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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tutorial1/">Tutorial 1: Model training (simple)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial2/">Tutorial 2: Model training (advanced)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial3/">Tutorial 3: Using a custom architecture</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
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  <section id="slideflow-cellseg">
<h1>slideflow.cellseg<a class="headerlink" href="#slideflow-cellseg" title="Permalink to this heading">¶</a></h1>
<p>This module contains utility functions for performing whole-slide image cell segmentation with Cellpose.</p>
<p>See <a class="reference internal" href="../cellseg/#cellseg"><span class="std std-ref">Cell Segmentation</span></a> for more information.</p>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.segment_slide">
<span class="sig-name descname"><span class="pre">segment_slide</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.wsi.WSI"><span class="pre">WSI</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">cellpose.models.Cellpose</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'cyto2'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diam_um</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diam_mean</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">window_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">downscale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpus</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(0,)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spawn_workers</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pb</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Progress</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pb_tasks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">TaskID</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_progress</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_flow</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cp_thresh</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flow_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#slideflow.cellseg.Segmentation" title="slideflow.cellseg.Segmentation"><span class="pre">Segmentation</span></a></span></span><a class="reference internal" href="../_modules/slideflow/cellseg/#segment_slide"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.cellseg.segment_slide" title="Permalink to this definition">¶</a></dt>
<dd><p>Segment cells in a whole-slide image, returning masks and centroids.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>slide</strong> (str, <code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.WSI</span></code>) – Whole-slide image. May be a path
(str) or WSI object (<cite>slideflow.WSI</cite>).</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>model</strong> (str, <code class="xref py py-class docutils literal notranslate"><span class="pre">cellpose.models.Cellpose</span></code>) – Cellpose model to use
for cell segmentation. May be any valid cellpose model. Defaults
to ‘cyto2’.</p></li>
<li><p><strong>diam_um</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Cell diameter to detect, in microns.
Determines tile extraction microns-per-pixel resolution to match
the given pixel diameter specified by <cite>diam_mean</cite>. Not used if
<cite>slide</cite> is a <cite>sf.WSI</cite> object.</p></li>
<li><p><strong>diam_mean</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Cell diameter to detect, in pixels (without
image resizing). If None, uses Cellpose defaults (17 for the
‘nuclei’ model, 30 for all others).</p></li>
<li><p><strong>window_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Window size, in pixels, at which to segment cells.
Not used if slide is a <cite>sf.WSI</cite> object.</p></li>
<li><p><strong>downscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Factor by which to downscale generated masks after
calculation. Defaults to None (keep masks at original size).</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Batch size for cell segmentation. Defaults to 8.</p></li>
<li><p><strong>gpus</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – GPUs to use for cell segmentation.
Defaults to 0 (first GPU).</p></li>
<li><p><strong>spawn_workers</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Enable spawn-based multiprocessing. Increases
cell segmentation speed at the cost of higher memory utilization.</p></li>
<li><p><strong>pb</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">rich.progress.Progress</span></code>, optional) – Progress bar instance.
Used for external progress bar tracking. Defaults to None.</p></li>
<li><p><strong>pb_tasks</strong> (list(<code class="xref py py-class docutils literal notranslate"><span class="pre">rich.progress.TaskID</span></code>)) – Progress bar tasks.
Used for external progress bar tracking. Defaults to None.</p></li>
<li><p><strong>show_progress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Show a tqdm progress bar. Defaults to True.</p></li>
<li><p><strong>save_flow</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save flow values for the whole-slide image.
Increases memory utilization. Defaults to True.</p></li>
<li><p><strong>cp_thresh</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Cell probability threshold. All pixels with value
above threshold kept for masks, decrease to find more and larger
masks. Defaults to 0.</p></li>
<li><p><strong>flow_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Flow error threshold (all cells with errors
below threshold are kept). Defaults to 0.4.</p></li>
<li><p><strong>interp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Interpolate during 2D dynamics. Defaults to True.</p></li>
<li><p><strong>tile</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Tiles image to decrease GPU/CPU memory usage.
Defaults to True.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Verbose log output at the INFO level. Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#slideflow.cellseg.Segmentation" title="slideflow.cellseg.Segmentation"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.cellseg.Segmentation</span></code></a></p>
</dd>
</dl>
</dd></dl>

<section id="segmentation">
<h2>Segmentation<a class="headerlink" href="#segmentation" title="Permalink to this heading">¶</a></h2>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Segmentation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">masks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.wsi.WSI"><span class="pre">WSI</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flows</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">styles</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diams</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wsi_dim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wsi_offset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/cellseg/#Segmentation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.cellseg.Segmentation" title="Permalink to this definition">¶</a></dt>
<dd><p>Organizes a collection of cell segmentation masks for a slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>masks</strong> (<em>np.ndarray</em>) – Array of masks, dtype int32, where 0 represents
non-segmented background, and each segmented mask is represented
by unique increasing integers.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>slide</strong> (<em>slideflow.WSI</em>) – If provided, <code class="docutils literal notranslate"><span class="pre">Segmentation</span></code> can coordinate
extracting tiles at mask centroids. Defaults to None.</p></li>
<li><p><strong>flows</strong> (<em>np.ndarray</em>) – Array of flows, dtype float32. Defaults to None.</p></li>
<li><p><strong>wsi_dim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.12)"><em>tuple</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – Size of <code class="docutils literal notranslate"><span class="pre">masks</span></code> in the slide
pixel space (highest magnification). Used to align the mask
array to a corresponding slide. Required for calculating
centroids. Defaults to None.</p></li>
<li><p><strong>wsi_offset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.12)"><em>tuple</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – Top-left starting location for
<code class="docutils literal notranslate"><span class="pre">masks</span></code>, in slide pixel space (highest magnification).
Used to align the mask array to a corresponding slide.
Required for calculating centroids. Defaults to None.</p></li>
<li><p><strong>styles</strong> (<em>np.ndarray</em>) – Array of styles, currently ignored.</p></li>
<li><p><strong>diams</strong> (<em>np.ndarray</em>) – Array of diameters, currently ignored.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.apply_rois">
<span class="sig-name descname"><span class="pre">apply_rois</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">annpolys</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">shapely.geometry.Polygon</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.apply_rois" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply regions of interest (ROIs), excluding masks outside ROIs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>scale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – ROI scale (roi size / WSI base dimension size).</p></li>
<li><p><strong>annpolys</strong> (list(<code class="docutils literal notranslate"><span class="pre">shapely.geometry.Polygon</span></code>)) – List of ROI
polygons, as available in <code class="docutils literal notranslate"><span class="pre">slideflow.WSI.rois</span></code>.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.calculate_centroids">
<span class="sig-name descname"><span class="pre">calculate_centroids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.calculate_centroids" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate centroids.</p>
<p>Centroid values are buffered into <code class="docutils literal notranslate"><span class="pre">Segmentation._centroids</span></code> to
reduce unnecessary recalculations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>force</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Recalculate centroids, even if calculated before.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.calculate_outlines">
<span class="sig-name descname"><span class="pre">calculate_outlines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.calculate_outlines" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate mask outlines.</p>
<p>Mask outlines are buffered into <code class="docutils literal notranslate"><span class="pre">Segmentation._outlines</span></code> to
reduce unnecessary recalculations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>force</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Recalculate outlines, even if calculated before.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.centroids">
<span class="sig-name descname"><span class="pre">centroids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wsi_dim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.centroids" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate and return mask centroids.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>wsi_dim</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Convert centroids from mask space to WSI space.
Requires that <code class="docutils literal notranslate"><span class="pre">wsi_dim</span></code> was provided during initialization.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A <code class="docutils literal notranslate"><span class="pre">np.ndarray</span></code> with shape <code class="docutils literal notranslate"><span class="pre">(2,</span> <span class="pre">num_masks)</span></code>.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.centroid_to_image">
<span class="sig-name descname"><span class="pre">centroid_to_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'green'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.centroid_to_image" title="Permalink to this definition">¶</a></dt>
<dd><p>Render an image with the location of all centroids as a point.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Centroid color. Defaults to ‘green’.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.extract_centroids">
<span class="sig-name descname"><span class="pre">extract_centroids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_px</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">128</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.extract_centroids" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a generator which extracts tiles from a slide at mask centroids.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to a slide.</p></li>
<li><p><strong>tile_px</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Height/width of tile to extract at centroids.
Defaults to 128.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>A generator which yields a numpy array, with shape</dt><dd><p><code class="docutils literal notranslate"><span class="pre">(tile_px,</span> <span class="pre">tile_px,</span> <span class="pre">3)</span></code>, at each mask centroid.</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.mask_to_image">
<span class="sig-name descname"><span class="pre">mask_to_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">centroid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'cyan'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">centroid_color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'green'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.cellseg.Segmentation.mask_to_image" title="Permalink to this definition">¶</a></dt>
<dd><p>Render an image of all masks.</p>
<p>Masks are rendered on a black background.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>centroid</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Include centroids as points on the image.
Defaults to False.</p></li>
<li><p><strong>color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Color of the masks. Defaults to ‘cyan’.</p></li>
<li><p><strong>centroid_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Color of centroid points. Defaults to ‘green’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.outline_to_image">
<span class="sig-name descname"><span class="pre">outline_to_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">centroid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'red'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">centroid_color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'green'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.cellseg.Segmentation.outline_to_image" title="Permalink to this definition">¶</a></dt>
<dd><p>Render an image with the outlines of all masks.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>centroid</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Include centroids as points on the image.
Defaults to False.</p></li>
<li><p><strong>color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Color of the mask outlines. Defaults to ‘red’.</p></li>
<li><p><strong>centroid_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Color of centroid points. Defaults to ‘green’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.cellseg.Segmentation.save">
<span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">centroids</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flows</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.cellseg.Segmentation.save" title="Permalink to this definition">¶</a></dt>
<dd><p>Save segmentation masks and metadata to *.zip.</p>
<p>A <a class="reference internal" href="#slideflow.cellseg.Segmentation" title="slideflow.cellseg.Segmentation"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.cellseg.Segmentation</span></code></a> object can be loaded from
this file with <code class="docutils literal notranslate"><span class="pre">.load()</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Destination filename (ends with *.zip)</p></li>
<li><p><strong>centroids</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save centroid locations.</p></li>
<li><p><strong>flows</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save flows.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

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<li><a class="reference internal" href="#slideflow.cellseg.segment_slide"><code class="docutils literal notranslate"><span class="pre">segment_slide()</span></code></a></li>
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