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4 changes: 2 additions & 2 deletions imprint.html
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<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>
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<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.
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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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>
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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>, July 8th, 2024</p>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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!
Most of my work has been done on tools and software for image analysis focused on microscopy data.</p>
<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>
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<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>
<li><p><a class="reference internal" href="entry_user_interf3/Readme.html"><span class="doc std std-doc">Creating advanced GUIs for napari</span></a></p></li>
<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>
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<h1>Links<a class="headerlink" href="#links" title="Permalink to this heading">#</a></h1>
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<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>
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<h1>BiA-PoL blog authors<a class="headerlink" href="#bia-pol-blog-authors" title="Permalink to this heading">#</a></h1>
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<li><p><a class="reference internal" href="robert_haase/readme.html"><span class="doc std std-doc">Robert Haase</span></a></p></li>
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<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>
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