

<Algorithms><Algorithm Name="IHC Nuclear v1" Description="IHC General Purpose Nuclear Image Analysis" SequenceOrder="0" Incremental="1" AlgorithmLicenseId="10029"><Parameter Title="View Width" Description="Width of processing box" Type="0" Value="1000"><ParameterAttribute><Min>0</Min><Max>2500</Max><Step>100</Step></ParameterAttribute></Parameter><Parameter Title="View Height" Description="Height of processing box" Type="0" Value="1000"><ParameterAttribute><Min>0</Min><Max>2500</Max><Step>100</Step></ParameterAttribute></Parameter><Parameter Title="Overlap Size" Description="Size of the overlap region for each view. This should be atleast as big as the average object size" Type="0" Value="100"><ParameterAttribute><Min>0</Min><Max>2500</Max><Step>10</Step></ParameterAttribute></Parameter><Parameter Title="Image Zoom" Description="Zoom level to be used. Higher zoom results in faster algorithm run but less accurate results." Type="1" Value="1"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Markup Compression Type" Description="This sets compression type for algorithm markup image. Choose better compression if you need it for a special purpose." Type="4" Value="0"><ParameterAttribute><List><Item Value="0" Description="Same as processed image" /><Item Value="1" Description="JPEG" /><Item Value="2" Description="JPEG2000" /></List></ParameterAttribute></Parameter><Parameter Title="Compression Quality" Description="Higher quality takes longer and yields bigger files. Does not apply to all compression types." Type="0" Value="30"><ParameterAttribute><Min>0</Min><Max>95</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Classifier Neighborhood" Description="Size (microns) of neighborhood to pad boundary of each view, as required by classifier." Type="1" Value="0"><ParameterAttribute><Min>0</Min><Max>200</Max><Step>10</Step></ParameterAttribute></Parameter><Parameter Title="Classifier" Description="Choose from the list of Classifiers available in eSlide Manager" Type="6" Value="None"><ParameterAttribute><List><Item Value="0" Description="None" /><Item Value="1" Description="10_Cote Samples" /><Item Value="2" Description="10_Vaccine Work Kif23" /><Item Value="3" Description="11_Alveolar Epithelium and Widened Alveoli" /><Item Value="4" Description="11_Pulmonary Edema" /><Item Value="5" Description="12_Ab39_Test" /><Item Value="6" Description="13_Ab39-try2" /><Item Value="7" Description="1_Practice-MEM" /><Item Value="8" Description="2_Test Classifier" /><Item Value="9" Description="3_Mouse-lung-tumor-H&amp;E" /><Item Value="10" Description="3_mouse lung H&amp;E_single slide" /><Item Value="11" Description="4_Caerulain mice" /><Item Value="12" Description="5_Pancreatic Cancer Mice" /><Item Value="13" Description="6_Fibrosis IV" /><Item Value="14" Description="6_Fibrosis V" /><Item Value="15" Description="6_HE Fibrosis 2" /><Item Value="16" Description="6_HE Fibrosis III" /><Item Value="17" Description="6_HE Immune Cells" /><Item Value="18" Description="6_Trichrome" /><Item Value="19" Description="8_HE Immune Cells 2" /><Item Value="20" Description="9_Training Set Test" /></List></ParameterAttribute></Parameter><Parameter Title="Class List" Description="Pick the classes to retain for further processing" Type="5" Value=""><ParameterAttribute /></Parameter><Parameter Title="Averaging Radius (um)" Description="Radius (microns) for Noise Reduction (0&lt;Value&lt;100)" Type="1" Value="1"><ParameterAttribute><Min>0</Min><Max>100</Max><Step>0.5</Step></ParameterAttribute></Parameter><Parameter Title="Curvature Threshold" Description="Curvature Threshold for Nuclear Declustering (0&lt;Value&lt;=25)" Type="1" Value="2.5"><ParameterAttribute><Min>0</Min><Max>25</Max><Step>0.5</Step></ParameterAttribute></Parameter><Parameter Title="Segmentation Type" Description="Use Nuclear Stain or Intensity to Segment Nuclei" Type="4" Value="2"><ParameterAttribute><List><Item Value="0" Description="Nuclear Stain" /><Item Value="1" Description="Intensity" /><Item Value="2" Description="Cytoplasmic Rejection" /></List></ParameterAttribute></Parameter><Parameter Title="Threshold Type" Description="Threshold Method" Type="4" Value="1"><ParameterAttribute><List><Item Value="0" Description="Amplitude Threshold Method" /><Item Value="1" Description="Edge Threshold Method" /><Item Value="2" Description="Manual Threshold Method" /></List></ParameterAttribute></Parameter><Parameter Title="Edge Trimming" Description="Trim Light Edges of Objects" Type="4" Value="2"><ParameterAttribute><List><Item Value="0" Description="None" /><Item Value="1" Description="Weighted" /><Item Value="2" Description="Un-Weighted" /></List></ParameterAttribute></Parameter><Parameter Title="Lower Threshold" Description="Lower-limit for Intensity Thresholding (0&lt;Value&lt;=255)" Type="0" Value="0"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Upper Threshold" Description="Upper-limit for Intensity Thresholding (0&lt;Value&lt;=255)" Type="0" Value="212"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Min Nuclear Size (um^2)" Description="Minimum Area for detectable Nuclei (micron-squared) (Value &gt; 0)" Type="1" Value="1"><ParameterAttribute><Min>0</Min><Max /><Step>10</Step></ParameterAttribute></Parameter><Parameter Title="Max Nuclear Size (um^2)" Description="Maximum Area for detectable Nuclei (micron-squared) (Value &gt; 0)" Type="1" Value="20"><ParameterAttribute><Min>0</Min><Max /><Step>10</Step></ParameterAttribute></Parameter><Parameter Title="Min Roundness" Description="Nuclei with roundness less than this are not reported. (0.0 &lt; Value &lt; 1.0)" Type="1" Value="0.2"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Min Compactness" Description="Nuclei with compactness less than this are not reported. (0.0 &lt; Value &lt; 1.0)" Type="1" Value="0.5"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Min Elongation" Description="Nuclei with aspect ratios less than this are not reported. (0.0 &lt; Value &lt; 1.0)" Type="1" Value="0.52"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Remove Light Objects" Description="Value=0 removes no nuclei, Value=1 removes all nuclei (0.0 &lt; Value &lt; 1.0)" Type="1" Value="0"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Clear Area Intensity" Description="Intensity of Clear Area (240 for ScanScope)" Type="0" Value="240"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Nuclear Stain (Red)" Description="OD for Nuclear Red: Default is Hematoxylin" Type="1" Value="0.7"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Nuclear Stain (Green)" Description="OD for Nuclear Green: Default is Hematoxylin" Type="1" Value="0.704"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Nuclear Stain (Blue)" Description="OD for Nuclear Blue: Default is Hematoxylin" Type="1" Value="0.286"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Positive Stain (Red)" Description="OD for Positive Red: Default is DAB" Type="1" Value="0.46"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Positive Stain (Green)" Description="OD for Positive Green: Default is DAB" Type="1" Value="0.79"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Positive Stain (Blue)" Description="OD for Positive Blue: Default is DAB" Type="1" Value="0.94"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="3rd Stain (Red)" Description="OD for Color(3) Red: Default is None" Type="1" Value="0"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="3rd Stain (Green)" Description="OD for Color(3) Green: Default is None" Type="1" Value="0"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="3rd Stain (Blue)" Description="OD for Color(3) Blue: Default is None" Type="1" Value="0"><ParameterAttribute><Min>0</Min><Max>1</Max><Step>0.01</Step></ParameterAttribute></Parameter><Parameter Title="Cytoplasmic Intensity Threshold" Description="Adjust Nuclear Intensity if Cytoplasm&lt;Threshold (0 Disables)" Type="0" Value="230"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Weak(1+) Threshold" Description="Intensity Threshold (Upper Limit) of WEAK Positive Nuclei" Type="0" Value="255"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Moderate(2+) Threshold" Description="Intensity Threshold (Upper Limit) of MEDIUM Positive Nuclei" Type="0" Value="250"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Strong(3+) Threshold" Description="Intensity Threshold (Upper Limit) of STRONG Positive Nuclei" Type="0" Value="160"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Black Threshold" Description="Intensity Threshold (Lower Limit) of STRONG Positive Nuclei" Type="0" Value="0"><ParameterAttribute><Min>0</Min><Max>255</Max><Step>1</Step></ParameterAttribute></Parameter><Parameter Title="Use Mode" Description="Select Training or Analysis/Tuning Mode" Type="4" Value="0"><ParameterAttribute><List><Item Value="0" Description="Analysis/Tuning" /><Item Value="1" Description="Training" /></List></ParameterAttribute></Parameter><Parameter Title="Mark-up Image Type" Description="Choose Type of Markup Image" Type="4" Value="2"><ParameterAttribute><List><Item Value="0" Description="Tuning" /><Item Value="1" Description="Analysis" /><Item Value="2" Description="Analysis (With Cell Edges)" /></List></ParameterAttribute></Parameter><Parameter Title="Classifier Type" Description="Select Type of Classifier" Type="4" Value="1"><ParameterAttribute><List><Item Value="0" Description="IHCMembrane" /><Item Value="1" Description="IHCNuclear" /></List></ParameterAttribute></Parameter><Parameter Title="Classifier Definition File" Description="Name of Classifier Definition File" Type="2" Value="IHC_Nuclear_Training"><ParameterAttribute /></Parameter><MacroOutputCollection><MacroOutput><RowState>Unchanged</RowState><Id>32431</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>Percent</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32432</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>Intensity</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32433</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>3+ %</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32434</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>2+ %</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32435</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>1+ %</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32436</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>0  %</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32437</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title>Intensity Value</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput><MacroOutput><RowState>Unchanged</RowState><Id>32438</Id><MacroAlgorithmId>2255</MacroAlgorithmId><Title># Cells</Title><IsIvd p3:nil="true" xmlns:p3="http://www.w3.org/2001/XMLSchema-instance" /></MacroOutput></MacroOutputCollection></Algorithm></Algorithms>