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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../installation/">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../overview/">Overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quickstart/">Quickstart</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Setting up a Project</a></li>
<li class="toctree-l1"><a class="reference internal" href="../datasets_and_val/">Datasets</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slide_processing/">Slide Processing</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../posthoc/">Layer Activations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../uq/">Uncertainty Quantification</a></li>
<li class="toctree-l1"><a class="reference internal" href="../features/">Generating Features</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mil/">Multiple-Instance Learning (MIL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../ssl/">Self-Supervised Learning (SSL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stylegan/">Generative Networks (GANs)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../saliency/">Saliency Maps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../segmentation/">Tissue Segmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../cellseg/">Cell Segmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../custom_loops/">Custom Training Loops</a></li>
<li class="toctree-l1"><a class="reference internal" href="../studio/">Slideflow Studio: Live Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="../troubleshooting/">Troubleshooting</a></li>
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<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tfrecords/">TFRecords: Reading and Writing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataloaders/">Dataloaders: Sampling and Augmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../custom_extractors/">Custom Feature Extractors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tile_labels/">Strong Supervision with Tile Labels</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/">Creating a Slideflow Plugin</a></li>
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<p class="caption" role="heading"><span class="caption-text">API</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../slideflow/">slideflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../project/">slideflow.Project</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataset/">slideflow.Dataset</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataset_features/">slideflow.DatasetFeatures</a></li>
<li class="toctree-l1"><a class="reference internal" href="../heatmap/">slideflow.Heatmap</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_params/">slideflow.ModelParams</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mosaic/">slideflow.Mosaic</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../biscuit/">slideflow.biscuit</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../io/">slideflow.io</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io_tensorflow/">slideflow.io.tensorflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io_torch/">slideflow.io.torch</a></li>
<li class="toctree-l1"><a class="reference internal" href="../gan/">slideflow.gan</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../mil_module/">slideflow.mil</a></li>
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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>
<li class="toctree-l1"><a class="reference internal" href="../tutorial4/">Tutorial 4: Model evaluation &amp; heatmaps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial6/">Tutorial 6: Custom slide filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial7/">Tutorial 7: Training with custom augmentations</a></li>
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  <section id="setting-up-a-project">
<span id="project-setup"></span><h1>Setting up a Project<a class="headerlink" href="#setting-up-a-project" title="Permalink to this heading">¶</a></h1>
<p>Slideflow <a class="reference internal" href="../project/#project"><span class="std std-ref">Projects</span></a> organize datasets, annotations, and results into a unified directory and provide a high-level API for common tasks.</p>
<p>Use <a class="reference internal" href="../slideflow/#slideflow.create_project" title="slideflow.create_project"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.create_project()</span></code></a> to create a new project, supplying an annotations file (with patient labels) and path to slides. A new dataset source (collection of slides and tfrecords) will be configured. Additional keyword arguments can be used to specify the location of trecords and saved models.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>

<span class="n">P</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">create_project</span><span class="p">(</span>
  <span class="n">root</span><span class="o">=</span><span class="s1">&#39;project_path&#39;</span><span class="p">,</span>
  <span class="n">annotations</span><span class="o">=</span><span class="s2">&quot;./annotations.csv&quot;</span>
  <span class="n">slides</span><span class="o">=</span><span class="s1">&#39;/path/to/slides/&#39;</span>
<span class="p">)</span>
</pre></div>
</div>
<p>Project settings are saved in a <code class="docutils literal notranslate"><span class="pre">settings.json</span></code> file in the root project directory. Each project will have the following settings:</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p><strong>name</strong></p></td>
<td><p>Project name.
Defaults to “MyProject”.</p></td>
</tr>
<tr class="row-even"><td><p><strong>annotations</strong></p></td>
<td><p>Path to CSV containing annotations.
Each line is a unique slide.
Defaults to “./annotations.csv”</p></td>
</tr>
<tr class="row-odd"><td><p><strong>dataset_config</strong></p></td>
<td><p>Path to JSON file containing dataset configuration.
Defaults to “./datasets.json”</p></td>
</tr>
<tr class="row-even"><td><p><strong>sources</strong></p></td>
<td><p>Names of dataset source(s) to include in the project.
Defaults to an empty list.</p></td>
</tr>
<tr class="row-odd"><td><p><strong>models_dir</strong></p></td>
<td><p>Path, where model files and results are saved.
Defaults to “./models”</p></td>
</tr>
<tr class="row-even"><td><p><strong>eval_dir</strong></p></td>
<td><p>Path, where model evaluation results are saved.
Defaults to “./eval”</p></td>
</tr>
</tbody>
</table>
<p>Once a project has been initialized at a directory, you may then load the project with the following syntax:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="n">P</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">load_project</span><span class="p">(</span><span class="s1">&#39;/path/to/project/directory&#39;</span><span class="p">)</span>
</pre></div>
</div>
<section id="dataset-sources">
<span id="id1"></span><h2>Dataset Sources<a class="headerlink" href="#dataset-sources" title="Permalink to this heading">¶</a></h2>
<p>A <a class="reference internal" href="../datasets_and_val/#datasets-and-validation"><span class="std std-ref">dataset source</span></a> is a collection of slides, Regions of Interest (ROI) annotations (if available), and extracted tiles. Sources are defined in the project dataset configuration file, which can be shared and used across multiple projects or saved locally within a project directory. These configuration files have the following format:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="o">{</span>
<span class="w">  </span><span class="s2">&quot;SOURCE&quot;</span>:
<span class="w">  </span><span class="o">{</span>
<span class="w">    </span><span class="s2">&quot;slides&quot;</span>:<span class="w"> </span><span class="s2">&quot;/directory&quot;</span>,
<span class="w">    </span><span class="s2">&quot;roi&quot;</span>:<span class="w"> </span><span class="s2">&quot;/directory&quot;</span>,
<span class="w">    </span><span class="s2">&quot;tiles&quot;</span>:<span class="w"> </span><span class="s2">&quot;/directory&quot;</span>,
<span class="w">    </span><span class="s2">&quot;tfrecords&quot;</span>:<span class="w"> </span><span class="s2">&quot;/directory&quot;</span>,
<span class="w">  </span><span class="o">}</span>
<span class="o">}</span>
</pre></div>
</div>
<p>When a project is created with <a class="reference internal" href="../slideflow/#slideflow.create_project" title="slideflow.create_project"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.create_project()</span></code></a>, a dataset source is automatically created. You can change where slides and extracted tiles are stored by editing the project’s dataset configuration file.</p>
<p>It is possible for a project to have multiple dataset sources - for example, you may choose to organize data from multiple institutions into separate sources. You can add a new dataset source to a project with <code class="xref py py-meth docutils literal notranslate"><span class="pre">Project.add_source()</span></code>, which will update the project dataset configuration file accordingly.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">P</span><span class="o">.</span><span class="n">add_source</span><span class="p">(</span>
  <span class="n">name</span><span class="o">=</span><span class="s2">&quot;SOURCE_NAME&quot;</span><span class="p">,</span>
  <span class="n">slides</span><span class="o">=</span><span class="s2">&quot;/slides/directory&quot;</span><span class="p">,</span>
  <span class="n">roi</span><span class="o">=</span><span class="s2">&quot;/roi/directory&quot;</span><span class="p">,</span>
  <span class="n">tiles</span><span class="o">=</span><span class="s2">&quot;/tiles/directory&quot;</span><span class="p">,</span>
  <span class="n">tfrecords</span><span class="o">=</span><span class="s2">&quot;/tfrecords/directory&quot;</span>
<span class="p">)</span>
</pre></div>
</div>
<p>Read more about <a class="reference internal" href="../datasets_and_val/#datasets-and-validation"><span class="std std-ref">working with datasets</span></a>.</p>
</section>
<section id="annotations">
<h2>Annotations<a class="headerlink" href="#annotations" title="Permalink to this heading">¶</a></h2>
<p>Your annotations file is used to label patients and slides with clinical data and/or other outcome variables that will be used for training. Each line in the annotations file should correspond to a unique slide. Patients may have more than one slide.</p>
<p>The annotations file may contain any number of columns, but it must contain the following headers at minimum:</p>
<ul class="simple">
<li><p><strong>patient</strong>: patient identifier</p></li>
<li><p><strong>slide</strong>: slide name / identifier (without the file extension)</p></li>
</ul>
<p>An example annotations file is given below:</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p><em>patient</em></p></td>
<td><p><em>category</em></p></td>
<td><p><em>dataset</em></p></td>
<td><p><em>slide</em></p></td>
</tr>
<tr class="row-even"><td><p>TCGA-EL-A23A</p></td>
<td><p>EGFR-mutant</p></td>
<td><p>train</p></td>
<td><p>TCGA-EL-A3CO-01Z-00-DX1-7BF5F</p></td>
</tr>
<tr class="row-odd"><td><p>TCGA-EL-A35B</p></td>
<td><p>EGFR-mutant</p></td>
<td><p>eval</p></td>
<td><p>TCGA-EL-A35B-01Z-00-DX1-89FCD</p></td>
</tr>
<tr class="row-even"><td><p>TCGA-EL-A26X</p></td>
<td><p>non-mutant</p></td>
<td><p>train</p></td>
<td><p>TCGA-EL-A26X-01Z-00-DX1-4HA2C</p></td>
</tr>
<tr class="row-odd"><td><p>TCGA-EL-B83L</p></td>
<td><p>non-mutant</p></td>
<td><p>eval</p></td>
<td><p>TCGA-EL-B83L-01Z-00-DX1-6BC5L</p></td>
</tr>
</tbody>
</table>
<p>An example annotations file is generated each time a new project is initialized. To manually generate an empty annotations file that contains all detected slides, use the bundled <code class="docutils literal notranslate"><span class="pre">Project</span></code> function:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">P</span><span class="o">.</span><span class="n">create_blank_annotations</span><span class="p">()</span>
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">slide</span></code> column may not need to be explicitly set in the annotations file by the user. Rather, once a dataset has been set up, slideflow will search through the linked slide directories and attempt to match slides to entries in the annotations file using <strong>patient</strong>. Entries that are blank in the <strong>slide</strong> column will be auto-populated with any detected and matching slides, if available.</p>
</section>
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