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‎build/doctrees/environment.pickle

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‎build/doctrees/index.doctree

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‎build/html/_sources/index.rst.txt

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@@ -29,16 +29,6 @@ about our research can be found on our `website <https://www.dean-lab.org>`_.
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- Cost-effective, easy-to-assemble, and performant light-sheet microscopes for interrogating live cells,
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expanded, and cleared tissue samples.
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**Software Repositories**
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================
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.. _navigate_repo:
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- `navigate <https://github.com/TheDeanLab/navigate>`_ - A Python package for intelligent light-sheet microscopy of complex tissue samples.
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- `navigate_plugin_template <https://github.com/TheDeanLab/navigate-plugin-template>`_ - A template repository for creating plugins for the **navigate** package.
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- `navigate_confocal_projection <https://github.com/TheDeanLab/navigate-confocal-projection>`_ - A plugin for the **navigate** package that acquires confocal projections with light-sheet microscopes.
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- `navigate_at_scale <https://github.com/TheDeanLab/navigate-at-scale>`_ - A plugin for the **navigate** package that enables high-throughput imaging of large tissue samples using robotic delivery of tissues to the microscope.
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**Educational Resources**
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================
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- `CI2023 <https://github.com/TheDeanLab/CI2023>`_ - An introduction to continuous integration and continuous deployment for scientific software.
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- NIH National Cancer Institute (1U54CA268072).
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- `Simmons Comprehensive Cancer Center <https://www.utsouthwestern.edu/departments/simmons/>`_ Translational Seed Grant.
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- `UTSW President's Research Council <https://engage.utsouthwestern.edu/pages/membership-giving/membership-giving---presidents-research-council>`_
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.. toctree::
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:caption: Software
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:maxdepth: 2
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navigate <https://github.com/TheDeanLab/navigate>
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navigate Plugin Template <https://github.com/TheDeanLab/navigate-plugin-template>
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navigate Confocal Projection Plugin <https://github.com/TheDeanLab/navigate-confocal-projection>
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navigate At Scale <https://github.com/TheDeanLab/navigate-at-scale>
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navigate MMCore Plugin <https://github.com/TheDeanLab/navigate-mmcore-plugin>
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navigate ilastik Server <https://github.com/TheDeanLab/navigate-ilastik-server>

‎build/html/genindex.html

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</form>
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</div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<!-- Local TOC -->
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<div class="local-toc"></div>
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<p class="caption" role="heading"><span class="caption-text">Software</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate">navigate</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-plugin-template">navigate Plugin Template</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-confocal-projection">navigate Confocal Projection Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-at-scale">navigate At Scale</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-mmcore-plugin">navigate MMCore Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-ilastik-server">navigate ilastik Server</a></li>
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</ul>
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</div>
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</div>
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</nav>

‎build/html/index.html

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</form>
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</div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<!-- Local TOC -->
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<div class="local-toc"><ul>
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<li><a class="reference internal" href="#">The Dean Lab at UTSW</a><ul>
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<li><a class="reference internal" href="#projects"><strong>Projects</strong></a></li>
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<li><a class="reference internal" href="#software-repositories"><strong>Software Repositories</strong></a></li>
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<li><a class="reference internal" href="#educational-resources"><strong>Educational Resources</strong></a></li>
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<li><a class="reference internal" href="#publication-repositories"><strong>Publication Repositories</strong></a></li>
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<li><a class="reference internal" href="#funding"><strong>Funding</strong></a></li>
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<p class="caption" role="heading"><span class="caption-text">Software</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate">navigate</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-plugin-template">navigate Plugin Template</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-confocal-projection">navigate Confocal Projection Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-at-scale">navigate At Scale</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-mmcore-plugin">navigate MMCore Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-ilastik-server">navigate ilastik Server</a></li>
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</ul>
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</li>
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</ul>
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</div>
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</div>
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</div>
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</nav>
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expanded, and cleared tissue samples.</p></li>
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</ul>
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</section>
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<section id="software-repositories">
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<h2><strong>Software Repositories</strong><a class="headerlink" href="#software-repositories" title="Permalink to this heading"></a></h2>
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<ul class="simple" id="navigate-repo">
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<li><p><a class="reference external" href="https://github.com/TheDeanLab/navigate">navigate</a> - A Python package for intelligent light-sheet microscopy of complex tissue samples.</p></li>
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<li><p><a class="reference external" href="https://github.com/TheDeanLab/navigate-plugin-template">navigate_plugin_template</a> - A template repository for creating plugins for the <strong>navigate</strong> package.</p></li>
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<li><p><a class="reference external" href="https://github.com/TheDeanLab/navigate-confocal-projection">navigate_confocal_projection</a> - A plugin for the <strong>navigate</strong> package that acquires confocal projections with light-sheet microscopes.</p></li>
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<li><p><a class="reference external" href="https://github.com/TheDeanLab/navigate-at-scale">navigate_at_scale</a> - A plugin for the <strong>navigate</strong> package that enables high-throughput imaging of large tissue samples using robotic delivery of tissues to the microscope.</p></li>
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</ul>
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</section>
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<section id="educational-resources">
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<h2><strong>Educational Resources</strong><a class="headerlink" href="#educational-resources" title="Permalink to this heading"></a></h2>
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<ul class="simple">
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<li><p><a class="reference external" href="https://www.utsouthwestern.edu/departments/simmons/">Simmons Comprehensive Cancer Center</a> Translational Seed Grant.</p></li>
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<li><p><a class="reference external" href="https://engage.utsouthwestern.edu/pages/membership-giving/membership-giving---presidents-research-council">UTSW President’s Research Council</a></p></li>
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</ul>
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<div class="toctree-wrapper compound">
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<p class="caption" role="heading"><span class="caption-text">Software</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate">navigate</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-plugin-template">navigate Plugin Template</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-confocal-projection">navigate Confocal Projection Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-at-scale">navigate At Scale</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-mmcore-plugin">navigate MMCore Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-ilastik-server">navigate ilastik Server</a></li>
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</ul>
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</div>
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</section>
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</section>
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‎build/html/objects.inv

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‎build/html/search.html

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</form>
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<!-- Local TOC -->
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<div class="local-toc"></div>
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<p class="caption" role="heading"><span class="caption-text">Software</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate">navigate</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-plugin-template">navigate Plugin Template</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-confocal-projection">navigate Confocal Projection Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-at-scale">navigate At Scale</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-mmcore-plugin">navigate MMCore Plugin</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/TheDeanLab/navigate-ilastik-server">navigate ilastik Server</a></li>
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</ul>
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</div>
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</div>
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</nav>

‎build/html/searchindex.js

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‎source/index.rst

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@@ -29,16 +29,6 @@ about our research can be found on our `website <https://www.dean-lab.org>`_.
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- Cost-effective, easy-to-assemble, and performant light-sheet microscopes for interrogating live cells,
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expanded, and cleared tissue samples.
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**Software Repositories**
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================
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.. _navigate_repo:
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- `navigate <https://github.com/TheDeanLab/navigate>`_ - A Python package for intelligent light-sheet microscopy of complex tissue samples.
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- `navigate_plugin_template <https://github.com/TheDeanLab/navigate-plugin-template>`_ - A template repository for creating plugins for the **navigate** package.
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- `navigate_confocal_projection <https://github.com/TheDeanLab/navigate-confocal-projection>`_ - A plugin for the **navigate** package that acquires confocal projections with light-sheet microscopes.
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- `navigate_at_scale <https://github.com/TheDeanLab/navigate-at-scale>`_ - A plugin for the **navigate** package that enables high-throughput imaging of large tissue samples using robotic delivery of tissues to the microscope.
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**Educational Resources**
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================
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- `CI2023 <https://github.com/TheDeanLab/CI2023>`_ - An introduction to continuous integration and continuous deployment for scientific software.
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- NIH National Cancer Institute (1U54CA268072).
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- `Simmons Comprehensive Cancer Center <https://www.utsouthwestern.edu/departments/simmons/>`_ Translational Seed Grant.
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- `UTSW President's Research Council <https://engage.utsouthwestern.edu/pages/membership-giving/membership-giving---presidents-research-council>`_
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.. toctree::
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:caption: Software
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:maxdepth: 2
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navigate <https://github.com/TheDeanLab/navigate>
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navigate Plugin Template <https://github.com/TheDeanLab/navigate-plugin-template>
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navigate Confocal Projection Plugin <https://github.com/TheDeanLab/navigate-confocal-projection>
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navigate At Scale <https://github.com/TheDeanLab/navigate-at-scale>
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navigate MMCore Plugin <https://github.com/TheDeanLab/navigate-mmcore-plugin>
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navigate ilastik Server <https://github.com/TheDeanLab/navigate-ilastik-server>

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