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<section id="tutorial-6-custom-slide-filtering">
<span id="tutorial6"></span><h1>Tutorial 6: Custom slide filtering<a class="headerlink" href="#tutorial-6-custom-slide-filtering" title="Permalink to this heading">¶</a></h1>
<p>In this brief tutorial, we’ll take a look at how you can implement and preview bespoke slide-level filtering methods.</p>
<p>The slide-level filtering (QC) methods Slideflow currently supports include Otsu’s thresholding and Gaussian blur filtering, which can be applied to a <a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.WSI"><code class="xref py py-class docutils literal notranslate"><span class="pre">WSI</span></code></a> object with <code class="xref py py-meth docutils literal notranslate"><span class="pre">WSI.qc()</span></code>. If you have a custom filtering algorithm you would like to apply to a slide, you can now use <code class="xref py py-meth docutils literal notranslate"><span class="pre">WSI.apply_qc_mask()</span></code> to apply a boolean mask to filter a slide.</p>
<p>For the purposes of this tutorial, we will generate a boolean mask using the already-available Otsu’s thresholding algorithm, but you can replace this with whatever masking algorithm you like.</p>
<p>First, we’ll load a slide:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="n">wsi</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">WSI</span><span class="p">(</span><span class="s1">'slide.svs'</span><span class="p">,</span> <span class="n">tile_px</span><span class="o">=</span><span class="mi">299</span><span class="p">,</span> <span class="n">tile_um</span><span class="o">=</span><span class="mi">302</span><span class="p">)</span>
</pre></div>
</div>
<p>Next, we’ll apply Otsu’s thresholding to get the boolean mask we’ll use in subsequent steps, then remove the QC once we have the mask:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="s1">'otsu'</span><span class="p">)</span>
<span class="n">qc_mask</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">wsi</span><span class="o">.</span><span class="n">qc_mask</span><span class="p">)</span>
<span class="n">wsi</span><span class="o">.</span><span class="n">remove_qc</span><span class="p">()</span>
</pre></div>
</div>
<p>Our mask should have two dimensions (y, x) and have a dtype of bool:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>>>><span class="w"> </span>qc_mask.shape
<span class="o">(</span><span class="m">1010</span>,<span class="w"> </span><span class="m">2847</span><span class="o">)</span>
>>><span class="w"> </span>qc_mask.dtype
dtype<span class="o">(</span><span class="s1">'bool'</span><span class="o">)</span>
</pre></div>
</div>
<p>Our <a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.WSI"><code class="xref py py-class docutils literal notranslate"><span class="pre">WSI</span></code></a> object now has no QC applied. We can manually apply this boolean mask with <code class="xref py py-meth docutils literal notranslate"><span class="pre">WSI.apply_qc_mask()</span></code>:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">wsi</span><span class="o">.</span><span class="n">apply_qc_mask</span><span class="p">(</span><span class="n">qc_mask</span><span class="p">)</span>
</pre></div>
</div>
<p>And that’s it! We can preview how our mask affects tile filtering by using <code class="xref py py-meth docutils literal notranslate"><span class="pre">WSI.preview()</span></code>:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">wsi</span><span class="o">.</span><span class="n">preview</span><span class="p">()</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
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