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 </pre></div> </div> <p>The <code class="docutils literal notranslate"><span class=pre >[all]</span></code> qualifier also installs <code class="docutils literal notranslate"><span class=pre >pyqt5</span></code> as the napari GUI backend, and a few additional napari plugins that you might find useful in your workflow:</p> <ul class=simple > <li><p><a class="reference external" href="https://github.com/brisvag/napari-properties-plotter">napari-properties-plotter</a></p> <li><p><a class="reference external" href="https://github.com/kevinyamauchi/napari-properties-viewer">napari-properties-viewer</a></p> <li><p><a class="reference external" href="https://github.com/brisvag/napari-label-interpolator">napari-label-interpolator</a></p> </ul> <section id=nightly-build > <h3 id=nightly-build >Nightly build<a class=headerlink  href="#nightly-build" title="Permalink to this heading">¶</a></h3> <p>If you’d like the most up to date <code class="docutils literal notranslate"><span class=pre >blik</span></code> possible, you can install directly from the <code class="docutils literal notranslate"><span class=pre >main</span></code> branch on github. This also uses napari <code class="docutils literal notranslate"><span class=pre >main</span></code>, so expect some instability!</p> <div class="highlight-default notranslate"><div class=highlight ><pre><span></span><span class=n >pip</span> <span class=n >install</span> <span class=s2 >"git+https://github.com/brisvag/blik.git@main#egg=blik[all]"</span>
 <span class=n >pip</span> <span class=n >install</span> <span class=s2 >"git+https://github.com/napari/napari.git@main#egg=napari[all]"</span>
 </pre></div> </div> </section> </section> <section id=basic-usage > <h2 id=basic-usage >Basic Usage<a class=headerlink  href="#basic-usage" title="Permalink to this heading">¶</a></h2> <p>From the command line:</p> <div class="highlight-bash notranslate"><div class=highlight ><pre><span></span>napari<span class=w > </span>-w<span class=w > </span>blik<span class=w > </span>--<span class=w > </span>/path/to.star<span class=w > </span>/path/to/mrc/files/*
-</pre></div> </div> <p>The <code class="docutils literal notranslate"><span class=pre >-w</span> <span class=pre >blik</span></code> is important for proper initialization of all the layers. Always open the main widget open to ensure nothing goes wrong!</p> <p><em><code class="docutils literal notranslate"><span class=pre >blik</span></code> is just <code class="docutils literal notranslate"><span class=pre >napari</span></code></em>. Particles and images are exposed as simple napari layers, which can be analysed and manipulated with simple python, and most importantly other <a class="reference external" href="https://napari-hub.org/">napari plugins</a>.</p> </section> <section id=widgets > <h2 id=widgets >Widgets<a class=headerlink  href="#widgets" title="Permalink to this heading">¶</a></h2> <p>The main widget has a few functions:</p> <ul class=simple > <li><p><code class="docutils literal notranslate"><span class=pre >experiment</span></code>: quickly switch to a different experiment id (typically, everything related to an individual tomogram such as volume, particles and segmentations)</p> <li><p><code class="docutils literal notranslate"><span class=pre >new</span></code>: generate a new <code class="docutils literal notranslate"><span class=pre >segmentation</span></code>, a new manually-picked set of <code class="docutils literal notranslate"><span class=pre >particles</span></code>, or a new <code class="docutils literal notranslate"><span class=pre >surface</span> <span class=pre >picking</span></code> or <code class="docutils literal notranslate"><span class=pre >filament</span> <span class=pre >picking</span></code> for segmentation, particle generation or volume resampling.</p> <li><p><code class="docutils literal notranslate"><span class=pre >add</span> <span class=pre >to</span> <span class=pre >exp</span></code>: add a layer to the currently selected <code class="docutils literal notranslate"><span class=pre >experiment</span></code> (just a shorthand for <code class="docutils literal notranslate"><span class=pre >layer.metadata['experiment_id']</span> <span class=pre >=</span> <span class=pre >current_exp_id</span></code>)</p> </ul> <p>There are also widgets for picking of both surfaces and filaments.</p> <ul class=simple > <li><p><code class="docutils literal notranslate"><span class=pre >surface</span></code>: process a previously picked <code class="docutils literal notranslate"><span class=pre >surface</span> <span class=pre >picking</span></code> layer to generate a surface mesh and distribute particles on it for subtomogram averaging, or resample a tomogram along the surface.</p> <li><p><code class="docutils literal notranslate"><span class=pre >filament</span></code>: process a previously picked <code class="docutils literal notranslate"><span class=pre >filament</span> <span class=pre >picking</span></code> layer to generate a filament and distribute particles on it for subtomogram averaging, or resample a tomogram along the filament.</p> </ul> </section> <div class="toctree-wrapper compound"> </div> </section> <script type="text/x-thebe-config"> { requestKernel: true, binderOptions: { repo: "binder-examples/jupyter-stacks-datascience", ref: "master", }, codeMirrorConfig: { theme: "abcdef", mode: "python" }, kernelOptions: { name: "python3", path: "./." }, predefinedOutput: true } </script> <script>kernelName = 'python3'</script> </article> </div> </div> </main> </div> <footer class=md-footer > <div class=md-footer-nav > <nav class="md-footer-nav__inner md-grid"> <a href=getting_started.html  title="Getting started" class="md-flex md-footer-nav__link md-footer-nav__link--next" rel=next > <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"><span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Next" </span> Getting started </span> </div> <div class="md-flex__cell md-flex__cell--shrink"><i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i> </div> </a> </nav> </div> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-footer-copyright > <div class=md-footer-copyright__highlight > &#169; Copyright 2020. </div> Created using <a href="http://www.sphinx-doc.org/">Sphinx</a> 5.0.2. and <a href="https://github.com/bashtage/sphinx-material/">Material for Sphinx</a> </div> </div> </div> </footer> <script src="_static/javascripts/application.js"></script> <script>app.initialize({version: "1.0.4", url: {base: ".."}})</script>
+</pre></div> </div> <p>The <code class="docutils literal notranslate"><span class=pre >-w</span> <span class=pre >blik</span></code> is important for proper initialization of all the layers. Always open the main widget open to ensure nothing goes wrong!</p> <p><em><code class="docutils literal notranslate"><span class=pre >blik</span></code> is just <code class="docutils literal notranslate"><span class=pre >napari</span></code></em>. Particles and images are exposed as simple napari layers, which can be analysed and manipulated with simple python, and most importantly other <a class="reference external" href="https://napari-hub.org/">napari plugins</a>.</p> </section> <section id=widgets > <h2 id=widgets >Widgets<a class=headerlink  href="#widgets" title="Permalink to this heading">¶</a></h2> <p>The main widget has a few functions:</p> <ul class=simple > <li><p><code class="docutils literal notranslate"><span class=pre >experiment</span></code>: quickly switch to a different experiment id (typically, everything related to an individual tomogram such as volume, particles and segmentations)</p> <li><p><code class="docutils literal notranslate"><span class=pre >new</span></code>: generate a new <code class="docutils literal notranslate"><span class=pre >segmentation</span></code>, a new manually-picked set of <code class="docutils literal notranslate"><span class=pre >particles</span></code>, or a new <code class="docutils literal notranslate"><span class=pre >surface</span> <span class=pre >picking</span></code> or <code class="docutils literal notranslate"><span class=pre >filament</span> <span class=pre >picking</span></code> for segmentation, particle generation or volume resampling.</p> <li><p><code class="docutils literal notranslate"><span class=pre >add</span> <span class=pre >to</span> <span class=pre >exp</span></code>: add a layer to the currently selected <code class="docutils literal notranslate"><span class=pre >experiment</span></code> (just a shorthand for <code class="docutils literal notranslate"><span class=pre >layer.metadata['experiment_id']</span> <span class=pre >=</span> <span class=pre >current_exp_id</span></code>)</p> <li><p><code class="docutils literal notranslate"><span class=pre >slice_thickness</span></code>: changes the slicing thickness in all dimensions in napari. Images will be averaged over that thickness, and all particles in the slice will be displayed.</p> </ul> <p>There are also widgets for picking of both surfaces and filaments.</p> <ul class=simple > <li><p><code class="docutils literal notranslate"><span class=pre >surface</span></code>: process a previously picked <code class="docutils literal notranslate"><span class=pre >surface</span> <span class=pre >picking</span></code> layer to generate a surface mesh and distribute particles on it for subtomogram averaging, or resample a tomogram along the surface.</p> <li><p><code class="docutils literal notranslate"><span class=pre >filament</span></code>: process a previously picked <code class="docutils literal notranslate"><span class=pre >filament</span> <span class=pre >picking</span></code> layer to generate a filament and distribute particles on it for subtomogram averaging, or resample a tomogram along the filament.</p> </ul> </section> <div class="toctree-wrapper compound"> </div> </section> <script type="text/x-thebe-config"> { requestKernel: true, binderOptions: { repo: "binder-examples/jupyter-stacks-datascience", ref: "master", }, codeMirrorConfig: { theme: "abcdef", mode: "python" }, kernelOptions: { name: "python3", path: "./." }, predefinedOutput: true } </script> <script>kernelName = 'python3'</script> </article> </div> </div> </main> </div> <footer class=md-footer > <div class=md-footer-nav > <nav class="md-footer-nav__inner md-grid"> <a href=getting_started.html  title="Getting started" class="md-flex md-footer-nav__link md-footer-nav__link--next" rel=next > <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"><span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Next" </span> Getting started </span> </div> <div class="md-flex__cell md-flex__cell--shrink"><i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i> </div> </a> </nav> </div> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-footer-copyright > <div class=md-footer-copyright__highlight > &#169; Copyright 2020. </div> Created using <a href="http://www.sphinx-doc.org/">Sphinx</a> 5.0.2. and <a href="https://github.com/bashtage/sphinx-material/">Material for Sphinx</a> </div> </div> </div> </footer> <script src="_static/javascripts/application.js"></script> <script>app.initialize({version: "1.0.4", url: {base: ".."}})</script>