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<h1 id="index">Index</h1>





  
  

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<div class="genindex-jumpbox">





  
  

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 <a href="#Symbols"><strong>Symbols</strong></a>





  
  

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 | <a href="#A"><strong>A</strong></a>





  
  

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 | <a href="#B"><strong>B</strong></a>





  
  

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 | <a href="#C"><strong>C</strong></a>





  
  

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 | <a href="#D"><strong>D</strong></a>





  
  

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 | <a href="#E"><strong>E</strong></a>





  
  

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 | <a href="#F"><strong>F</strong></a>





  
  

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 | <a href="#G"><strong>G</strong></a>





  
  

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 | <a href="#I"><strong>I</strong></a>





  
  

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 | <a href="#L"><strong>L</strong></a>





  
  

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 | <a href="#N"><strong>N</strong></a>





  
  

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 | <a href="#O"><strong>O</strong></a>





  
  

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 | <a href="#P"><strong>P</strong></a>





  
  

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 | <a href="#R"><strong>R</strong></a>





  
  

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 | <a href="#S"><strong>S</strong></a>





  
  

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 | <a href="#T"><strong>T</strong></a>





  
  

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 | <a href="#U"><strong>U</strong></a>





  
  

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</div>





  
  

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<h2 id="Symbols">Symbols</h2>





  
  

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<table style="width: 100%" class="indextable genindextable"><tr>





  
  

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  <td style="width: 33%; vertical-align: top;"><ul>





  
  

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      <li>





  
  

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    --version





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-monitor-version">pathflowai-monitor command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-version">pathflowai-preprocess command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-version">pathflowai-visualize command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -a, --annotation_txt &lt;annotation_txt&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-a">pathflowai-visualize-overlay_new_annotations command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -a, --annotations &lt;annotations&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-a">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-a">pathflowai-visualize-plot_embeddings command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -ac, --annotation_col &lt;annotation_col&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ac">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -al, --alpha &lt;alpha&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-al">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -am, --adjust_mask





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-am">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -an, --annotations





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-an">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -b, --basename &lt;basename&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-b">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-b">pathflowai-preprocess-remove_basename_from_db command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-b">pathflowai-visualize-extract_patch command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-b">pathflowai-visualize-plot_embeddings command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-b">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-b">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -bp, --basic_preprocess





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-bp">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -bs, --batch_size &lt;batch_size&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-bs">pathflowai-visualize-shapley_plot command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -c, --custom_segmentation &lt;custom_segmentation&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-c">pathflowai-visualize-extract_patch command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-c">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -cf, --compression_factor &lt;compression_factor&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-cf">pathflowai-visualize-overlay_new_annotations command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-cf">pathflowai-visualize-plot_image command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-cf">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -csv, --records_output_csv &lt;records_output_csv&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-csv">pathflowai-monitor-monitor_usage command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -dt, --delay_time &lt;delay_time&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-dt">pathflowai-monitor-monitor_usage command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -e, --embeddings_file &lt;embeddings_file&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-e">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -fr, --from_annotations &lt;from_annotations&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-fr">pathflowai-preprocess-alter_masks command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-fr">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -g, --generate_finetune_segmentation





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-g">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -i, --embeddings_file &lt;embeddings_file&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-i">pathflowai-visualize-plot_embeddings command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -i, --image_file &lt;image_file&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-i">pathflowai-visualize-plot_image command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -i, --img_file &lt;img_file&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-i">pathflowai-visualize-overlay_new_annotations command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -i, --input_dir &lt;input_dir&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-i">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-i">pathflowai-visualize-extract_patch command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-i">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

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</li>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-i">pathflowai-visualize-plot_predictions command line option</a>





  
  

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</li>





  
  

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      </ul></li>





  
  

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      <li>





  
  

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    -i, --input_patch_db &lt;input_patch_db&gt;





  
  

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      <ul>





  
  

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        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-i">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

  353
  
</li>





  
  

  354
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-i">pathflowai-preprocess-remove_basename_from_db command line option</a>





  
  

  355
  
</li>





  
  

  356
  
      </ul></li>





  
  

  357
  
      <li>





  
  

  358
  
    -i, --mask_dir &lt;mask_dir&gt;





  
  

  359
  





  
  

  360
  
      <ul>





  
  

  361
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-i">pathflowai-preprocess-alter_masks command line option</a>





  
  

  362
  
</li>





  
  

  363
  
      </ul></li>





  
  

  364
  
      <li>





  
  

  365
  
    -it, --intensity_threshold &lt;intensity_threshold&gt;





  
  

  366
  





  
  

  367
  
      <ul>





  
  

  368
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-it">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  369
  
</li>





  
  

  370
  
      </ul></li>





  
  

  371
  
      <li>





  
  

  372
  
    -l, --local_smoothing &lt;local_smoothing&gt;





  
  

  373
  





  
  

  374
  
      <ul>





  
  

  375
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-l">pathflowai-visualize-shapley_plot command line option</a>





  
  

  376
  
</li>





  
  

  377
  
      </ul></li>





  
  

  378
  
      <li>





  
  

  379
  
    -m, --model_pkl &lt;model_pkl&gt;





  
  

  380
  





  
  

  381
  
      <ul>





  
  

  382
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-m">pathflowai-visualize-shapley_plot command line option</a>





  
  

  383
  
</li>





  
  

  384
  
      </ul></li>





  
  

  385
  
      <li>





  
  

  386
  
    -ma, --max_background_area &lt;max_background_area&gt;





  
  

  387
  





  
  

  388
  
      <ul>





  
  

  389
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ma">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

  390
  
</li>





  
  

  391
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-ma">pathflowai-visualize-plot_embeddings command line option</a>





  
  

  392
  
</li>





  
  

  393
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-ma">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  394
  
</li>





  
  

  395
  
      </ul></li>





  
  

  396
  
      <li>





  
  

  397
  
    -mpl, --mpl_scatter





  
  

  398
  





  
  

  399
  
      <ul>





  
  

  400
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-mpl">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  401
  
</li>





  
  

  402
  
      </ul></li>





  
  

  403
  
      <li>





  
  

  404
  
    -mth, --method &lt;method&gt;





  
  

  405
  





  
  

  406
  
      <ul>





  
  

  407
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-mth">pathflowai-visualize-shapley_plot command line option</a>





  
  

  408
  
</li>





  
  

  409
  
      </ul></li>





  
  

  410
  
  </ul></td>





  
  

  411
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  412
  
      <li>





  
  

  413
  
    -nn, --n_neighbors &lt;n_neighbors&gt;





  
  

  414
  





  
  

  415
  
      <ul>





  
  

  416
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-nn">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  417
  
</li>





  
  

  418
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-nn">pathflowai-visualize-plot_embeddings command line option</a>





  
  

  419
  
</li>





  
  

  420
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-nn">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  421
  
</li>





  
  

  422
  
      </ul></li>





  
  

  423
  
      <li>





  
  

  424
  
    -npy, --img2npy





  
  

  425
  





  
  

  426
  
      <ul>





  
  

  427
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-npy">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  428
  
</li>





  
  

  429
  
      </ul></li>





  
  

  430
  
      <li>





  
  

  431
  
    -ns, --n_samples &lt;n_samples&gt;





  
  

  432
  





  
  

  433
  
      <ul>





  
  

  434
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-ns">pathflowai-visualize-shapley_plot command line option</a>





  
  

  435
  
</li>





  
  

  436
  
      </ul></li>





  
  

  437
  
      <li>





  
  

  438
  
    -o, --output_dir &lt;output_dir&gt;





  
  

  439
  





  
  

  440
  
      <ul>





  
  

  441
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-o">pathflowai-preprocess-alter_masks command line option</a>





  
  

  442
  
</li>





  
  

  443
  
      </ul></li>





  
  

  444
  
      <li>





  
  

  445
  
    -o, --output_patch_db &lt;output_patch_db&gt;





  
  

  446
  





  
  

  447
  
      <ul>





  
  

  448
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-o">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

  449
  
</li>





  
  

  450
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-o">pathflowai-preprocess-remove_basename_from_db command line option</a>





  
  

  451
  
</li>





  
  

  452
  
      </ul></li>





  
  

  453
  
      <li>





  
  

  454
  
    -o, --outputfilename &lt;outputfilename&gt;





  
  

  455
  





  
  

  456
  
      <ul>





  
  

  457
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-o">pathflowai-visualize-overlay_new_annotations command line option</a>





  
  

  458
  
</li>





  
  

  459
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-o">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  460
  
</li>





  
  

  461
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-o">pathflowai-visualize-shapley_plot command line option</a>





  
  

  462
  
</li>





  
  

  463
  
      </ul></li>





  
  

  464
  
      <li>





  
  

  465
  
    -o, --outputfname &lt;outputfname&gt;





  
  

  466
  





  
  

  467
  
      <ul>





  
  

  468
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-o">pathflowai-visualize-extract_patch command line option</a>





  
  

  469
  
</li>





  
  

  470
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-o">pathflowai-visualize-plot_image command line option</a>





  
  

  471
  
</li>





  
  

  472
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-o">pathflowai-visualize-plot_predictions command line option</a>





  
  

  473
  
</li>





  
  

  474
  
      </ul></li>





  
  

  475
  
      <li>





  
  

  476
  
    -o, --plotly_output_file &lt;plotly_output_file&gt;





  
  

  477
  





  
  

  478
  
      <ul>





  
  

  479
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-o">pathflowai-visualize-plot_embeddings command line option</a>





  
  

  480
  
</li>





  
  

  481
  
      </ul></li>





  
  

  482
  
      <li>





  
  

  483
  
    -ocf, --original_compression_factor &lt;original_compression_factor&gt;





  
  

  484
  





  
  

  485
  
      <ul>





  
  

  486
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-ocf">pathflowai-visualize-overlay_new_annotations command line option</a>





  
  

  487
  
</li>





  
  

  488
  
      </ul></li>





  
  

  489
  
      <li>





  
  

  490
  
    -odb, --out_db &lt;out_db&gt;





  
  

  491
  





  
  

  492
  
      <ul>





  
  

  493
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-odb">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  494
  
</li>





  
  

  495
  
      </ul></li>





  
  

  496
  
      <li>





  
  

  497
  
    -p, --patch_info_file &lt;patch_info_file&gt;





  
  

  498
  





  
  

  499
  
      <ul>





  
  

  500
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-p">pathflowai-visualize-extract_patch command line option</a>





  
  

  501
  
</li>





  
  

  502
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-p">pathflowai-visualize-plot_predictions command line option</a>





  
  

  503
  
</li>





  
  

  504
  
      </ul></li>





  
  

  505
  
      <li>





  
  

  506
  
    -p, --pred_out &lt;pred_out&gt;





  
  

  507
  





  
  

  508
  
      <ul>





  
  

  509
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-p">pathflowai-visualize-shapley_plot command line option</a>





  
  

  510
  
</li>





  
  

  511
  
      </ul></li>





  
  

  512
  
      <li>





  
  

  513
  
    -pa, --patches





  
  

  514
  





  
  

  515
  
      <ul>





  
  

  516
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pa">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  517
  
</li>





  
  

  518
  
      </ul></li>





  
  

  519
  
      <li>





  
  

  520
  
    -pr, --preprocess





  
  

  521
  





  
  

  522
  
      <ul>





  
  

  523
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pr">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  524
  
</li>





  
  

  525
  
      </ul></li>





  
  

  526
  
      <li>





  
  

  527
  
    -ps, --patch_size &lt;patch_size&gt;





  
  

  528
  





  
  

  529
  
      <ul>





  
  

  530
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ps">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

  531
  
</li>





  
  

  532
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-ps">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  533
  
</li>





  
  

  534
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-ps">pathflowai-preprocess-remove_basename_from_db command line option</a>





  
  

  535
  
</li>





  
  

  536
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-ps">pathflowai-visualize-extract_patch command line option</a>





  
  

  537
  
</li>





  
  

  538
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ps">pathflowai-visualize-plot_predictions command line option</a>





  
  

  539
  
</li>





  
  

  540
  
      </ul></li>





  
  

  541
  
      <li>





  
  

  542
  
    -rb, --remove_background_annotation &lt;remove_background_annotation&gt;





  
  

  543
  





  
  

  544
  
      <ul>





  
  

  545
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-rb">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

  546
  
</li>





  
  

  547
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-rb">pathflowai-visualize-plot_embeddings command line option</a>





  
  

  548
  
</li>





  
  

  549
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-rb">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  550
  
</li>





  
  

  551
  
      </ul></li>





  
  

  552
  
      <li>





  
  

  553
  
    -s, --segmentation





  
  

  554
  





  
  

  555
  
      <ul>





  
  

  556
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-s">pathflowai-visualize-extract_patch command line option</a>





  
  

  557
  
</li>





  
  

  558
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-s">pathflowai-visualize-plot_predictions command line option</a>





  
  

  559
  
</li>





  
  

  560
  
      </ul></li>





  
  

  561
  
      <li>





  
  

  562
  
    -sc, --n_segmentation_classes &lt;n_segmentation_classes&gt;





  
  

  563
  





  
  

  564
  
      <ul>





  
  

  565
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-sc">pathflowai-visualize-extract_patch command line option</a>





  
  

  566
  
</li>





  
  

  567
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sc">pathflowai-visualize-plot_predictions command line option</a>





  
  

  568
  
</li>





  
  

  569
  
      </ul></li>





  
  

  570
  
      <li>





  
  

  571
  
    -sc, --sort_col &lt;sort_col&gt;





  
  

  572
  





  
  

  573
  
      <ul>





  
  

  574
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sc">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  575
  
</li>





  
  

  576
  
      </ul></li>





  
  

  577
  
      <li>





  
  

  578
  
    -sf, --scaling_factor &lt;scaling_factor&gt;





  
  

  579
  





  
  

  580
  
      <ul>





  
  

  581
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sf">pathflowai-visualize-plot_predictions command line option</a>





  
  

  582
  
</li>





  
  

  583
  
      </ul></li>





  
  

  584
  
      <li>





  
  

  585
  
    -sm, --sort_mode &lt;sort_mode&gt;





  
  

  586
  





  
  

  587
  
      <ul>





  
  

  588
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sm">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  589
  
</li>





  
  

  590
  
      </ul></li>





  
  

  591
  
      <li>





  
  

  592
  
    -t, --threshold &lt;threshold&gt;





  
  

  593
  





  
  

  594
  
      <ul>





  
  

  595
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-t">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  596
  
</li>





  
  

  597
  
      </ul></li>





  
  

  598
  
      <li>





  
  

  599
  
    -tc, --target_segmentation_class &lt;target_segmentation_class&gt;





  
  

  600
  





  
  

  601
  
      <ul>





  
  

  602
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tc">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  603
  
</li>





  
  

  604
  
      </ul></li>





  
  

  605
  
      <li>





  
  

  606
  
    -tif, --tif_file





  
  

  607
  





  
  

  608
  
      <ul>





  
  

  609
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-tif">pathflowai-visualize-plot_predictions command line option</a>





  
  

  610
  
</li>





  
  

  611
  
      </ul></li>





  
  

  612
  
      <li>





  
  

  613
  
    -to, --to_annotations &lt;to_annotations&gt;





  
  

  614
  





  
  

  615
  
      <ul>





  
  

  616
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-to">pathflowai-preprocess-alter_masks command line option</a>





  
  

  617
  
</li>





  
  

  618
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-to">pathflowai-preprocess-collapse_annotations command line option</a>





  
  

  619
  
</li>





  
  

  620
  
      </ul></li>





  
  

  621
  
      <li>





  
  

  622
  
    -tt, --target_threshold &lt;target_threshold&gt;





  
  

  623
  





  
  

  624
  
      <ul>





  
  

  625
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tt">pathflowai-preprocess-preprocess_pipeline command line option</a>





  
  

  626
  
</li>





  
  

  627
  
      </ul></li>





  
  

  628
  
      <li>





  
  

  629
  
    -tt, --total_time &lt;total_time&gt;





  
  

  630
  





  
  

  631
  
      <ul>





  
  

  632
  
        <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-tt">pathflowai-monitor-monitor_usage command line option</a>





  
  

  633
  
</li>





  
  

  634
  
      </ul></li>





  
  

  635
  
      <li>





  
  

  636
  
    -x, --x &lt;x&gt;





  
  

  637
  





  
  

  638
  
      <ul>





  
  

  639
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-x">pathflowai-visualize-extract_patch command line option</a>





  
  

  640
  
</li>





  
  

  641
  
      </ul></li>





  
  

  642
  
      <li>





  
  

  643
  
    -y, --y &lt;y&gt;





  
  

  644
  





  
  

  645
  
      <ul>





  
  

  646
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-y">pathflowai-visualize-extract_patch command line option</a>





  
  

  647
  
</li>





  
  

  648
  
      </ul></li>





  
  

  649
  
      <li>





  
  

  650
  
    -z, --zoom &lt;zoom&gt;





  
  

  651
  





  
  

  652
  
      <ul>





  
  

  653
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-z">pathflowai-visualize-plot_image_umap_embeddings command line option</a>





  
  

  654
  
</li>





  
  

  655
  
      </ul></li>





  
  

  656
  
  </ul></td>





  
  

  657
  
</tr></table>





  
  

  658
  





  
  

  659
  
<h2 id="A">A</h2>





  
  

  660
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  661
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  662
  
      <li><a href="index.html#pathflowai.visualize.PredictionPlotter.add_custom_segmentation">add_custom_segmentation() (pathflowai.visualize.PredictionPlotter method)</a>





  
  

  663
  
</li>





  
  

  664
  
      <li><a href="index.html#pathflowai.visualize.PlotlyPlot.add_plot">add_plot() (pathflowai.visualize.PlotlyPlot method)</a>





  
  

  665
  
</li>





  
  

  666
  
      <li><a href="index.html#pathflowai.utils.add_purple_mask">add_purple_mask() (in module pathflowai.utils)</a>





  
  

  667
  
</li>





  
  

  668
  
  </ul></td>





  
  

  669
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  670
  
      <li><a href="index.html#pathflowai.utils.adjust_mask">adjust_mask() (in module pathflowai.utils)</a>





  
  

  671
  
</li>





  
  

  672
  
      <li><a href="index.html#pathflowai.visualize.annotation2rgb">annotation2rgb() (in module pathflowai.visualize)</a>





  
  

  673
  
</li>





  
  

  674
  
      <li><a href="index.html#pathflowai.losses.assert_">assert_() (in module pathflowai.losses)</a>





  
  

  675
  
</li>





  
  

  676
  
  </ul></td>





  
  

  677
  
</tr></table>





  
  

  678
  





  
  

  679
  
<h2 id="B">B</h2>





  
  

  680
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  681
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  682
  
      <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.binarize_annotations">binarize_annotations() (pathflowai.datasets.DynamicImageDataset method)</a>





  
  

  683
  
</li>





  
  

  684
  
  </ul></td>





  
  

  685
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  686
  
      <li><a href="index.html#pathflowai.visualize.blend">blend() (in module pathflowai.visualize)</a>





  
  

  687
  
</li>





  
  

  688
  
      <li><a href="index.html#pathflowai.utils.boxes2interior">boxes2interior() (in module pathflowai.utils)</a>





  
  

  689
  
</li>





  
  

  690
  
  </ul></td>





  
  

  691
  
</tr></table>





  
  

  692
  





  
  

  693
  
<h2 id="C">C</h2>





  
  

  694
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  695
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  696
  
      <li><a href="index.html#pathflowai.losses.class2one_hot">class2one_hot() (in module pathflowai.losses)</a>





  
  

  697
  
</li>





  
  

  698
  
      <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.concat">concat() (pathflowai.datasets.DynamicImageDataset method)</a>





  
  

  699
  
</li>





  
  

  700
  
      <li><a href="index.html#pathflowai.schedulers.CosineAnnealingWithRestartsLR">CosineAnnealingWithRestartsLR (class in pathflowai.schedulers)</a>





  
  

  701
  
</li>





  
  

  702
  
  </ul></td>





  
  

  703
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  704
  
      <li><a href="index.html#pathflowai.utils.create_purple_mask">create_purple_mask() (in module pathflowai.utils)</a>





  
  

  705
  
</li>





  
  

  706
  
      <li><a href="index.html#pathflowai.utils.create_sparse_annotation_arrays">create_sparse_annotation_arrays() (in module pathflowai.utils)</a>





  
  

  707
  
</li>





  
  

  708
  
      <li><a href="index.html#pathflowai.utils.create_train_val_test">create_train_val_test() (in module pathflowai.utils)</a>





  
  

  709
  
</li>





  
  

  710
  
      <li><a href="index.html#pathflowai.datasets.create_transforms">create_transforms() (in module pathflowai.datasets)</a>





  
  

  711
  
</li>





  
  

  712
  
  </ul></td>





  
  

  713
  
</tr></table>





  
  

  714
  





  
  

  715
  
<h2 id="D">D</h2>





  
  

  716
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  717
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  718
  
      <li><a href="index.html#pathflowai.utils.df2sql">df2sql() (in module pathflowai.utils)</a>





  
  

  719
  
</li>





  
  

  720
  
  </ul></td>





  
  

  721
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  722
  
      <li><a href="index.html#pathflowai.utils.dir2images">dir2images() (in module pathflowai.utils)</a>





  
  

  723
  
</li>





  
  

  724
  
      <li><a href="index.html#pathflowai.datasets.DynamicImageDataset">DynamicImageDataset (class in pathflowai.datasets)</a>





  
  

  725
  
</li>





  
  

  726
  
  </ul></td>





  
  

  727
  
</tr></table>





  
  

  728
  





  
  

  729
  
<h2 id="E">E</h2>





  
  

  730
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  731
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  732
  
      <li><a href="index.html#pathflowai.losses.eq">eq() (in module pathflowai.losses)</a>





  
  

  733
  
</li>





  
  

  734
  
  </ul></td>





  
  

  735
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  736
  
      <li><a href="index.html#pathflowai.utils.extract_patch_information">extract_patch_information() (in module pathflowai.utils)</a>





  
  

  737
  
</li>





  
  

  738
  
  </ul></td>





  
  

  739
  
</tr></table>





  
  

  740
  





  
  

  741
  
<h2 id="F">F</h2>





  
  

  742
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  743
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  744
  
      <li><a href="index.html#pathflowai.utils.fix_name">fix_name() (in module pathflowai.utils)</a>





  
  

  745
  
</li>





  
  

  746
  
      <li><a href="index.html#pathflowai.utils.fix_names">fix_names() (in module pathflowai.utils)</a>





  
  

  747
  
</li>





  
  

  748
  
      <li><a href="index.html#pathflowai.losses.flatten_samples">flatten_samples() (in module pathflowai.losses)</a>





  
  

  749
  
</li>





  
  

  750
  
  </ul></td>





  
  

  751
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  752
  
      <li><a href="index.html#pathflowai.losses.FocalLoss">FocalLoss (class in pathflowai.losses)</a>





  
  

  753
  
</li>





  
  

  754
  
      <li><a href="index.html#pathflowai.losses.FocalLoss.forward">forward() (pathflowai.losses.FocalLoss method)</a>





  
  

  755
  





  
  

  756
  
      <ul>





  
  

  757
  
        <li><a href="index.html#pathflowai.losses.GeneralizedDiceLoss.forward">(pathflowai.losses.GeneralizedDiceLoss method)</a>





  
  

  758
  
</li>





  
  

  759
  
      </ul></li>





  
  

  760
  
  </ul></td>





  
  

  761
  
</tr></table>





  
  

  762
  





  
  

  763
  
<h2 id="G">G</h2>





  
  

  764
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  765
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  766
  
      <li><a href="index.html#pathflowai.losses.GeneralizedDice">GeneralizedDice (class in pathflowai.losses)</a>





  
  

  767
  
</li>





  
  

  768
  
      <li><a href="index.html#pathflowai.losses.GeneralizedDiceLoss">GeneralizedDiceLoss (class in pathflowai.losses)</a>





  
  

  769
  
</li>





  
  

  770
  
      <li><a href="index.html#pathflowai.visualize.PredictionPlotter.generate_image">generate_image() (pathflowai.visualize.PredictionPlotter method)</a>





  
  

  771
  
</li>





  
  

  772
  
      <li><a href="index.html#pathflowai.utils.generate_patch_pipeline">generate_patch_pipeline() (in module pathflowai.utils)</a>





  
  

  773
  
</li>





  
  

  774
  
  </ul></td>





  
  

  775
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  776
  
      <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.get_class_weights">get_class_weights() (pathflowai.datasets.DynamicImageDataset method)</a>





  
  

  777
  
</li>





  
  

  778
  
      <li><a href="index.html#pathflowai.datasets.get_data_transforms">get_data_transforms() (in module pathflowai.datasets)</a>





  
  

  779
  
</li>





  
  

  780
  
      <li><a href="index.html#pathflowai.schedulers.Scheduler.get_lr">get_lr() (pathflowai.schedulers.Scheduler method)</a>





  
  

  781
  
</li>





  
  

  782
  
      <li><a href="index.html#pathflowai.datasets.get_normalizer">get_normalizer() (in module pathflowai.datasets)</a>





  
  

  783
  
</li>





  
  

  784
  
      <li><a href="index.html#pathflowai.utils.grab_interior_points">grab_interior_points() (in module pathflowai.utils)</a>





  
  

  785
  
</li>





  
  

  786
  
  </ul></td>





  
  

  787
  
</tr></table>





  
  

  788
  





  
  

  789
  
<h2 id="I">I</h2>





  
  

  790
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  791
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  792
  
      <li><a href="index.html#pathflowai.utils.image2coords">image2coords() (in module pathflowai.utils)</a>





  
  

  793
  
</li>





  
  

  794
  
      <li><a href="index.html#pathflowai.utils.images2coord_dict">images2coord_dict() (in module pathflowai.utils)</a>





  
  

  795
  
</li>





  
  

  796
  
      <li><a href="index.html#pathflowai.sampler.ImbalancedDatasetSampler">ImbalancedDatasetSampler (class in pathflowai.sampler)</a>





  
  

  797
  
</li>





  
  

  798
  
  </ul></td>





  
  

  799
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  800
  
      <li><a href="index.html#pathflowai.utils.img2npy_">img2npy_() (in module pathflowai.utils)</a>





  
  

  801
  
</li>





  
  

  802
  
      <li><a href="index.html#pathflowai.utils.is_coords_in_box">is_coords_in_box() (in module pathflowai.utils)</a>





  
  

  803
  
</li>





  
  

  804
  
      <li><a href="index.html#pathflowai.utils.is_image_in_boxes">is_image_in_boxes() (in module pathflowai.utils)</a>





  
  

  805
  
</li>





  
  

  806
  
      <li><a href="index.html#pathflowai.utils.is_valid_patch">is_valid_patch() (in module pathflowai.utils)</a>





  
  

  807
  
</li>





  
  

  808
  
  </ul></td>





  
  

  809
  
</tr></table>





  
  

  810
  





  
  

  811
  
<h2 id="L">L</h2>





  
  

  812
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  813
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  814
  
      <li><a href="index.html#pathflowai.utils.load_dataset">load_dataset() (in module pathflowai.utils)</a>





  
  

  815
  
</li>





  
  

  816
  
      <li><a href="index.html#pathflowai.utils.load_image">load_image() (in module pathflowai.utils)</a>





  
  

  817
  
</li>





  
  

  818
  
  </ul></td>





  
  

  819
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  820
  
      <li><a href="index.html#pathflowai.utils.load_process_image">load_process_image() (in module pathflowai.utils)</a>





  
  

  821
  
</li>





  
  

  822
  
      <li><a href="index.html#pathflowai.utils.load_sql_df">load_sql_df() (in module pathflowai.utils)</a>





  
  

  823
  
</li>





  
  

  824
  
  </ul></td>





  
  

  825
  
</tr></table>





  
  

  826
  





  
  

  827
  
<h2 id="N">N</h2>





  
  

  828
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  829
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  830
  
      <li><a href="index.html#pathflowai.utils.npy2da">npy2da() (in module pathflowai.utils)</a>





  
  

  831
  
</li>





  
  

  832
  
  </ul></td>





  
  

  833
  
</tr></table>





  
  

  834
  





  
  

  835
  
<h2 id="O">O</h2>





  
  

  836
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  837
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  838
  
      <li><a href="index.html#pathflowai.losses.one_hot">one_hot() (in module pathflowai.losses)</a>





  
  

  839
  
</li>





  
  

  840
  
  </ul></td>





  
  

  841
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  842
  
      <li><a href="index.html#pathflowai.losses.one_hot2dist">one_hot2dist() (in module pathflowai.losses)</a>





  
  

  843
  
</li>





  
  

  844
  
      <li><a href="index.html#pathflowai.visualize.PredictionPlotter.output_image">output_image() (pathflowai.visualize.PredictionPlotter method)</a>





  
  

  845
  
</li>





  
  

  846
  
  </ul></td>





  
  

  847
  
</tr></table>





  
  

  848
  





  
  

  849
  
<h2 id="P">P</h2>





  
  

  850
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  851
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  852
  
      <li><a href="index.html#pathflowai.utils.parse_coord_return_boxes">parse_coord_return_boxes() (in module pathflowai.utils)</a>





  
  

  853
  
</li>





  
  

  854
  
      <li>





  
  

  855
  
    pathflowai-monitor command line option





  
  

  856
  





  
  

  857
  
      <ul>





  
  

  858
  
        <li><a href="index.html#cmdoption-pathflowai-monitor-version">--version</a>





  
  

  859
  
</li>





  
  

  860
  
      </ul></li>





  
  

  861
  
      <li>





  
  

  862
  
    pathflowai-monitor-monitor_usage command line option





  
  

  863
  





  
  

  864
  
      <ul>





  
  

  865
  
        <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-csv">-csv, --records_output_csv &lt;records_output_csv&gt;</a>





  
  

  866
  
</li>





  
  

  867
  
        <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-dt">-dt, --delay_time &lt;delay_time&gt;</a>





  
  

  868
  
</li>





  
  

  869
  
        <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-tt">-tt, --total_time &lt;total_time&gt;</a>





  
  

  870
  
</li>





  
  

  871
  
      </ul></li>





  
  

  872
  
      <li>





  
  

  873
  
    pathflowai-preprocess command line option





  
  

  874
  





  
  

  875
  
      <ul>





  
  

  876
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-version">--version</a>





  
  

  877
  
</li>





  
  

  878
  
      </ul></li>





  
  

  879
  
      <li>





  
  

  880
  
    pathflowai-preprocess-alter_masks command line option





  
  

  881
  





  
  

  882
  
      <ul>





  
  

  883
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-fr">-fr, --from_annotations &lt;from_annotations&gt;</a>





  
  

  884
  
</li>





  
  

  885
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-i">-i, --mask_dir &lt;mask_dir&gt;</a>





  
  

  886
  
</li>





  
  

  887
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-o">-o, --output_dir &lt;output_dir&gt;</a>





  
  

  888
  
</li>





  
  

  889
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-to">-to, --to_annotations &lt;to_annotations&gt;</a>





  
  

  890
  
</li>





  
  

  891
  
      </ul></li>





  
  

  892
  
      <li>





  
  

  893
  
    pathflowai-preprocess-collapse_annotations command line option





  
  

  894
  





  
  

  895
  
      <ul>





  
  

  896
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-fr">-fr, --from_annotations &lt;from_annotations&gt;</a>





  
  

  897
  
</li>





  
  

  898
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-i">-i, --input_patch_db &lt;input_patch_db&gt;</a>





  
  

  899
  
</li>





  
  

  900
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ma">-ma, --max_background_area &lt;max_background_area&gt;</a>





  
  

  901
  
</li>





  
  

  902
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-o">-o, --output_patch_db &lt;output_patch_db&gt;</a>





  
  

  903
  
</li>





  
  

  904
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ps">-ps, --patch_size &lt;patch_size&gt;</a>





  
  

  905
  
</li>





  
  

  906
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-rb">-rb, --remove_background_annotation &lt;remove_background_annotation&gt;</a>





  
  

  907
  
</li>





  
  

  908
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-to">-to, --to_annotations &lt;to_annotations&gt;</a>





  
  

  909
  
</li>





  
  

  910
  
      </ul></li>





  
  

  911
  
      <li>





  
  

  912
  
    pathflowai-preprocess-preprocess_pipeline command line option





  
  

  913
  





  
  

  914
  
      <ul>





  
  

  915
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-a">-a, --annotations &lt;annotations&gt;</a>





  
  

  916
  
</li>





  
  

  917
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-am">-am, --adjust_mask</a>





  
  

  918
  
</li>





  
  

  919
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-b">-b, --basename &lt;basename&gt;</a>





  
  

  920
  
</li>





  
  

  921
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-bp">-bp, --basic_preprocess</a>





  
  

  922
  
</li>





  
  

  923
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-g">-g, --generate_finetune_segmentation</a>





  
  

  924
  
</li>





  
  

  925
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-i">-i, --input_dir &lt;input_dir&gt;</a>





  
  

  926
  
</li>





  
  

  927
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-it">-it, --intensity_threshold &lt;intensity_threshold&gt;</a>





  
  

  928
  
</li>





  
  

  929
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-nn">-nn, --n_neighbors &lt;n_neighbors&gt;</a>





  
  

  930
  
</li>





  
  

  931
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-npy">-npy, --img2npy</a>





  
  

  932
  
</li>





  
  

  933
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-odb">-odb, --out_db &lt;out_db&gt;</a>





  
  

  934
  
</li>





  
  

  935
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pa">-pa, --patches</a>





  
  

  936
  
</li>





  
  

  937
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pr">-pr, --preprocess</a>





  
  

  938
  
</li>





  
  

  939
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-ps">-ps, --patch_size &lt;patch_size&gt;</a>





  
  

  940
  
</li>





  
  

  941
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-t">-t, --threshold &lt;threshold&gt;</a>





  
  

  942
  
</li>





  
  

  943
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tc">-tc, --target_segmentation_class &lt;target_segmentation_class&gt;</a>





  
  

  944
  
</li>





  
  

  945
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tt">-tt, --target_threshold &lt;target_threshold&gt;</a>





  
  

  946
  
</li>





  
  

  947
  
      </ul></li>





  
  

  948
  
      <li>





  
  

  949
  
    pathflowai-preprocess-remove_basename_from_db command line option





  
  

  950
  





  
  

  951
  
      <ul>





  
  

  952
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-b">-b, --basename &lt;basename&gt;</a>





  
  

  953
  
</li>





  
  

  954
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-i">-i, --input_patch_db &lt;input_patch_db&gt;</a>





  
  

  955
  
</li>





  
  

  956
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-o">-o, --output_patch_db &lt;output_patch_db&gt;</a>





  
  

  957
  
</li>





  
  

  958
  
        <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-ps">-ps, --patch_size &lt;patch_size&gt;</a>





  
  

  959
  
</li>





  
  

  960
  
      </ul></li>





  
  

  961
  
      <li>





  
  

  962
  
    pathflowai-visualize command line option





  
  

  963
  





  
  

  964
  
      <ul>





  
  

  965
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-version">--version</a>





  
  

  966
  
</li>





  
  

  967
  
      </ul></li>





  
  

  968
  
      <li>





  
  

  969
  
    pathflowai-visualize-extract_patch command line option





  
  

  970
  





  
  

  971
  
      <ul>





  
  

  972
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-b">-b, --basename &lt;basename&gt;</a>





  
  

  973
  
</li>





  
  

  974
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-c">-c, --custom_segmentation &lt;custom_segmentation&gt;</a>





  
  

  975
  
</li>





  
  

  976
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-i">-i, --input_dir &lt;input_dir&gt;</a>





  
  

  977
  
</li>





  
  

  978
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-o">-o, --outputfname &lt;outputfname&gt;</a>





  
  

  979
  
</li>





  
  

  980
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-p">-p, --patch_info_file &lt;patch_info_file&gt;</a>





  
  

  981
  
</li>





  
  

  982
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-ps">-ps, --patch_size &lt;patch_size&gt;</a>





  
  

  983
  
</li>





  
  

  984
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-s">-s, --segmentation</a>





  
  

  985
  
</li>





  
  

  986
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-sc">-sc, --n_segmentation_classes &lt;n_segmentation_classes&gt;</a>





  
  

  987
  
</li>





  
  

  988
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-x">-x, --x &lt;x&gt;</a>





  
  

  989
  
</li>





  
  

  990
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-y">-y, --y &lt;y&gt;</a>





  
  

  991
  
</li>





  
  

  992
  
      </ul></li>





  
  

  993
  
      <li>





  
  

  994
  
    pathflowai-visualize-overlay_new_annotations command line option





  
  

  995
  





  
  

  996
  
      <ul>





  
  

  997
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-a">-a, --annotation_txt &lt;annotation_txt&gt;</a>





  
  

  998
  
</li>





  
  

  999
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-cf">-cf, --compression_factor &lt;compression_factor&gt;</a>





  
  

  1000
  
</li>





  
  

  1001
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-i">-i, --img_file &lt;img_file&gt;</a>





  
  

  1002
  
</li>





  
  

  1003
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-o">-o, --outputfilename &lt;outputfilename&gt;</a>





  
  

  1004
  
</li>





  
  

  1005
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-ocf">-ocf, --original_compression_factor &lt;original_compression_factor&gt;</a>





  
  

  1006
  
</li>





  
  

  1007
  
      </ul></li>





  
  

  1008
  
  </ul></td>





  
  

  1009
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  1010
  
      <li>





  
  

  1011
  
    pathflowai-visualize-plot_embeddings command line option





  
  

  1012
  





  
  

  1013
  
      <ul>





  
  

  1014
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-a">-a, --annotations &lt;annotations&gt;</a>





  
  

  1015
  
</li>





  
  

  1016
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-b">-b, --basename &lt;basename&gt;</a>





  
  

  1017
  
</li>





  
  

  1018
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-i">-i, --embeddings_file &lt;embeddings_file&gt;</a>





  
  

  1019
  
</li>





  
  

  1020
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-ma">-ma, --max_background_area &lt;max_background_area&gt;</a>





  
  

  1021
  
</li>





  
  

  1022
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-nn">-nn, --n_neighbors &lt;n_neighbors&gt;</a>





  
  

  1023
  
</li>





  
  

  1024
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-o">-o, --plotly_output_file &lt;plotly_output_file&gt;</a>





  
  

  1025
  
</li>





  
  

  1026
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-rb">-rb, --remove_background_annotation &lt;remove_background_annotation&gt;</a>





  
  

  1027
  
</li>





  
  

  1028
  
      </ul></li>





  
  

  1029
  
      <li>





  
  

  1030
  
    pathflowai-visualize-plot_image command line option





  
  

  1031
  





  
  

  1032
  
      <ul>





  
  

  1033
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-cf">-cf, --compression_factor &lt;compression_factor&gt;</a>





  
  

  1034
  
</li>





  
  

  1035
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-i">-i, --image_file &lt;image_file&gt;</a>





  
  

  1036
  
</li>





  
  

  1037
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-o">-o, --outputfname &lt;outputfname&gt;</a>





  
  

  1038
  
</li>





  
  

  1039
  
      </ul></li>





  
  

  1040
  
      <li>





  
  

  1041
  
    pathflowai-visualize-plot_image_umap_embeddings command line option





  
  

  1042
  





  
  

  1043
  
      <ul>





  
  

  1044
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-b">-b, --basename &lt;basename&gt;</a>





  
  

  1045
  
</li>





  
  

  1046
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-e">-e, --embeddings_file &lt;embeddings_file&gt;</a>





  
  

  1047
  
</li>





  
  

  1048
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-i">-i, --input_dir &lt;input_dir&gt;</a>





  
  

  1049
  
</li>





  
  

  1050
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-ma">-ma, --max_background_area &lt;max_background_area&gt;</a>





  
  

  1051
  
</li>





  
  

  1052
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-mpl">-mpl, --mpl_scatter</a>





  
  

  1053
  
</li>





  
  

  1054
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-nn">-nn, --n_neighbors &lt;n_neighbors&gt;</a>





  
  

  1055
  
</li>





  
  

  1056
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-o">-o, --outputfilename &lt;outputfilename&gt;</a>





  
  

  1057
  
</li>





  
  

  1058
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-rb">-rb, --remove_background_annotation &lt;remove_background_annotation&gt;</a>





  
  

  1059
  
</li>





  
  

  1060
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sc">-sc, --sort_col &lt;sort_col&gt;</a>





  
  

  1061
  
</li>





  
  

  1062
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sm">-sm, --sort_mode &lt;sort_mode&gt;</a>





  
  

  1063
  
</li>





  
  

  1064
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-z">-z, --zoom &lt;zoom&gt;</a>





  
  

  1065
  
</li>





  
  

  1066
  
      </ul></li>





  
  

  1067
  
      <li>





  
  

  1068
  
    pathflowai-visualize-plot_predictions command line option





  
  

  1069
  





  
  

  1070
  
      <ul>





  
  

  1071
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ac">-ac, --annotation_col &lt;annotation_col&gt;</a>





  
  

  1072
  
</li>





  
  

  1073
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-al">-al, --alpha &lt;alpha&gt;</a>





  
  

  1074
  
</li>





  
  

  1075
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-an">-an, --annotations</a>





  
  

  1076
  
</li>





  
  

  1077
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-b">-b, --basename &lt;basename&gt;</a>





  
  

  1078
  
</li>





  
  

  1079
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-c">-c, --custom_segmentation &lt;custom_segmentation&gt;</a>





  
  

  1080
  
</li>





  
  

  1081
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-cf">-cf, --compression_factor &lt;compression_factor&gt;</a>





  
  

  1082
  
</li>





  
  

  1083
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-i">-i, --input_dir &lt;input_dir&gt;</a>





  
  

  1084
  
</li>





  
  

  1085
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-o">-o, --outputfname &lt;outputfname&gt;</a>





  
  

  1086
  
</li>





  
  

  1087
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-p">-p, --patch_info_file &lt;patch_info_file&gt;</a>





  
  

  1088
  
</li>





  
  

  1089
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ps">-ps, --patch_size &lt;patch_size&gt;</a>





  
  

  1090
  
</li>





  
  

  1091
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-s">-s, --segmentation</a>





  
  

  1092
  
</li>





  
  

  1093
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sc">-sc, --n_segmentation_classes &lt;n_segmentation_classes&gt;</a>





  
  

  1094
  
</li>





  
  

  1095
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sf">-sf, --scaling_factor &lt;scaling_factor&gt;</a>





  
  

  1096
  
</li>





  
  

  1097
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-tif">-tif, --tif_file</a>





  
  

  1098
  
</li>





  
  

  1099
  
      </ul></li>





  
  

  1100
  
      <li>





  
  

  1101
  
    pathflowai-visualize-shapley_plot command line option





  
  

  1102
  





  
  

  1103
  
      <ul>





  
  

  1104
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-bs">-bs, --batch_size &lt;batch_size&gt;</a>





  
  

  1105
  
</li>





  
  

  1106
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-l">-l, --local_smoothing &lt;local_smoothing&gt;</a>





  
  

  1107
  
</li>





  
  

  1108
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-m">-m, --model_pkl &lt;model_pkl&gt;</a>





  
  

  1109
  
</li>





  
  

  1110
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-mth">-mth, --method &lt;method&gt;</a>





  
  

  1111
  
</li>





  
  

  1112
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-ns">-ns, --n_samples &lt;n_samples&gt;</a>





  
  

  1113
  
</li>





  
  

  1114
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-o">-o, --outputfilename &lt;outputfilename&gt;</a>





  
  

  1115
  
</li>





  
  

  1116
  
        <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-p">-p, --pred_out &lt;pred_out&gt;</a>





  
  

  1117
  
</li>





  
  

  1118
  
      </ul></li>





  
  

  1119
  
      <li><a href="index.html#module-pathflowai.datasets">pathflowai.datasets (module)</a>





  
  

  1120
  
</li>





  
  

  1121
  
      <li><a href="index.html#module-pathflowai.losses">pathflowai.losses (module)</a>





  
  

  1122
  
</li>





  
  

  1123
  
      <li><a href="index.html#module-pathflowai.sampler">pathflowai.sampler (module)</a>





  
  

  1124
  
</li>





  
  

  1125
  
      <li><a href="index.html#module-pathflowai.schedulers">pathflowai.schedulers (module)</a>





  
  

  1126
  
</li>





  
  

  1127
  
      <li><a href="index.html#module-pathflowai.utils">pathflowai.utils (module)</a>





  
  

  1128
  
</li>





  
  

  1129
  
      <li><a href="index.html#module-pathflowai.visualize">pathflowai.visualize (module)</a>





  
  

  1130
  
</li>





  
  

  1131
  
      <li><a href="index.html#pathflowai.visualize.PlotlyPlot.plot">plot() (pathflowai.visualize.PlotlyPlot method)</a>





  
  

  1132
  
</li>





  
  

  1133
  
      <li><a href="index.html#pathflowai.visualize.plot_image_">plot_image_() (in module pathflowai.visualize)</a>





  
  

  1134
  
</li>





  
  

  1135
  
      <li><a href="index.html#pathflowai.visualize.plot_shap">plot_shap() (in module pathflowai.visualize)</a>





  
  

  1136
  
</li>





  
  

  1137
  
      <li><a href="index.html#pathflowai.visualize.plot_umap_images">plot_umap_images() (in module pathflowai.visualize)</a>





  
  

  1138
  
</li>





  
  

  1139
  
      <li><a href="index.html#pathflowai.visualize.PlotlyPlot">PlotlyPlot (class in pathflowai.visualize)</a>





  
  

  1140
  
</li>





  
  

  1141
  
      <li><a href="index.html#pathflowai.visualize.PredictionPlotter">PredictionPlotter (class in pathflowai.visualize)</a>





  
  

  1142
  
</li>





  
  

  1143
  
      <li><a href="index.html#pathflowai.visualize.prob2rbg">prob2rbg() (in module pathflowai.visualize)</a>





  
  

  1144
  
</li>





  
  

  1145
  
      <li><a href="index.html#pathflowai.utils.process_svs">process_svs() (in module pathflowai.utils)</a>





  
  

  1146
  
</li>





  
  

  1147
  
  </ul></td>





  
  

  1148
  
</tr></table>





  
  

  1149
  





  
  

  1150
  
<h2 id="R">R</h2>





  
  

  1151
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  1152
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  1153
  
      <li><a href="index.html#pathflowai.datasets.RandomRotate90">RandomRotate90() (in module pathflowai.datasets)</a>





  
  

  1154
  
</li>





  
  

  1155
  
      <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.retain_ID">retain_ID() (pathflowai.datasets.DynamicImageDataset method)</a>





  
  

  1156
  
</li>





  
  

  1157
  
      <li><a href="index.html#pathflowai.utils.retain_images">retain_images() (in module pathflowai.utils)</a>





  
  

  1158
  
</li>





  
  

  1159
  
  </ul></td>





  
  

  1160
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  1161
  
      <li><a href="index.html#pathflowai.utils.return_image_coord">return_image_coord() (in module pathflowai.utils)</a>





  
  

  1162
  
</li>





  
  

  1163
  
      <li><a href="index.html#pathflowai.utils.return_image_in_boxes_dict">return_image_in_boxes_dict() (in module pathflowai.utils)</a>





  
  

  1164
  
</li>





  
  

  1165
  
      <li><a href="index.html#pathflowai.visualize.PredictionPlotter.return_patch">return_patch() (pathflowai.visualize.PredictionPlotter method)</a>





  
  

  1166
  
</li>





  
  

  1167
  
      <li><a href="index.html#pathflowai.utils.run_preprocessing_pipeline">run_preprocessing_pipeline() (in module pathflowai.utils)</a>





  
  

  1168
  
</li>





  
  

  1169
  
  </ul></td>





  
  

  1170
  
</tr></table>





  
  

  1171
  





  
  

  1172
  
<h2 id="S">S</h2>





  
  

  1173
  
<table style="width: 100%" class="indextable genindextable"><tr>





  
  

  1174
  
  <td style="width: 33%; vertical-align: top;"><ul>





  
  

  1175
  
      <li><a href="index.html#pathflowai.utils.save_all_patch_info">save_all_patch_info() (in module pathflowai.utils)</a>





  
  

  1176
  
</li>





  
  

  1177
  
      <li><a href="index.html#pathflowai.utils.save_dataset">save_dataset() (in module pathflowai.utils)</a>





  
  

  1178
  
</li>





  
  

  1179
  
      <li><a href="index.html#pathflowai.schedulers.Scheduler">Scheduler (class in pathflowai.schedulers)</a>





  
  

  1180
  
</li>





  
  

  1181
  
      <li><a href="index.html#pathflowai.visualize.seg2rgb">seg2rgb() (in module pathflowai.visualize)</a>





  
  

  1182
  
</li>





  
  

  1183
  
      <li><a href="index.html#pathflowai.utils.segmentation_predictions2npy">segmentation_predictions2npy() (in module pathflowai.utils)</a>





  
  

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