<?xml version="1.0"?>
<Configuration xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <Processing>
    <FilterAndAlignCycle>25</FilterAndAlignCycle>
    <NumberOfThreads>20</NumberOfThreads>
    <DataManager>DataManagerAllInMem</DataManager>
    <InterOpManager>InterOpManagerTwoChannel</InterOpManager>
    <WorkProviderTypes>
      <WorkProviderOptions>ServiceMultiImageBased</WorkProviderOptions>
    </WorkProviderTypes>
    <TileMatch />
    <CifQValTileMatch>1[13].03|12.09|2[13].09|22.03</CifQValTileMatch>
    <PostProcessEventFile />
    <MaxExceptionsCopying>3</MaxExceptionsCopying>
    <ServiceBasedTimeoutMinutes>5</ServiceBasedTimeoutMinutes>
    <AggregateOutput>true</AggregateOutput>
    <ThumbnailTileMatch>...0[16]|...12</ThumbnailTileMatch>
    <FixTapBoundaries>false</FixTapBoundaries>
    <InterOpOutCopyMaxRetries>2</InterOpOutCopyMaxRetries>
    <WorkSourceUrl>http://localhost:8080/</WorkSourceUrl>
    <WorkProviderServicePort>8081</WorkProviderServicePort>
    <FileCopyEndpoint>http://localhost:8090/</FileCopyEndpoint>
    <MaxMinsForRequeueOnError>60</MaxMinsForRequeueOnError>
  </Processing>
  <Logging>
    <MaxQueueLength>200</MaxQueueLength>
    <LogFileChunkingSize>5242880</LogFileChunkingSize>
    <UseProfiler>true</UseProfiler>
    <DebugLogging>false</DebugLogging>
  </Logging>
  <TemplateGeneration>
    <TemplateStartCycle>1</TemplateStartCycle>
    <TemplateEndCycle>5</TemplateEndCycle>
    <TemplateChastityCutoff>0.75</TemplateChastityCutoff>
    <TightRadius>1</TightRadius>
    <LooseRadius>5</LooseRadius>
    <SpotLocationsMax>1000000</SpotLocationsMax>
    <LowDiversityChanceCutoff>0.2</LowDiversityChanceCutoff>
    <TightRadiusLowDiversity>1.5</TightRadiusLowDiversity>
    <TemplateImageSharpening>LaplacianCross</TemplateImageSharpening>
    <TemplateGenerationType>Random</TemplateGenerationType>
    <PatternedAreaSelection>FullImage</PatternedAreaSelection>
    <TemplateImageSharpeningMask>
      <float>0</float>
      <float>-2</float>
      <float>0</float>
      <float>-2</float>
      <float>9</float>
      <float>-2</float>
      <float>0</float>
      <float>-2</float>
      <float>0</float>
    </TemplateImageSharpeningMask>
    <SpotFindingRegionWidth>128</SpotFindingRegionWidth>
    <SpotFindingRegionHeight>128</SpotFindingRegionHeight>
    <TruthMapUpperLeftX>-1</TruthMapUpperLeftX>
    <TruthMapUpperLeftY>-1</TruthMapUpperLeftY>
    <TruthMapRegionWidth>256</TruthMapRegionWidth>
    <TruthMapRegionHeight>256</TruthMapRegionHeight>
    <TruthMapSamplingFactor>3</TruthMapSamplingFactor>
  </TemplateGeneration>
  <ColorMatrix>
    <EstimateColorMatrixCycles>3</EstimateColorMatrixCycles>
    <SaveCifs>false</SaveCifs>
  </ColorMatrix>
  <ImageAnalysis>
    <UseRoi>false</UseRoi>
    <PixelSize>1.5</PixelSize>
    <RoiRadiusInPixels>1000</RoiRadiusInPixels>
    <UseBackgroundCorrection>true</UseBackgroundCorrection>
    <SkipNonPfExtraction>true</SkipNonPfExtraction>
    <ExtractionMethod>OnePointFivePixel</ExtractionMethod>
    <ExtractionImageSharpeningMask>
      <float>0</float>
      <float>-2</float>
      <float>0</float>
      <float>-2</float>
      <float>9</float>
      <float>-2</float>
      <float>0</float>
      <float>-2</float>
      <float>0</float>
    </ExtractionImageSharpeningMask>
    <UpperLeftFiducialXInPixels>0</UpperLeftFiducialXInPixels>
    <UpperLeftFiducialYInPixels>0</UpperLeftFiducialYInPixels>
    <bgBoxWidth>64</bgBoxWidth>
    <bgBoxHeight>64</bgBoxHeight>
    <RegistrationDebugTileMatch />
    <RegistrationDebugCycleMatch>^[1-5]{1}$</RegistrationDebugCycleMatch>
    <RegistratorType>Random</RegistratorType>
    <HexagonalPatternOrientation>Horizontal</HexagonalPatternOrientation>
    <NumberOfCameras>1</NumberOfCameras>
    <NonlinearTransformType>XFieldOfView</NonlinearTransformType>
    <RigidRegistrationNumberOfColumns>0</RigidRegistrationNumberOfColumns>
    <RigidRegistrationNumberOfRows>0</RigidRegistrationNumberOfRows>
    <RigidRegistrationPitchInPixels>0</RigidRegistrationPitchInPixels>
    <RadialDistortionPolynomOrder>0</RadialDistortionPolynomOrder>
    <SpatialNormalizationRowSize>256</SpatialNormalizationRowSize>
    <SpatialNormalizationColumnSize>256</SpatialNormalizationColumnSize>
    <SubRegionBorderPaddingX>-1</SubRegionBorderPaddingX>
    <SubRegionBorderPaddingY>-1</SubRegionBorderPaddingY>
    <SubRegionSize>512</SubRegionSize>
  </ImageAnalysis>
  <NeighborCorrection>
    <EnableNeighborCorrection>false</EnableNeighborCorrection>
    <EstimateNeighborCorrectionCycles>1</EstimateNeighborCorrectionCycles>
    <NumberOfBinsInX>10</NumberOfBinsInX>
  </NeighborCorrection>
  <Basecalling>
    <Basecaller>BasecallerTwoChannel</Basecaller>
    <WindowBeforeAndAfter>1</WindowBeforeAndAfter>
    <CodingScheme>GTCA</CodingScheme>
    <ScatterPlotTileMatch />
    <AreaPerPixelmm2>5.96E-07</AreaPerPixelmm2>
    <ChastityCutoff>0.63</ChastityCutoff>
    <LoadFilter>false</LoadFilter>
    <SaveQvals>false</SaveQvals>
    <QscoreBinning>true</QscoreBinning>
    <QualityModelType>V9</QualityModelType>
    <NumPFGridBinsY>6</NumPFGridBinsY>
    <NumPFGridBinsX>8</NumPFGridBinsX>
    <EmptyFilterCycle>0</EmptyFilterCycle>
    <AllowedNotEmpty>0</AllowedNotEmpty>
    <SaveEmptyFile>false</SaveEmptyFile>
  </Basecalling>
  <SequenceAlignment>
    <Aligner>SequenceAlignerBits</Aligner>
    <SaveAlignments>false</SaveAlignments>
  </SequenceAlignment>
  <LoggingOptions>
    <LogOptions>Console</LogOptions>
    <LogOptions>FileByTile</LogOptions>
  </LoggingOptions>
</Configuration>