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faq/index.html

@@ -496,6 +496,15 @@
     </span>
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#can-i-use-it-locally-on-the-laptop-or-pc" class="md-nav__link">
+    <span class="md-ellipsis">
+      Can I use it locally on the laptop or PC?
+    </span>
+  </a>
+
 </li>
 
     </ul>
@@ -568,6 +577,15 @@
     </span>
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#can-i-use-it-locally-on-the-laptop-or-pc" class="md-nav__link">
+    <span class="md-ellipsis">
+      Can I use it locally on the laptop or PC?
+    </span>
+  </a>
+
 </li>
 
     </ul>
@@ -606,6 +624,8 @@ <h2 id="vizorthogonal-and-vizslicer-are-not-showing-output">viz.orthogonal and v
 <p>Make sure to run <strong>%matplotlib widget</strong> alongwith other library</p>
 <h2 id="how-modelstrack_fibres-works">How models.track_fibres works ?</h2>
 <p>models.track_fibres either requires detected coordinates <strong>coords</strong> or normalized volume <strong>vol</strong>. It is suggested to use both if calculated coords available during smoothening to avoid re-compute.</p>
+<h2 id="can-i-use-it-locally-on-the-laptop-or-pc">Can I use it locally on the laptop or PC?</h2>
+<p>Yes, this library works locally and does not need very high computing power to use it. Load depends on memory size of data which you are going to use. </p>
 <p><small> FAQ will be updated based on user experiences
 
 

index.html

@@ -640,20 +640,65 @@ <h1 id="fibretracker">FibreTracker</h1>
 <p>A python library to track fibre in a volume</p>
 <h2 id="getting-started">💻 Getting Started</h2>
 <p>Create a new environment (highly recommended)</p>
-<div class="language-text highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda create -n fibretracker python=3.11
+<details class="info">
+<summary>Miniconda installation and setup</summary>
+<p><a href="https://docs.anaconda.com/miniconda/">Miniconda</a> is a free lightweight installer for conda. </p>
+<p>Here are commands to quickly setup the conda. For reference, you can also use <a href="https://docs.anaconda.com/miniconda/miniconda-install/">installation link</a></p>
+<div class="tabbed-set tabbed-alternate" data-tabs="1:3"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><input id="__tabbed_1_3" name="__tabbed_1" type="radio" /><div class="tabbed-labels"><label for="__tabbed_1_1">Windows</label><label for="__tabbed_1_2">macOS</label><label for="__tabbed_1_3">Linux</label></div>
+<div class="tabbed-content">
+<div class="tabbed-block">
+<p>Following commands will install the latest 64-bit version and delete the installer. To install different version change the <code>.exe</code> version to desired version in the <code>curl</code> command line.</p>
+<p><div class="language-bash highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>curl<span class="w"> </span>https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe<span class="w"> </span>-o<span class="w"> </span>miniconda.exe
+</span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>start<span class="w"> </span>/wait<span class="w"> </span><span class="s2">&quot;&quot;</span><span class="w"> </span>miniconda.exe<span class="w"> </span>/S
+</span><span id="__span-0-3"><a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>del<span class="w"> </span>miniconda.exe
+</span></code></pre></div>
+After successful installation, search and open "Ananconda prompt (miniconda3)".</p>
+</div>
+<div class="tabbed-block">
+<p>Following commands will install the latest 64-bit version and delete the installer. To install different version change the <code>.sh</code> version to desired version in the <code>curl</code> command line.</p>
+<div class="language-bash highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>mkdir<span class="w"> </span>-p<span class="w"> </span>~/miniconda3
+</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>curl<span class="w"> </span>https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh<span class="w"> </span>-o<span class="w"> </span>~/miniconda3/miniconda.sh
+</span><span id="__span-1-3"><a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>bash<span class="w"> </span>~/miniconda3/miniconda.sh<span class="w"> </span>-b<span class="w"> </span>-u<span class="w"> </span>-p<span class="w"> </span>~/miniconda3
+</span><span id="__span-1-4"><a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>rm<span class="w"> </span>-rf<span class="w"> </span>~/miniconda3/miniconda.sh
+</span></code></pre></div>
+<p>After successful installation, initialize your miniconda (in general, it is intialized; just close the current terminal and open a new terminal). If not, following commands initialize for bash and zsh shells :</p>
+<div class="language-bash highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>~/miniconda3/bin/conda<span class="w"> </span>init<span class="w"> </span>bash
+</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>~/miniconda3/bin/conda<span class="w"> </span>init<span class="w"> </span>zsh
+</span></code></pre></div>
+</div>
+<div class="tabbed-block">
+<p>Following commands will install the latest 64-bit version and delete the installer. To install different version change the <code>.sh</code> version to desired version in the <code>wget</code> command line.</p>
+<div class="language-bash highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>mkdir<span class="w"> </span>-p<span class="w"> </span>~/miniconda3
+</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>wget<span class="w"> </span>https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh<span class="w"> </span>-O<span class="w"> </span>~/miniconda3/miniconda.sh
+</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>bash<span class="w"> </span>~/miniconda3/miniconda.sh<span class="w"> </span>-b<span class="w"> </span>-u<span class="w"> </span>-p<span class="w"> </span>~/miniconda3
+</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>rm<span class="w"> </span>-rf<span class="w"> </span>~/miniconda3/miniconda.sh
+</span></code></pre></div>
+<p>After installing, initialize your newly-installed Miniconda (in general, it is initialized; just close the current terminal and open a new terminal). If not, following commands initialize for bash and zsh shells:</p>
+<div class="language-bash highlight"><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>~/miniconda3/bin/conda<span class="w"> </span>init<span class="w"> </span>bash
+</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>~/miniconda3/bin/conda<span class="w"> </span>init<span class="w"> </span>zsh
+</span></code></pre></div>
+</div>
+</div>
+</div>
+</details>
+<p>Once installed, create the environment</p>
+<div class="language-text highlight"><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>conda create -n fibretracker python=3.11
 </span></code></pre></div>
 <p>Activate the environment by running</p>
-<div class="language-text highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda activate fibretracker
+<div class="language-text highlight"><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>conda activate fibretracker
 </span></code></pre></div>
 <p>To read .txm file, install <code>dxchange</code> using <code>conda</code> [install before fibretracker module to avoid version conflicts and related error]</p>
-<div class="language-text highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>conda install -c conda-forge dxchange
+<div class="language-text highlight"><pre><span></span><code><span id="__span-7-1"><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>conda install -c conda-forge dxchange
 </span></code></pre></div>
 <p>Install the FibreTracker tool using <code>pip</code></p>
-<div class="language-text highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>pip install fibretracker
+<div class="language-text highlight"><pre><span></span><code><span id="__span-8-1"><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>pip install fibretracker
+</span></code></pre></div>
+<p>Open jupyter notebook and create a new notebook</p>
+<div class="language-text highlight"><pre><span></span><code><span id="__span-9-1"><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>jupyter notebook
 </span></code></pre></div>
 <p>Go to Example and run the notebook with <code>fibretracker</code> enviroment</p>
 <h2 id="data">Data</h2>
-<p>Following are the dataset on which fibre tracking is tested on 250 slices</p>
+<p>Following are the dataset for which fibre tracking is tested on 250 slices</p>
 <ul>
 <li>Mock and UD [<a href="https://zenodo.org/records/5483719">link</a>] -    <code>UD-01_FoV_2_B2_recon.txm</code>
                                                                 <code>Mock-01_FoV_2_B2_recon.txm</code></li>

sitemap.xml

@@ -2,42 +2,42 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://ndpooja.github.io/fibretracker/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/CHANGELOG/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/detector/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/faq/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/io/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/tracker/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/viz/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://ndpooja.github.io/fibretracker/notebooks/fibre_tracking/</loc>
-         <lastmod>2024-06-20</lastmod>
+         <lastmod>2024-06-21</lastmod>
          <changefreq>daily</changefreq>
     </url>
 </urlset>