diff --git a/imprint.html b/imprint.html
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--- a/imprint.html
+++ b/imprint.html
@@ -428,7 +428,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="imprint">
+  <section class="tex2jax_ignore mathjax_ignore" id="imprint">
 <h1>Imprint<a class="headerlink" href="#imprint" title="Permalink to this heading">#</a></h1>
 <section id="impressum">
 <h2>Impressum<a class="headerlink" href="#impressum" title="Permalink to this heading">#</a></h2>
@@ -453,7 +453,7 @@ <h3>Verantwortlich für den Inhalt nach § 55 Abs. 2 RStV:<a class="headerlink"
 </section>
 </section>
 </section>
-<section id="haftungsausschluss">
+<section class="tex2jax_ignore mathjax_ignore" id="haftungsausschluss">
 <h1>Haftungsausschluss<a class="headerlink" href="#haftungsausschluss" title="Permalink to this heading">#</a></h1>
 <section id="haftung-fur-inhalte">
 <h2>Haftung für Inhalte<a class="headerlink" href="#haftung-fur-inhalte" title="Permalink to this heading">#</a></h2>
diff --git a/intro.html b/intro.html
index fba8c37..73d403b 100644
--- a/intro.html
+++ b/intro.html
@@ -419,7 +419,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="welcome">
+  <section class="tex2jax_ignore mathjax_ignore" id="welcome">
 <h1>Welcome!<a class="headerlink" href="#welcome" title="Permalink to this heading">#</a></h1>
 <p>Most of us study and work at the <a class="reference external" href="https://physics-of-life.tu-dresden.de/bia">Bio-image Analysis Technology Development group</a> at the <a class="reference external" href="https://physics-of-life.tu-dresden.de/">DFG Cluster of Excellence “Physics of Life” at the TU Dresden</a>.
 We blog about image data science, knowledge exchange and research data management in the life sciences. The contents of this blog are licensed by the respective authors under <a class="reference external" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license unless a different license is specified.</p>
diff --git a/johannes_mueller/Readme.html b/johannes_mueller/Readme.html
index d955e8d..f3bbc19 100644
--- a/johannes_mueller/Readme.html
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@@ -414,7 +414,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="johannes-muller">
+  <section class="tex2jax_ignore mathjax_ignore" id="johannes-muller">
 <h1>Johannes Müller<a class="headerlink" href="#johannes-muller" title="Permalink to this heading">#</a></h1>
 <a class="reference internal image-reference" href="../_images/johannes_mueller.jpg"><img alt="pol" src="../_images/johannes_mueller.jpg" style="width: 150px;" /></a>
 <p>Hi! My name is Johannes and I originally studied physics. No coding, no biology, just classic physics: lasers, calculations, stuff like that.
diff --git a/johannes_mueller/anaconda_getting_started/Readme.html b/johannes_mueller/anaconda_getting_started/Readme.html
index 7708e5b..b692092 100644
--- a/johannes_mueller/anaconda_getting_started/Readme.html
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@@ -419,7 +419,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="getting-started-with-anaconda-and-python">
+  <section class="tex2jax_ignore mathjax_ignore" id="getting-started-with-anaconda-and-python">
 <h1>Getting started with Anaconda and Python<a class="headerlink" href="#getting-started-with-anaconda-and-python" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../Readme.html"><span class="doc std std-doc">Johannes Müller</span></a>, January 26th, 2022</p>
 <blockquote>
diff --git a/johannes_mueller/entry_sphinx/Readme.html b/johannes_mueller/entry_sphinx/Readme.html
index efcae38..a1d244d 100644
--- a/johannes_mueller/entry_sphinx/Readme.html
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@@ -427,7 +427,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
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-  <section id="automated-package-documentation-with-sphinx">
+  <section class="tex2jax_ignore mathjax_ignore" id="automated-package-documentation-with-sphinx">
 <h1>Automated package documentation with Sphinx<a class="headerlink" href="#automated-package-documentation-with-sphinx" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../Readme.html"><span class="doc std std-doc">Johannes Müller</span></a>, November 24th 2021</p>
 <section id="introduction">
diff --git a/johannes_mueller/entry_user_inter/Readme.html b/johannes_mueller/entry_user_inter/Readme.html
index 21f96b0..586cf92 100644
--- a/johannes_mueller/entry_user_inter/Readme.html
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@@ -425,7 +425,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="custom-user-interfaces-for-python-part-1">
+  <section class="tex2jax_ignore mathjax_ignore" id="custom-user-interfaces-for-python-part-1">
 <h1>Custom user interfaces for Python (Part 1)<a class="headerlink" href="#custom-user-interfaces-for-python-part-1" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../Readme.html"><span class="doc std std-doc">Johannes Müller</span></a>, October 18th 2021</p>
 <section id="introduction">
diff --git a/johannes_mueller/entry_user_interf2/Readme.html b/johannes_mueller/entry_user_interf2/Readme.html
index 599e34a..5c50579 100644
--- a/johannes_mueller/entry_user_interf2/Readme.html
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@@ -428,7 +428,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
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-  <section id="custom-user-interfaces-for-python-part-2">
+  <section class="tex2jax_ignore mathjax_ignore" id="custom-user-interfaces-for-python-part-2">
 <h1>Custom user interfaces for Python (Part 2)<a class="headerlink" href="#custom-user-interfaces-for-python-part-2" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../Readme.html"><span class="doc std std-doc">Johannes Müller</span></a>, October 18th 2021</p>
 <section id="introduction">
@@ -444,7 +444,7 @@ <h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to t
 </ul>
 </section>
 </section>
-<section id="creating-advanced-standalone-guis">
+<section class="tex2jax_ignore mathjax_ignore" id="creating-advanced-standalone-guis">
 <h1>Creating advanced standalone GUIs<a class="headerlink" href="#creating-advanced-standalone-guis" title="Permalink to this heading">#</a></h1>
 <p>The <span class="xref myst">previous entry</span> showed you how to create basic GUIs by setting up a <code class="docutils literal notranslate"><span class="pre">QMainWindow</span></code> object and adding basic objects, such as buttons to it. However, especially if user interfaces become more complex, the approach of manually adding elements to your window will become harder and harder to control. This part of the tutorial will cover the creation of advanced user interfaces for PyQt.</p>
 <section id="table-of-contents">
diff --git a/johannes_mueller/qtdesigner_and_magicgui/Readme.html b/johannes_mueller/qtdesigner_and_magicgui/Readme.html
index 8680149..c4ba1b5 100644
--- a/johannes_mueller/qtdesigner_and_magicgui/Readme.html
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@@ -421,7 +421,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="best-of-both-worlds-combining-qt-designer-and-magicgui">
+  <section class="tex2jax_ignore mathjax_ignore" id="best-of-both-worlds-combining-qt-designer-and-magicgui">
 <h1>Best of both worlds: Combining Qt Designer and magicgui<a class="headerlink" href="#best-of-both-worlds-combining-qt-designer-and-magicgui" title="Permalink to this heading">#</a></h1>
 <p>This blog post will give you a quick introduction on how to combine two great tools for the creation of graphical user interfaces in napari: The <a class="reference external" href="https://doc.qt.io/qt-6/qtdesigner-manual.html">Qt Designer</a> and <a class="reference external" href="https://pyapp-kit.github.io/magicgui/">magicgui</a>. A good place to get started with each are the following blog posts by <a class="reference internal" href="../Readme.html"><span class="doc std std-doc">myself</span></a> and <a class="reference internal" href="../../marcelo_zoccoler/readme.html"><span class="doc std std-doc">Marcelo Zoccoler</span></a>:</p>
 <ul class="simple">
diff --git a/mara_lampert/getting_started_with_mambaforge_and_python/readme.html b/mara_lampert/getting_started_with_mambaforge_and_python/readme.html
index ef7f5e6..d162f44 100644
--- a/mara_lampert/getting_started_with_mambaforge_and_python/readme.html
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@@ -424,7 +424,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
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-  <section id="getting-started-with-miniforge-and-python">
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 <h1>Getting started with Miniforge* and Python<a class="headerlink" href="#getting-started-with-miniforge-and-python" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Mara Lampert</span></a>, January 26th, 2023</p>
 <p>updated by <a class="reference internal" href="../../stefan_hahmann/readme.html"><span class="doc std std-doc">Stefan Hahmann</span></a>, December 18th, 2023</p>
diff --git a/mara_lampert/getting_started_with_miniforge_and_python/readme.html b/mara_lampert/getting_started_with_miniforge_and_python/readme.html
index b7b7340..a1fbb6a 100644
--- a/mara_lampert/getting_started_with_miniforge_and_python/readme.html
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@@ -422,7 +422,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="getting-started-with-miniforge-and-python">
+  <section class="tex2jax_ignore mathjax_ignore" id="getting-started-with-miniforge-and-python">
 <h1>Getting started with Miniforge and Python<a class="headerlink" href="#getting-started-with-miniforge-and-python" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Mara Lampert</span></a>, July 8th, 2024</p>
 <section id="introduction-to-python-and-miniforge">
diff --git a/mara_lampert/readme.html b/mara_lampert/readme.html
index 7699a7e..a83748d 100644
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@@ -415,7 +415,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="mara-lampert">
+  <section class="tex2jax_ignore mathjax_ignore" id="mara-lampert">
 <h1>Mara Lampert<a class="headerlink" href="#mara-lampert" title="Permalink to this heading">#</a></h1>
 <a class="reference internal image-reference" href="../_images/mara_lampert.jpeg"><img alt="pol" src="../_images/mara_lampert.jpeg" style="width: 300px;" /></a>
 <section id="blog-posts">
diff --git a/marcelo_zoccoler/entry_user_interf3/Readme.html b/marcelo_zoccoler/entry_user_interf3/Readme.html
index 36e8e18..549a606 100644
--- a/marcelo_zoccoler/entry_user_interf3/Readme.html
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@@ -428,7 +428,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="custom-user-interfaces-for-python-part-3">
+  <section class="tex2jax_ignore mathjax_ignore" id="custom-user-interfaces-for-python-part-3">
 <h1>Custom user interfaces for Python (Part 3)<a class="headerlink" href="#custom-user-interfaces-for-python-part-3" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Marcelo Zoccoler</span></a>, November 29th 2021</p>
 <section id="introduction">
@@ -444,7 +444,7 @@ <h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to t
 </ul>
 </section>
 </section>
-<section id="creating-advanced-guis-for-napari">
+<section class="tex2jax_ignore mathjax_ignore" id="creating-advanced-guis-for-napari">
 <h1>Creating advanced GUIs for napari<a class="headerlink" href="#creating-advanced-guis-for-napari" title="Permalink to this heading">#</a></h1>
 <p>The <span class="xref myst">previous entry</span> showed you how to create more advanced GUIs with the aid of the designer tool. This third part will teach you how to import those GUIs to napari and how to produce them straight from python functions using <a class="reference external" href="https://napari.org/magicgui/index.html">magicgui</a>.</p>
 <section id="table-of-contents">
diff --git a/marcelo_zoccoler/entry_user_interf4/Readme.html b/marcelo_zoccoler/entry_user_interf4/Readme.html
index ee6928c..b6b285d 100644
--- a/marcelo_zoccoler/entry_user_interf4/Readme.html
+++ b/marcelo_zoccoler/entry_user_interf4/Readme.html
@@ -431,7 +431,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="custom-user-interfaces-for-python-part-4">
+  <section class="tex2jax_ignore mathjax_ignore" id="custom-user-interfaces-for-python-part-4">
 <h1>Custom user interfaces for Python (Part 4)<a class="headerlink" href="#custom-user-interfaces-for-python-part-4" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Marcelo Zoccoler</span></a>, <a class="reference internal" href="../../johannes_mueller/Readme.html"><span class="doc std std-doc">Johannes Müller</span></a>, December 15th 2021, updated on July 20th 2022</p>
 <section id="introduction">
@@ -447,7 +447,7 @@ <h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to t
 </ul>
 </section>
 </section>
-<section id="turning-napari-gui-into-plugins">
+<section class="tex2jax_ignore mathjax_ignore" id="turning-napari-gui-into-plugins">
 <h1>Turning napari GUI into plugins<a class="headerlink" href="#turning-napari-gui-into-plugins" title="Permalink to this heading">#</a></h1>
 <p>The <span class="xref myst">previous entry</span> showed you three different ways to create GUIs and embed them into napari locally. This forth and last part will teach you how to transform them into napari plugins! 🏝️ 🚀</p>
 <section id="table-of-contents">
diff --git a/marcelo_zoccoler/jamovi/jamovi.html b/marcelo_zoccoler/jamovi/jamovi.html
index 1e9b24b..78882b9 100644
--- a/marcelo_zoccoler/jamovi/jamovi.html
+++ b/marcelo_zoccoler/jamovi/jamovi.html
@@ -420,7 +420,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="jamovi-statistical-analysis-made-visual-and-easy-powered-with-r">
+  <section class="tex2jax_ignore mathjax_ignore" id="jamovi-statistical-analysis-made-visual-and-easy-powered-with-r">
 <h1>Jamovi: statistical analysis made visual and easy (powered with R)<a class="headerlink" href="#jamovi-statistical-analysis-made-visual-and-easy-powered-with-r" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Marcelo Zoccoler</span></a>, October 7th 2021</p>
 <p>Statistical analysis software exist for decades. So why care about “just another one”. Well, for one main reason: simplicity. And I mean simplicity by a clean interface and an easy usage. Besides that, <a class="reference external" href="https://www.jamovi.org/">Jamovi</a> is open-source and developed in R, a powerful programming language to perform statistical tests.</p>
diff --git a/marcelo_zoccoler/mini_sabbatical_rike/Readme.html b/marcelo_zoccoler/mini_sabbatical_rike/Readme.html
index b9f85b2..b8b98a1 100644
--- a/marcelo_zoccoler/mini_sabbatical_rike/Readme.html
+++ b/marcelo_zoccoler/mini_sabbatical_rike/Readme.html
@@ -403,7 +403,7 @@ <h1>Mini-Sabbatical Experience at Bia-PoL</h1>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="mini-sabbatical-experience-at-bia-pol">
+  <section class="tex2jax_ignore mathjax_ignore" id="mini-sabbatical-experience-at-bia-pol">
 <h1>Mini-Sabbatical Experience at Bia-PoL<a class="headerlink" href="#mini-sabbatical-experience-at-bia-pol" title="Permalink to this heading">#</a></h1>
 <p>Friederike Kessel, February 28th 2022</p>
 <p>Hello, my name is Rike. For the last four years I have been a PhD student in experimental nephrology at the University Hospital Carl Gustav Carus in Dresden. During this time I started diving into the possibilities of bioimage analysis with Fiji. By using the ImageJ Macro language I helped colleagues to automatize workflows for the quantification of fluorescent signals in histology and intravital microscopy in mice.</p>
diff --git a/marcelo_zoccoler/omero_scripts/readme.html b/marcelo_zoccoler/omero_scripts/readme.html
index 0abe620..64a4924 100644
--- a/marcelo_zoccoler/omero_scripts/readme.html
+++ b/marcelo_zoccoler/omero_scripts/readme.html
@@ -416,7 +416,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="running-deep-learning-scripts-in-the-bia-pol-omero-server">
+  <section class="tex2jax_ignore mathjax_ignore" id="running-deep-learning-scripts-in-the-bia-pol-omero-server">
 <h1>Running Deep-Learning Scripts in the BiA-PoL Omero Server<a class="headerlink" href="#running-deep-learning-scripts-in-the-bia-pol-omero-server" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Marcelo Zoccoler</span></a>, May 2nd 2022</p>
 <section id="omero-server">
diff --git a/marcelo_zoccoler/readme.html b/marcelo_zoccoler/readme.html
index fb5158b..2b01085 100644
--- a/marcelo_zoccoler/readme.html
+++ b/marcelo_zoccoler/readme.html
@@ -416,7 +416,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="marcelo-zoccoler">
+  <section class="tex2jax_ignore mathjax_ignore" id="marcelo-zoccoler">
 <h1>Marcelo Zoccoler<a class="headerlink" href="#marcelo-zoccoler" title="Permalink to this heading">#</a></h1>
 <p><img alt="" src="../_images/marcelo_zoccoler_photo.jpg" /></p>
 <p>Hi! My name is Marcelo and I am an Electrical Engineer who has specialized in Life Sciences and Image Analysis!
@@ -424,7 +424,7 @@ <h1>Marcelo Zoccoler<a class="headerlink" href="#marcelo-zoccoler" title="Permal
 <p>During my Masters and PhD in Biomedical Engineering, I have worked with measuring microtubules stiffness by image analysis and modeling at UJF (now Université Grenoble Alpes) in France. After that, I have performed experiments with single cardiomyocytes under electrical fields in a <a class="reference external" href="https://doi.org/10.1007/978-3-319-19387-8_318">fluorescence microscope that was assembled by our group</a> at UNICAMP in Brazil. There, I started developing algorithms and software for bio-image analysis in MATLAB and Python. I also used a lot of Fiji as well! The goals were to quantify calcium concentration and membrane potential in these cells. Since some of these signals are very weak, I developed a software to extract these signals from noisy images called <a class="reference external" href="https://doi.org/10.1186/s12859-020-03661-9">METROID</a>. Most recently, I have contributed to develop a software called <a class="reference external" href="https://doi.org/10.1093/bioadv/vbab037">PoET</a> that automatically measures Giant Unilamellar Vesicles (GUV) pores and I have designed an online simulator as a tool to teach students about electrochemical balance across a semipermeable membrane.</p>
 <p>Since 2021, as a researcher for the Bio-image Analysis Technology Development group (BiA-PoL) at the DFG Cluster of Excellence “Physics of Life” at TU Dresden, I am developing courses and tools, mostly in Python and Fiji, that are intended to break down the barriers that biologists and biophysicists might experience when delving into the data science jungle. Below you will find some links to content related to my studies and how to find me.</p>
 </section>
-<section id="blog-posts">
+<section class="tex2jax_ignore mathjax_ignore" id="blog-posts">
 <h1>Blog posts<a class="headerlink" href="#blog-posts" title="Permalink to this heading">#</a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="jamovi/jamovi.html"><span class="doc std std-doc">Jamovi: statistical analysis made visual and easy (powered with R)</span></a></p></li>
@@ -432,7 +432,7 @@ <h1>Blog posts<a class="headerlink" href="#blog-posts" title="Permalink to this
 <li><p><a class="reference internal" href="entry_user_interf4/Readme.html"><span class="doc std std-doc">Turning napari GUI into plugins</span></a></p></li>
 </ul>
 </section>
-<section id="links">
+<section class="tex2jax_ignore mathjax_ignore" id="links">
 <h1>Links<a class="headerlink" href="#links" title="Permalink to this heading">#</a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="https://pbs.twimg.com/media/DoG8b8CX0AANQo8.jpg"><img alt="pol" src="https://pbs.twimg.com/media/DoG8b8CX0AANQo8.jpg" style="width: 25px;" /></a> <a class="reference external" href="https://physics-of-life.tu-dresden.de/en/research/core-groups/bio-image-analysis">BiA-PoL website</a></p></li>
diff --git a/people.html b/people.html
index 99c08a2..b99d4a8 100644
--- a/people.html
+++ b/people.html
@@ -403,7 +403,7 @@ <h1>BiA-PoL blog authors</h1>
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-  <section id="bia-pol-blog-authors">
+  <section class="tex2jax_ignore mathjax_ignore" id="bia-pol-blog-authors">
 <h1>BiA-PoL blog authors<a class="headerlink" href="#bia-pol-blog-authors" title="Permalink to this heading">#</a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="robert_haase/readme.html"><span class="doc std std-doc">Robert Haase</span></a></p></li>
diff --git a/robert_haase/browsing_idr/readme.html b/robert_haase/browsing_idr/readme.html
index 6ed3580..7e4055a 100644
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@@ -414,7 +414,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="browsing-the-open-microscopy-image-data-resource-with-python">
+  <section class="tex2jax_ignore mathjax_ignore" id="browsing-the-open-microscopy-image-data-resource-with-python">
 <h1>Browsing the Open Microscopy Image Data Resource with Python<a class="headerlink" href="#browsing-the-open-microscopy-image-data-resource-with-python" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Robert Haase</span></a>, June 6th 2021;
 <a class="reference internal" href="../../marcelo_zoccoler/readme.html"><span class="doc std std-doc">Marcelo Zoccoler</span></a>, updated on December 10th 2021</p>
diff --git a/robert_haase/clesperanto_google_colab/readme.html b/robert_haase/clesperanto_google_colab/readme.html
index 94940e5..97ac049 100644
--- a/robert_haase/clesperanto_google_colab/readme.html
+++ b/robert_haase/clesperanto_google_colab/readme.html
@@ -429,7 +429,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="gpu-accelerated-image-processing-in-the-cloud-using-google-colab-and-clesperanto">
+  <section class="tex2jax_ignore mathjax_ignore" id="gpu-accelerated-image-processing-in-the-cloud-using-google-colab-and-clesperanto">
 <h1>GPU-accelerated image processing in the cloud using Google Colab and clEsperanto<a class="headerlink" href="#gpu-accelerated-image-processing-in-the-cloud-using-google-colab-and-clesperanto" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Robert Haase</span></a>, June 5th 2021</p>
 <p>Not every computer has a powerful graphics processing unit (GPU) and thus,
@@ -573,11 +573,11 @@ <h3>How much memory is currently in use?<a class="headerlink" href="#how-much-me
 </section>
 </section>
 </section>
-<section id="disclosure">
+<section class="tex2jax_ignore mathjax_ignore" id="disclosure">
 <h1>Disclosure<a class="headerlink" href="#disclosure" title="Permalink to this heading">#</a></h1>
 <p>When reading this blog post, please have in mind that I’m one of the core developers of <a class="reference external" href="https://clesperanto.net">clesperanto</a>. I may be biased on the one side and even more interested on feedback on the other side.</p>
 </section>
-<section id="acknowledgements">
+<section class="tex2jax_ignore mathjax_ignore" id="acknowledgements">
 <h1>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this heading">#</a></h1>
 <p>I would like to thank Florian Jug and Wei Ouyang for introducing me to Google Colab and showing me tips and tricks.</p>
 </section>
diff --git a/robert_haase/cupy_cucim/cupy_cucim.html b/robert_haase/cupy_cucim/cupy_cucim.html
index 19eee6b..7bd8ff2 100644
--- a/robert_haase/cupy_cucim/cupy_cucim.html
+++ b/robert_haase/cupy_cucim/cupy_cucim.html
@@ -412,7 +412,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="gpu-accelerated-image-processing-using-cupy-and-cucim">
+  <section class="tex2jax_ignore mathjax_ignore" id="gpu-accelerated-image-processing-using-cupy-and-cucim">
 <h1>GPU-accelerated image processing using CUPY and CUCIM<a class="headerlink" href="#gpu-accelerated-image-processing-using-cupy-and-cucim" title="Permalink to this heading">#</a></h1>
 <p>Processing large images with python can take time. In order to accelerate processing, graphics processing units (GPUs) can be exploited, for example using <a class="reference external" href="https://en.wikipedia.org/wiki/CUDA">NVidia CUDA</a>. For processing images with CUDA, there are a couple of libraries available. We will take a closer look at <a class="reference external" href="https://cupy.dev/">cupy</a>, which brings more general computing capabilities for CUDA compatible GPUs, and <a class="reference external" href="https://github.com/rapidsai/cucim">cucim</a>, a library of image processing specific operations using CUDA. Both together can serve as GPU-surrogate for <a class="reference external" href="https://scikit-image.org/">scikit-image</a>.</p>
 <p>See also</p>
diff --git a/robert_haase/cupy_cucim/readme.html b/robert_haase/cupy_cucim/readme.html
index 8805d45..49bfdd6 100644
--- a/robert_haase/cupy_cucim/readme.html
+++ b/robert_haase/cupy_cucim/readme.html
@@ -414,7 +414,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="gpu-accelerated-image-processing-using-cupy-and-cucim">
+  <section class="tex2jax_ignore mathjax_ignore" id="gpu-accelerated-image-processing-using-cupy-and-cucim">
 <h1>GPU-accelerated image processing using cupy and cucim<a class="headerlink" href="#gpu-accelerated-image-processing-using-cupy-and-cucim" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Robert Haase</span></a>, June 6th 2021</p>
 <p>Processing large images with python can take time. In order to accelerate processing, graphics processing units (GPUs) can be exploited, for example using <a class="reference external" href="https://en.wikipedia.org/wiki/CUDA">NVidia CUDA</a>. For processing images with CUDA, there are a couple of libraries available. We will take a closer look at <a class="reference external" href="https://cupy.dev/">cupy</a>, which brings more general computing capabilities for CUDA compatible GPUs, and <a class="reference external" href="https://github.com/rapidsai/cucim">cucim</a>, a library of image processing specific operations using CUDA. Both together can serve as GPU-surrogate for <a class="reference external" href="https://scikit-image.org/">scikit-image</a>.</p>
diff --git a/robert_haase/ms_build_tools/readme.html b/robert_haase/ms_build_tools/readme.html
index 8374d4e..23f9539 100644
--- a/robert_haase/ms_build_tools/readme.html
+++ b/robert_haase/ms_build_tools/readme.html
@@ -416,7 +416,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="installing-microsoft-buildtools-on-windows">
+  <section class="tex2jax_ignore mathjax_ignore" id="installing-microsoft-buildtools-on-windows">
 <h1>Installing Microsoft buildtools on Windows<a class="headerlink" href="#installing-microsoft-buildtools-on-windows" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Robert Haase</span></a>, July 9th 2021</p>
 <p>Installing python libraries on Windows can be tricky. When using <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span></code> on a Windows computer that is not regularly visited by a hardcore programmer, a typical error message is “error: Microsoft Visual C++ 14.0 or greater is required.”.
diff --git a/robert_haase/readme.html b/robert_haase/readme.html
index e8fd728..c7a76eb 100644
--- a/robert_haase/readme.html
+++ b/robert_haase/readme.html
@@ -414,7 +414,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="robert-haase">
+  <section class="tex2jax_ignore mathjax_ignore" id="robert-haase">
 <h1>Robert Haase<a class="headerlink" href="#robert-haase" title="Permalink to this heading">#</a></h1>
 <img alt="../_images/robert_haase.png" src="../_images/robert_haase.png" />
 <p>My name is Robert and I am computer scientist by training.
diff --git a/robert_haase/stardist_gpu/readme.html b/robert_haase/stardist_gpu/readme.html
index 17eb287..de9b11f 100644
--- a/robert_haase/stardist_gpu/readme.html
+++ b/robert_haase/stardist_gpu/readme.html
@@ -421,7 +421,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="using-stardist-in-napari-with-gpu-support-in-windows">
+  <section class="tex2jax_ignore mathjax_ignore" id="using-stardist-in-napari-with-gpu-support-in-windows">
 <h1>Using StarDist in napari with GPU-support in Windows<a class="headerlink" href="#using-stardist-in-napari-with-gpu-support-in-windows" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Robert Haase</span></a>, June 19th 2021</p>
 <p>3D segmentation using deep learning is computationally costly, it might be necessary from a practical perspective to do it on computers
diff --git a/robert_haase/why_we_blog/readme.html b/robert_haase/why_we_blog/readme.html
index c6beb7a..87a6d6c 100644
--- a/robert_haase/why_we_blog/readme.html
+++ b/robert_haase/why_we_blog/readme.html
@@ -403,7 +403,7 @@ <h1>Why we blog</h1>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="why-we-blog">
+  <section class="tex2jax_ignore mathjax_ignore" id="why-we-blog">
 <h1>Why we blog<a class="headerlink" href="#why-we-blog" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Robert Haase</span></a>, May 30th 2021</p>
 <p>Bio-image analysis is an emerging field.
diff --git a/ryan_savill/01_intro_to_python/readme.html b/ryan_savill/01_intro_to_python/readme.html
index 5b6513a..d1eb16b 100644
--- a/ryan_savill/01_intro_to_python/readme.html
+++ b/ryan_savill/01_intro_to_python/readme.html
@@ -424,7 +424,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
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-  <section id="introduction-to-using-python-for-image-analysis">
+  <section class="tex2jax_ignore mathjax_ignore" id="introduction-to-using-python-for-image-analysis">
 <h1>Introduction to Using Python for Image Analysis<a class="headerlink" href="#introduction-to-using-python-for-image-analysis" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Ryan Savill</span></a>, June 17th 2021</p>
 <section id="setting-up-your-environment">
diff --git a/ryan_savill/02_intro_to_skimage/Introduction to Image Analysis Basics in Python with Scikit Image.html b/ryan_savill/02_intro_to_skimage/Introduction to Image Analysis Basics in Python with Scikit Image.html
index f17c5de..8c4c90f 100644
--- a/ryan_savill/02_intro_to_skimage/Introduction to Image Analysis Basics in Python with Scikit Image.html	
+++ b/ryan_savill/02_intro_to_skimage/Introduction to Image Analysis Basics in Python with Scikit Image.html	
@@ -401,7 +401,7 @@ <h1>Introduction to Image Analysis Basics in Python with Scikit Image</h1>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="introduction-to-image-analysis-basics-in-python-with-scikit-image">
+  <section class="tex2jax_ignore mathjax_ignore" id="introduction-to-image-analysis-basics-in-python-with-scikit-image">
 <h1>Introduction to Image Analysis Basics in Python with Scikit Image<a class="headerlink" href="#introduction-to-image-analysis-basics-in-python-with-scikit-image" title="Permalink to this heading">#</a></h1>
 <p>Now that we have a grasp of the basics of python it’s time to get started with some proper image analysis! For the purposes of trying out image analysis I have a picture of a tribolium embryo with stained nuclei. It previously was a 3D image but we are working with a maximum projection to keep it simple (This means the maximum intensity over all slices of the embryo were taken). Now to see how processing is done in python the explanation will be shown with this example.
 The first step in any program is to import the libraries needed. You can import whole libraries for example numpy:</p>
diff --git a/ryan_savill/02_intro_to_skimage/readme.html b/ryan_savill/02_intro_to_skimage/readme.html
index 0c7442b..7bc36e5 100644
--- a/ryan_savill/02_intro_to_skimage/readme.html
+++ b/ryan_savill/02_intro_to_skimage/readme.html
@@ -413,7 +413,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="introduction-to-image-analysis-basics-in-python-with-scikit-image">
+  <section class="tex2jax_ignore mathjax_ignore" id="introduction-to-image-analysis-basics-in-python-with-scikit-image">
 <h1>Introduction to Image Analysis Basics in Python with Scikit Image<a class="headerlink" href="#introduction-to-image-analysis-basics-in-python-with-scikit-image" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Ryan Savill</span></a>, June 25th 2021</p>
 <p>Now that we have a grasp of the basics of python it’s time to get started with some proper image analysis! For the purpose of trying out image analysis I have a picture of a tribolium embryo with stained nuclei. It previously was a 3D image but we are working with a maximum projection to keep it simple (This means the maximum intensity over all slices of the embryo were taken).  The dataset was acquired by Daniela Vorkel, Myers lab, MPI-CBG / CSBD Dresden. Now to see how processing is done in python the explanation will be shown with this example.
diff --git a/ryan_savill/03_background_subtraction/background subtraction in scipy and scikit image.html b/ryan_savill/03_background_subtraction/background subtraction in scipy and scikit image.html
index 280fa6a..647fe3e 100644
--- a/ryan_savill/03_background_subtraction/background subtraction in scipy and scikit image.html	
+++ b/ryan_savill/03_background_subtraction/background subtraction in scipy and scikit image.html	
@@ -417,7 +417,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="background-subtraction">
+  <section class="tex2jax_ignore mathjax_ignore" id="background-subtraction">
 <h1>Background Subtraction<a class="headerlink" href="#background-subtraction" title="Permalink to this heading">#</a></h1>
 <p>In the <a class="reference external" href="https://biapol.github.io/blog/02_intro_to_skimage">previous blog post</a> we saw how background subtraction can improve segmentation substantially. We will now take a more in depth look at how background subtraction works by showing the top-hat filter and Difference of Gaussian (DoG) filter, which both can achieve background subtraction. In general, we want to use background subtraction if there is a sharp signal (high localised intensity) we want to isolate from moderate signal that is evenly distributed in the background. Some simple functions allow us to find the background image and subtract it from our original image, only leaving the signals we want to isolate.</p>
 <section id="top-hat-filter">
diff --git a/ryan_savill/03_background_subtraction/readme.html b/ryan_savill/03_background_subtraction/readme.html
index 8a12a32..054848e 100644
--- a/ryan_savill/03_background_subtraction/readme.html
+++ b/ryan_savill/03_background_subtraction/readme.html
@@ -419,7 +419,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="background-subtraction">
+  <section class="tex2jax_ignore mathjax_ignore" id="background-subtraction">
 <h1>Background Subtraction<a class="headerlink" href="#background-subtraction" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Ryan Savill</span></a>, June 25th 2021</p>
 <p>In the <a class="reference external" href="https://biapol.github.io/blog/02_intro_to_skimage">previous blog post</a> we saw how background subtraction can improve segmentation substantially. We will now take a more in depth look at how background subtraction works by showing the top-hat filter and Difference of Gaussian (DoG) filter, which both can achieve background subtraction. In general, we want to use background subtraction if there is a sharp signal (high localised intensity) we want to isolate from moderate signal that is evenly distributed in the background. Some simple functions allow us to find the background image and subtract it from our original image, only leaving the signals we want to isolate.</p>
diff --git a/ryan_savill/principal_feature_analysis/readme.html b/ryan_savill/principal_feature_analysis/readme.html
index c598117..3682c46 100644
--- a/ryan_savill/principal_feature_analysis/readme.html
+++ b/ryan_savill/principal_feature_analysis/readme.html
@@ -414,7 +414,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="principal-feature-analysis">
+  <section class="tex2jax_ignore mathjax_ignore" id="principal-feature-analysis">
 <h1>Principal Feature Analysis<a class="headerlink" href="#principal-feature-analysis" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Ryan Savill</span></a>, July 8th 2021</p>
 <section id="background">
diff --git a/ryan_savill/readme.html b/ryan_savill/readme.html
index 5dde05c..d299c28 100644
--- a/ryan_savill/readme.html
+++ b/ryan_savill/readme.html
@@ -420,7 +420,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="ryan-savill">
+  <section class="tex2jax_ignore mathjax_ignore" id="ryan-savill">
 <h1>Ryan Savill<a class="headerlink" href="#ryan-savill" title="Permalink to this heading">#</a></h1>
 <section id="image-analysis-in-python-from-a-biologist-for-biologists">
 <h2>Image Analysis in Python from a Biologist for Biologists<a class="headerlink" href="#image-analysis-in-python-from-a-biologist-for-biologists" title="Permalink to this heading">#</a></h2>
diff --git a/stefan_hahmann/elephant_server_installation_windows/readme.html b/stefan_hahmann/elephant_server_installation_windows/readme.html
index 8ee8209..bfc21f3 100644
--- a/stefan_hahmann/elephant_server_installation_windows/readme.html
+++ b/stefan_hahmann/elephant_server_installation_windows/readme.html
@@ -427,7 +427,7 @@ <h2> Contents </h2>
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-  <section id="installation-of-elephant-server-on-windows">
+  <section class="tex2jax_ignore mathjax_ignore" id="installation-of-elephant-server-on-windows">
 <h1>Installation of Elephant Server on Windows<a class="headerlink" href="#installation-of-elephant-server-on-windows" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Stefan Hahmann</span></a>, April 24th 2024
 <a class="reference internal" href="../../johannes_mueller/Readme.html"><span class="doc std std-doc">Johannes Soltwedel</span></a>, April 24th 2024</p>
diff --git a/stefan_hahmann/github_desktop_jupyter_notebook/readme.html b/stefan_hahmann/github_desktop_jupyter_notebook/readme.html
index a67fbf5..645c02b 100644
--- a/stefan_hahmann/github_desktop_jupyter_notebook/readme.html
+++ b/stefan_hahmann/github_desktop_jupyter_notebook/readme.html
@@ -423,7 +423,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="running-bio-image-analysis-workflows-on-your-machine">
+  <section class="tex2jax_ignore mathjax_ignore" id="running-bio-image-analysis-workflows-on-your-machine">
 <h1>Running bio image analysis workflows on your machine<a class="headerlink" href="#running-bio-image-analysis-workflows-on-your-machine" title="Permalink to this heading">#</a></h1>
 <p><a class="reference internal" href="../readme.html"><span class="doc std std-doc">Stefan Hahmann</span></a>, December 21st 2023</p>
 <section id="introduction">
diff --git a/stefan_hahmann/readme.html b/stefan_hahmann/readme.html
index 378d540..36fe675 100644
--- a/stefan_hahmann/readme.html
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@@ -416,7 +416,7 @@ <h2> Contents </h2>
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-  <section id="stefan-hahmann">
+  <section class="tex2jax_ignore mathjax_ignore" id="stefan-hahmann">
 <h1>Stefan Hahmann<a class="headerlink" href="#stefan-hahmann" title="Permalink to this heading">#</a></h1>
 <p><img alt="stefan_hahmann.jpg" src="../_images/stefan_hahmann.jpg" /></p>
 <p>Hi! My name is Stefan.</p>
@@ -425,13 +425,13 @@ <h1>Stefan Hahmann<a class="headerlink" href="#stefan-hahmann" title="Permalink
 During my Postdoc, I worked at <a class="reference external" href="https://www.geog.uni-heidelberg.de/gis/">Heidelberg University</a>, where I contributed to the route planning service <a class="reference external" href="https://maps.openrouteservice.org/#/">OpenRouteService.org</a> and at <a class="reference external" href="https://www.ivi.fraunhofer.de/">Fraunhofer IVI</a>, where I contributed to <a class="reference external" href="https://www.mobikat.net/en.html">Mobikat</a>, a decision support tool for fire departments, rescue services and police.</p>
 <p>Since 2022, I work as a <a class="reference external" href="https://de-rse.org/en/">research software engineer</a> for the Bio-image Analysis Technology Development group (<a class="reference external" href="https://physics-of-life.tu-dresden.de/research/core-groups/bio-image-analysis/people">BiA-PoL</a>) at the DFG Cluster of Excellence “<a class="reference external" href="https://physics-of-life.tu-dresden.de/">Physics of Life</a>” at TU Dresden. I am developing plugins for the image analysis software <a class="reference external" href="https://imagej.net/software/fiji/">Fiji</a> and workflows for the image analysis software <a class="reference external" href="https://napari.org/stable/">Napari</a>, where currently most of the time I am <a class="reference external" href="https://github.com/mastodon-sc/mastodon-deep-lineage">extending</a> the (cell) tracking module <a class="reference external" href="https://mastodon.readthedocs.io/en/latest/">Mastodon</a>.</p>
 </section>
-<section id="blog-posts">
+<section class="tex2jax_ignore mathjax_ignore" id="blog-posts">
 <h1>Blog posts<a class="headerlink" href="#blog-posts" title="Permalink to this heading">#</a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="github_desktop_jupyter_notebook/readme.html"><span class="doc std std-doc">Running bio image analysis workflows on your machine</span></a></p></li>
 </ul>
 </section>
-<section id="links">
+<section class="tex2jax_ignore mathjax_ignore" id="links">
 <h1>Links<a class="headerlink" href="#links" title="Permalink to this heading">#</a></h1>
 <ul class="simple">
 <li><p><a class="reference external" href="https://twitter.com/stefanhahmann">Twitter</a></p></li>
diff --git a/till_korten/devbio-napari_cluster/readme.html b/till_korten/devbio-napari_cluster/readme.html
index 599f47f..4cf3e5f 100644
--- a/till_korten/devbio-napari_cluster/readme.html
+++ b/till_korten/devbio-napari_cluster/readme.html
@@ -424,7 +424,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
                   
-  <section id="using-gpu-accelerated-image-processing-on-the-tud-hpc-cluster">
+  <section class="tex2jax_ignore mathjax_ignore" id="using-gpu-accelerated-image-processing-on-the-tud-hpc-cluster">
 <h1>Using GPU-accelerated image processing on the TUD HPC cluster<a class="headerlink" href="#using-gpu-accelerated-image-processing-on-the-tud-hpc-cluster" title="Permalink to this heading">#</a></h1>
 <p><a class="reference external" href="https://biapol.github.io/blog/till_korten">Till Korten</a>, Oct 21st 2022</p>
 <p>The <a class="reference external" href="https://tu-dresden.de/zih/hochleistungsrechnen/hpc?set_language=en">High Performance Computing (HPC) cluster at the compute center (ZIH) of the TU Dresden</a> provides a lot of computational resources including GPU support, which we can use for analyzing data in the life-sciences.
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-  <section id="setting-up-gpu-accelerated-image-processing-on-the-tud-hpc-cluster">
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 <h1>Setting up GPU-accelerated image processing on the TUD HPC cluster<a class="headerlink" href="#setting-up-gpu-accelerated-image-processing-on-the-tud-hpc-cluster" title="Permalink to this heading">#</a></h1>
 <p><a class="reference external" href="https://biapol.github.io/blog/till_korten">Till Korten</a>, July 29th 2022</p>
 <p>The <a class="reference external" href="https://tu-dresden.de/zih/hochleistungsrechnen/hpc?set_language=en">High Performance Computing (HPC) cluster at the compute center (ZIH) of the TU Dresden</a> provides a lot of computational resources including GPU support, which we can use for analyzing data in the life-sciences.