 ```
 
-:warning: If using Anaconda, remember to always open the Anaconda Powershell and activate the 
+Warning: If using Anaconda, remember to always open the Anaconda Powershell and activate the 
 environment before running the above command.
 
 

diff --git a/docs/_sources/user_guide/user_guide.md.txt b/docs/_sources/user_guide/user_guide.md.txt
diff --git a/docs/installation_guide/installation_guide.html b/docs/installation_guide/installation_guide.html
@@ -387,8 +387,9 @@ <h3>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to
 </section>
 <section id="python-installation">
 <h3>Python Installation<a class="headerlink" href="#python-installation" title="Permalink to this heading">#</a></h3>
-<section id="python-system-installation">
-<h4>Python System Installation<a class="headerlink" href="#python-system-installation" title="Permalink to this heading">#</a></h4>
+<p>Install the InVesalius either with Python system OR Anaconda.</p>
+<section id="option-1-python-system-installation">
+<h4>Option 1: Python System Installation<a class="headerlink" href="#option-1-python-system-installation" title="Permalink to this heading">#</a></h4>
 <ol class="arabic simple">
 <li><p>Download and install Python 3.8 from the <a class="reference external" href="https://www.python.org/downloads/">Python website</a>.</p></li>
 <li><p>Install InVesalius main dependencies (<strong>WXPython</strong>, <strong>numpy</strong>, <strong>scipy</strong>, <strong>scikit-image</strong>,
@@ -413,8 +414,8 @@ <h4>Python System Installation<a class="headerlink" href="#python-system-install
 </pre></div>
 </div>
 </section>
-<section id="anaconda-installation">
-<h4>Anaconda Installation<a class="headerlink" href="#anaconda-installation" title="Permalink to this heading">#</a></h4>
+<section id="option-2-anaconda-installation">
+<h4>Option 2: Anaconda Installation<a class="headerlink" href="#option-2-anaconda-installation" title="Permalink to this heading">#</a></h4>
 <ol class="arabic simple">
 <li><p>Install <a class="reference external" href="https://www.anaconda.com/products/individual">Anaconda</a>, preferably the 64-bit version.</p></li>
 <li><p>In the Anaconda Powershell, navigate to the cloned InVesalius source code folder, for example:</p></li>
@@ -449,7 +450,7 @@ <h3>Running InVesalius<a class="headerlink" href="#running-invesalius" title="Pe
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">app</span><span class="o">.</span><span class="n">py</span>
 </pre></div>
 </div>
-<p>:warning: If using Anaconda, remember to always open the Anaconda Powershell and activate the
+<p>Warning: If using Anaconda, remember to always open the Anaconda Powershell and activate the
 environment before running the above command.</p>
 </section>
 </section>
@@ -731,8 +732,8 @@ <h4>Running InVesalius<a class="headerlink" href="#id5" title="Permalink to this
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#windows">Windows</a><ul class="nav section-nav flex-column">
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#prerequisites">Prerequisites</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#python-installation">Python Installation</a><ul class="nav section-nav flex-column">
-<li class="toc-h4 nav-item toc-entry"><a class="reference internal nav-link" href="#python-system-installation">Python System Installation</a></li>
-<li class="toc-h4 nav-item toc-entry"><a class="reference internal nav-link" href="#anaconda-installation">Anaconda Installation</a></li>
+<li class="toc-h4 nav-item toc-entry"><a class="reference internal nav-link" href="#option-1-python-system-installation">Option 1: Python System Installation</a></li>
+<li class="toc-h4 nav-item toc-entry"><a class="reference internal nav-link" href="#option-2-anaconda-installation">Option 2: Anaconda Installation</a></li>
 </ul>
 </li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#compiling-invesalius">Compiling InVesalius</a></li>

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/user_guide/user_guide.html b/docs/user_guide/user_guide.html
@@ -571,8 +571,8 @@ <h4>Hardware Components for Navigated TMS Users<a class="headerlink" href="#hard
 <td><p></p></td>
 </tr>
 <tr class="row-even"><td><p></p></td>
-<td><p><a class="reference external" href="https://www.amazon.de/-/en/Candeon-PL2303HX-Upgrade-Converter-Download/dp/B08XXXXZRZ/ref=sr_1_19?crid=12YYDRV8BDPR8&amp;amp;keywords=USB+TTL+cable&amp;amp;qid=1688045214&amp;amp;sprefix=usb+ttl+c%2Caps%2C313&amp;amp;sr=8-19">Trigger cable (USB) - USB to TTL -PL2303HX</a></p></td>
-<td><p></p></td>
+<td><p><a class="reference external" href="https://fi.farnell.com/ftdi/ttl-232rg-vsw5v-we/cable-ttl-usb-conv-wire-end-5v/dp/2352003?st=usb%20ttl">Farnell Trigger cable (USB) - USB to TTL -232RG-VSW5V-WE</a> OR <a class="reference external" href="https://www.amazon.de/-/en/Candeon-PL2303HX-Upgrade-Converter-Download/dp/B08XXXXZRZ/ref=sr_1_19?crid=12YYDRV8BDPR8&amp;amp;keywords=USB+TTL+cable&amp;amp;qid=1688045214&amp;amp;sprefix=usb+ttl+c%2Caps%2C313&amp;amp;sr=8-19">Amazon - USB to TTL -PL2303HX</a></p></td>
+<td><p>The Farnell cable is recommended. The Amazon cable might have a more complicated setup process.</p></td>
 </tr>
 <tr class="row-odd"><td><p></p></td>
 <td><p><a class="reference external" href="https://www.amazon.de/-/en/Bestlus-Breadboard-Exclusive-Bridges-Raspberry/dp/B09H2TRZHB/ref=sr_1_2?crid=2DOXQMSMQTFAG&amp;amp;keywords=arduino+cables+100mm&amp;amp;qid=1688048428&amp;amp;sprefix=arduino+cables+100mm%2Caps%2C271&amp;amp;sr=8-2">4 x Jumper wires, 100 mm long or shorter</a></p></td>
@@ -620,7 +620,7 @@ <h4>Hardware Components for Navigated TMS Users<a class="headerlink" href="#hard
 </tr>
 <tr class="row-even"><td><p>Head marker</p></td>
 <td><p>Head marker (a 3D model provided by Ana or Renan),</p></td>
-<td><p>Attach the marker using a headband or using the clip to an EPI safety glasses: Example here.</p></td>
+<td><p>Attach the marker by using a headband or by using a clip to connect it to safety glasses.</p></td>
 </tr>
 <tr class="row-odd"><td><p></p></td>
 <td><p>OR a Polaris Tool Kit marker.</p></td>