SuperpixelClassification.xml

<?xml version="1.0" encoding="UTF-8"?>
<executable>
  <category>HistomicsTK</category>
  <title>Superpixel Classification</title>
  <description>Classify Superpixels</description>
  <version>0.1.0</version>
  <documentation-url>https://digitalslidearchive.github.io/HistomicsTK</documentation-url>
  <license>Apache 2.0</license>
  <contributor>David Manthey (Kitware Inc)</contributor>
  <acknowledgements>This work is part of the HistomicsTK project.</acknowledgements>
  <parameters>
    <label>I/O</label>
    <description>Input/output parameters.</description>
    <directory reference="_girder_id_" defaultRelativePath="..">
      <name>images</name>
      <description>The directory of images to use for prediction or training</description>
      <label>Image Directory</label>
      <channel>input</channel>
      <index>0</index>
    </directory>
    <string>
      <name>annotationName</name>
      <longflag>annotationame</longflag>
      <label>Annotation Base Name</label>
      <description>Annotations with this name will be used for finding user labels and generating features</description>
      <default>Superpixel</default>
    </string>

    <directory reference="_girder_id_" defaultRelativePath=".." defaultNameMatch="[fF]eature">
      <name>features</name>
      <longflag>features</longflag>
      <description>A directory to store and load features extracted from the images</description>
      <label>Feature Directory</label>
      <channel>input</channel>
    </directory>
    <integer>
      <name>patchSize</name>
      <longflag>patchsize</longflag>
      <label>Patch Size</label>
      <channel>input</channel>
      <default>100</default>
      <description>The image size used for feature extraction</description>
    </integer>
    <directory reference="_girder_id_" defaultRelativePath=".." defaultNameMatch="[mM]odel">
      <name>modeldir</name>
      <longflag>modeldir</longflag>
      <description>A directory to store and load the model</description>
      <label>Model Directory</label>
      <channel>input</channel>
    </directory>
    <boolean>
      <name>progress</name>
      <longflag>progress</longflag>
      <description>Report progress</description>
      <label>Progress</label>
      <default>true</default>
    </boolean>
  </parameters>
  <parameters>
    <label>Superpixels</label>
    <description>Superpixel parameters</description>
    <boolean>
      <name>gensuperpixels</name>
      <longflag>generate-superpixels</longflag>
      <description>If an image does not have an annotation with superpixels, generate one</description>
      <label>Generate superpixels</label>
      <default>true</default>
    </boolean>
    <integer>
      <name>radius</name>
      <longflag>radius</longflag>
      <label>Approximate radius</label>
      <channel>input</channel>
      <default>100</default>
      <description>Approximate superpixel radius is pixels</description>
    </integer>
    <float>
      <name>magnification</name>
      <longflag>magnification</longflag>
      <label>Magnification</label>
      <channel>input</channel>
      <default>5</default>
      <description>Image magnification for superpixel generation</description>
    </float>
    <directory reference="_girder_id_" defaultRelativePath=".." defaultNameMatch="[aA]nnotation">
      <name>annotationDir</name>
      <longflag>annotationdir</longflag>
      <description>A directory to store superpixel annotation images</description>
      <label>Annotation Directory</label>
      <channel>input</channel>
    </directory>
  </parameters>
  <parameters>
    <label>Training</label>
    <description>Training parameters</description>
    <boolean>
      <name>train</name>
      <longflag>train</longflag>
      <description>Train the model based on the newest user annotations</description>
      <label>Train model</label>
      <default>true</default>
    </boolean>
    <boolean>
      <name>useCuda</name>
      <longflag>usecuda</longflag>
      <description>Whether or not to use GPU/cuda (true) or cpu (false).</description>
      <label>Use CUDA</label>
      <default>false</default>
    </boolean>
    <integer>
      <name>batchSize</name>
      <longflag>batchsize</longflag>
      <label>Batch Size</label>
      <channel>input</channel>
      <default>-1</default>
      <description>Training batch size (-1 indicates optimal batch size)</description>
    </integer>
    <integer>
      <name>epochs</name>
      <longflag>epochs</longflag>
      <label>Epochs</label>
      <channel>input</channel>
      <default>100</default>
      <description>Training epochs</description>
    </integer>
    <float>
      <name>split</name>
      <longflag>split</longflag>
      <label>Training Split</label>
      <channel>input</channel>
      <default>0.8</default>
      <description>Training / validation split (0 to 1)</description>
    </float>
    <boolean>
      <name>randominput</name>
      <longflag>randomInput</longflag>
      <label>Random Input</label>
      <description>Start with random input</description>
      <default>false</default>
    </boolean>
    <string-vector>
      <name>labels</name>
      <longflag>labels</longflag>
      <label>Labels</label>
      <description>Labels for random input</description>
      <default>Tissue,Background,Marker</default>
    </string-vector>
    <string-vector>
      <name>exclude</name>
      <longflag>exclude</longflag>
      <label>Exclude Labels</label>
      <description>Labels excluded from training.  Any feature with this label is treated as unlabelled for the purposes of training</description>
      <default>Exclude</default>
    </string-vector>
    <boolean>
      <name>heatmaps</name>
      <longflag>heatmaps</longflag>
      <description>Generate heatmap annotations</description>
      <label>Generate heatmaps for attention and uncertainty</label>
      <default>false</default>
    </boolean>
    <string-enumeration>
      <name>certainty</name>
      <label>Certainty Metric</label>
      <description>The method used to deterime which superpixels have the most certain labels</description>
      <longflag>certainty</longflag>
      <default>confidence</default>
      <element>confidence</element>
      <element>margin</element>
      <element>negative_entropy</element>
      <element>batchbald</element>
    </string-enumeration>
    <string-enumeration>
      <name>feature</name>
      <label>Feature Shape</label>
      <description>Whether a feature is superpixel image data or a foundation model vector</description>
      <longflag>feature</longflag>
      <default>image</default>
      <element>image</element>
      <element>vector</element>
    </string-enumeration>
  </parameters>
  <parameters advanced="true">
    <label>Girder API URL and Key</label>
    <description>A Girder API URL and token for Girder client</description>
    <string>
      <name>girderApiUrl</name>
      <longflag>api-url</longflag>
      <label>Girder API URL</label>
      <description>A Girder API URL (e.g., https://girder.example.com:443/api/v1)</description>
      <default></default>
    </string>
    <string>
      <name>girderToken</name>
      <longflag>girder-token</longflag>
      <label>Girder Token</label>
      <description>A Girder token</description>
      <default></default>
    </string>
    <integer>
      <name>numWorkers</name>
      <longflag>workers</longflag>
      <label>Number of Workers</label>
      <channel>input</channel>
      <default>4</default>
      <description>The number of worker threads for superpixel and feature generation</description>
    </integer>
    <integer>
      <name>cutoff</name>
      <longflag>cutoff</longflag>
      <label>Number of annotations per slide</label>
      <default>500</default>
      <description>Number of unannotated superpixels to use per slide for features, training and predictions</description>
    </integer>
  </parameters>
</executable>