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clearmap.idx
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\indexentry{ClearMap (module)|hyperpage}{35}
\indexentry{ClearMap.IO (module)|hyperpage}{35}
\indexentry{ClearMap.IO.IO (module)|hyperpage}{37}
\indexentry{pointFileExtensions (in module ClearMap.IO.IO)|hyperpage}{37}
\indexentry{pointFileTypes (in module ClearMap.IO.IO)|hyperpage}{37}
\indexentry{pointFileExtensionToType (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{dataFileExtensions (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{dataFileTypes (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{dataFileExtensionToType (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{fileExtension() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{isFile() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{isFileExpression() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{isPointFile() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{isDataFile() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{createDirectory() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{pointFileNameToType() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{dataFileNameToType() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{dataFileNameToModule() (in module ClearMap.IO.IO)|hyperpage}{38}
\indexentry{pointFileNameToModule() (in module ClearMap.IO.IO)|hyperpage}{39}
\indexentry{dataSize() (in module ClearMap.IO.IO)|hyperpage}{39}
\indexentry{dataZSize() (in module ClearMap.IO.IO)|hyperpage}{39}
\indexentry{toDataRange() (in module ClearMap.IO.IO)|hyperpage}{39}
\indexentry{toDataSize() (in module ClearMap.IO.IO)|hyperpage}{39}
\indexentry{dataSizeFromDataRange() (in module ClearMap.IO.IO)|hyperpage}{39}
\indexentry{dataToRange() (in module ClearMap.IO.IO)|hyperpage}{40}
\indexentry{readData() (in module ClearMap.IO.IO)|hyperpage}{40}
\indexentry{writeData() (in module ClearMap.IO.IO)|hyperpage}{40}
\indexentry{copyFile() (in module ClearMap.IO.IO)|hyperpage}{40}
\indexentry{copyData() (in module ClearMap.IO.IO)|hyperpage}{41}
\indexentry{convertData() (in module ClearMap.IO.IO)|hyperpage}{41}
\indexentry{toMultiChannelData() (in module ClearMap.IO.IO)|hyperpage}{41}
\indexentry{pointsToCoordinates() (in module ClearMap.IO.IO)|hyperpage}{41}
\indexentry{pointsToProperties() (in module ClearMap.IO.IO)|hyperpage}{41}
\indexentry{pointsToCoordinatesAndProperties() (in module ClearMap.IO.IO)|hyperpage}{42}
\indexentry{pointsToCoordinatesAndPropertiesFileNames() (in module ClearMap.IO.IO)|hyperpage}{42}
\indexentry{pointShiftFromRange() (in module ClearMap.IO.IO)|hyperpage}{42}
\indexentry{pointsToRange() (in module ClearMap.IO.IO)|hyperpage}{42}
\indexentry{readPoints() (in module ClearMap.IO.IO)|hyperpage}{42}
\indexentry{writePoints() (in module ClearMap.IO.IO)|hyperpage}{43}
\indexentry{writeTable() (in module ClearMap.IO.IO)|hyperpage}{43}
\indexentry{ClearMap.IO.CSV (module)|hyperpage}{43}
\indexentry{writePoints() (in module ClearMap.IO.CSV)|hyperpage}{43}
\indexentry{readPoints() (in module ClearMap.IO.CSV)|hyperpage}{44}
\indexentry{test() (in module ClearMap.IO.CSV)|hyperpage}{44}
\indexentry{ClearMap.IO.FileList (module)|hyperpage}{44}
\indexentry{readFileList() (in module ClearMap.IO.FileList)|hyperpage}{44}
\indexentry{splitFileExpression() (in module ClearMap.IO.FileList)|hyperpage}{44}
\indexentry{fileExpressionToFileName() (in module ClearMap.IO.FileList)|hyperpage}{44}
\indexentry{dataSize() (in module ClearMap.IO.FileList)|hyperpage}{45}
\indexentry{dataZSize() (in module ClearMap.IO.FileList)|hyperpage}{45}
\indexentry{readDataFiles() (in module ClearMap.IO.FileList)|hyperpage}{45}
\indexentry{readData() (in module ClearMap.IO.FileList)|hyperpage}{45}
\indexentry{writeData() (in module ClearMap.IO.FileList)|hyperpage}{45}
\indexentry{copyData() (in module ClearMap.IO.FileList)|hyperpage}{45}
\indexentry{test() (in module ClearMap.IO.FileList)|hyperpage}{46}
\indexentry{ClearMap.IO.Imaris (module)|hyperpage}{46}
\indexentry{openFile() (in module ClearMap.IO.Imaris)|hyperpage}{46}
\indexentry{closeFile() (in module ClearMap.IO.Imaris)|hyperpage}{46}
\indexentry{readDataSet() (in module ClearMap.IO.Imaris)|hyperpage}{46}
\indexentry{dataSize() (in module ClearMap.IO.Imaris)|hyperpage}{46}
\indexentry{dataZSize() (in module ClearMap.IO.Imaris)|hyperpage}{47}
\indexentry{readData() (in module ClearMap.IO.Imaris)|hyperpage}{47}
\indexentry{getDataSize() (in module ClearMap.IO.Imaris)|hyperpage}{47}
\indexentry{getDataExtent() (in module ClearMap.IO.Imaris)|hyperpage}{47}
\indexentry{getScaleAndOffset() (in module ClearMap.IO.Imaris)|hyperpage}{47}
\indexentry{transformPointsToImaris() (in module ClearMap.IO.Imaris)|hyperpage}{47}
\indexentry{writePoints() (in module ClearMap.IO.Imaris)|hyperpage}{48}
\indexentry{writeData() (in module ClearMap.IO.Imaris)|hyperpage}{48}
\indexentry{readPoints() (in module ClearMap.IO.Imaris)|hyperpage}{48}
\indexentry{copyData() (in module ClearMap.IO.Imaris)|hyperpage}{48}
\indexentry{test() (in module ClearMap.IO.Imaris)|hyperpage}{48}
\indexentry{ClearMap.IO.NPY (module)|hyperpage}{48}
\indexentry{writePoints() (in module ClearMap.IO.NPY)|hyperpage}{49}
\indexentry{readPoints() (in module ClearMap.IO.NPY)|hyperpage}{49}
\indexentry{test() (in module ClearMap.IO.NPY)|hyperpage}{49}
\indexentry{ClearMap.IO.NRRD (module)|hyperpage}{49}
\indexentry{NrrdError|hyperpage}{49}
\indexentry{parse\_nrrdvector() (in module ClearMap.IO.NRRD)|hyperpage}{49}
\indexentry{parse\_optional\_nrrdvector() (in module ClearMap.IO.NRRD)|hyperpage}{49}
\indexentry{readHeader() (in module ClearMap.IO.NRRD)|hyperpage}{49}
\indexentry{readData() (in module ClearMap.IO.NRRD)|hyperpage}{50}
\indexentry{writeData() (in module ClearMap.IO.NRRD)|hyperpage}{50}
\indexentry{dataSize() (in module ClearMap.IO.NRRD)|hyperpage}{50}
\indexentry{dataZSize() (in module ClearMap.IO.NRRD)|hyperpage}{50}
\indexentry{copyData() (in module ClearMap.IO.NRRD)|hyperpage}{50}
\indexentry{test() (in module ClearMap.IO.NRRD)|hyperpage}{51}
\indexentry{ClearMap.IO.RAW (module)|hyperpage}{51}
\indexentry{dataSize() (in module ClearMap.IO.RAW)|hyperpage}{51}
\indexentry{dataZSize() (in module ClearMap.IO.RAW)|hyperpage}{51}
\indexentry{readData() (in module ClearMap.IO.RAW)|hyperpage}{51}
\indexentry{writeHeader() (in module ClearMap.IO.RAW)|hyperpage}{51}
\indexentry{writeRawData() (in module ClearMap.IO.RAW)|hyperpage}{52}
\indexentry{writeData() (in module ClearMap.IO.RAW)|hyperpage}{52}
\indexentry{copyData() (in module ClearMap.IO.RAW)|hyperpage}{52}
\indexentry{test() (in module ClearMap.IO.RAW)|hyperpage}{52}
\indexentry{ClearMap.IO.TIF (module)|hyperpage}{52}
\indexentry{dataSize() (in module ClearMap.IO.TIF)|hyperpage}{52}
\indexentry{dataZSize() (in module ClearMap.IO.TIF)|hyperpage}{53}
\indexentry{readData() (in module ClearMap.IO.TIF)|hyperpage}{53}
\indexentry{writeData() (in module ClearMap.IO.TIF)|hyperpage}{53}
\indexentry{copyData() (in module ClearMap.IO.TIF)|hyperpage}{53}
\indexentry{test() (in module ClearMap.IO.TIF)|hyperpage}{53}
\indexentry{ClearMap.IO.VTK (module)|hyperpage}{53}
\indexentry{writePoints() (in module ClearMap.IO.VTK)|hyperpage}{53}
\indexentry{readPoints() (in module ClearMap.IO.VTK)|hyperpage}{54}
\indexentry{ClearMap.Alignment (module)|hyperpage}{54}
\indexentry{ClearMap.Alignment.Elastix (module)|hyperpage}{54}
\indexentry{ElastixBinary (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{ElastixLib (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{TransformixBinary (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{Initialized (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{printSettings() (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{setElastixLibraryPath() (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{initializeElastix() (in module ClearMap.Alignment.Elastix)|hyperpage}{55}
\indexentry{checkElastixInitialized() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{getTransformParameterFile() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{setPathTransformParameterFiles() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{parseElastixOutputPoints() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{getTransformFileSizeAndSpacing() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{getResultDataFile() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{setTransformFileSizeAndSpacing() (in module ClearMap.Alignment.Elastix)|hyperpage}{56}
\indexentry{rescaleSizeAndSpacing() (in module ClearMap.Alignment.Elastix)|hyperpage}{57}
\indexentry{alignData() (in module ClearMap.Alignment.Elastix)|hyperpage}{57}
\indexentry{transformData() (in module ClearMap.Alignment.Elastix)|hyperpage}{57}
\indexentry{deformationField() (in module ClearMap.Alignment.Elastix)|hyperpage}{57}
\indexentry{deformationDistance() (in module ClearMap.Alignment.Elastix)|hyperpage}{58}
\indexentry{writePoints() (in module ClearMap.Alignment.Elastix)|hyperpage}{58}
\indexentry{transformPoints() (in module ClearMap.Alignment.Elastix)|hyperpage}{58}
\indexentry{test() (in module ClearMap.Alignment.Elastix)|hyperpage}{58}
\indexentry{ClearMap.Alignment.Resampling (module)|hyperpage}{59}
\indexentry{fixOrientation() (in module ClearMap.Alignment.Resampling)|hyperpage}{59}
\indexentry{inverseOrientation() (in module ClearMap.Alignment.Resampling)|hyperpage}{60}
\indexentry{orientationToPermuation() (in module ClearMap.Alignment.Resampling)|hyperpage}{60}
\indexentry{orientResolution() (in module ClearMap.Alignment.Resampling)|hyperpage}{60}
\indexentry{orientResolutionInverse() (in module ClearMap.Alignment.Resampling)|hyperpage}{60}
\indexentry{orientDataSize() (in module ClearMap.Alignment.Resampling)|hyperpage}{60}
\indexentry{orientDataSizeInverse() (in module ClearMap.Alignment.Resampling)|hyperpage}{61}
\indexentry{resampleDataSize() (in module ClearMap.Alignment.Resampling)|hyperpage}{61}
\indexentry{fixInterpolation() (in module ClearMap.Alignment.Resampling)|hyperpage}{61}
\indexentry{resampleXY() (in module ClearMap.Alignment.Resampling)|hyperpage}{61}
\indexentry{resampleData() (in module ClearMap.Alignment.Resampling)|hyperpage}{61}
\indexentry{resampleDataInverse() (in module ClearMap.Alignment.Resampling)|hyperpage}{62}
\indexentry{resamplePoints() (in module ClearMap.Alignment.Resampling)|hyperpage}{63}
\indexentry{resamplePointsInverse() (in module ClearMap.Alignment.Resampling)|hyperpage}{63}
\indexentry{sagittalToCoronalData() (in module ClearMap.Alignment.Resampling)|hyperpage}{64}
\indexentry{ClearMap.ImageProcessing (module)|hyperpage}{64}
\indexentry{ClearMap.ImageProcessing.StackProcessing (module)|hyperpage}{65}
\indexentry{printSubStackInfo() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{66}
\indexentry{writeSubStack() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{66}
\indexentry{joinPoints() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{66}
\indexentry{calculateChunkSize() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{66}
\indexentry{calculateSubStacks() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{67}
\indexentry{noProcessing() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{67}
\indexentry{parallelProcessStack() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{67}
\indexentry{sequentiallyProcessStack() (in module ClearMap.ImageProcessing.StackProcessing)|hyperpage}{68}
\indexentry{ClearMap.ImageProcessing.CellDetection (module)|hyperpage}{68}
\indexentry{detectCells() (in module ClearMap.ImageProcessing.CellDetection)|hyperpage}{69}
\indexentry{ClearMap.ImageProcessing.CellSizeDetection (module)|hyperpage}{69}
\indexentry{detectCellShape() (in module ClearMap.ImageProcessing.CellSizeDetection)|hyperpage}{69}
\indexentry{findCellSize() (in module ClearMap.ImageProcessing.CellSizeDetection)|hyperpage}{70}
\indexentry{findCellIntensity() (in module ClearMap.ImageProcessing.CellSizeDetection)|hyperpage}{70}
\indexentry{ClearMap.ImageProcessing.Filter (module)|hyperpage}{71}
\indexentry{ClearMap.ImageProcessing.Filter.LinearFilter (module)|hyperpage}{71}
\indexentry{filterLinear() (in module ClearMap.ImageProcessing.Filter.LinearFilter)|hyperpage}{71}
\indexentry{ClearMap.ImageProcessing.Filter.DoGFilter (module)|hyperpage}{71}
\indexentry{filterDoG() (in module ClearMap.ImageProcessing.Filter.DoGFilter)|hyperpage}{71}
\indexentry{ClearMap.ImageProcessing.Filter.Convolution (module)|hyperpage}{72}
\indexentry{convolve() (in module ClearMap.ImageProcessing.Filter.Convolution)|hyperpage}{72}
\indexentry{ClearMap.ImageProcessing.Filter.FilterKernel (module)|hyperpage}{72}
\indexentry{filterKernel() (in module ClearMap.ImageProcessing.Filter.FilterKernel)|hyperpage}{72}
\indexentry{filterKernel2D() (in module ClearMap.ImageProcessing.Filter.FilterKernel)|hyperpage}{73}
\indexentry{filterKernel3D() (in module ClearMap.ImageProcessing.Filter.FilterKernel)|hyperpage}{73}
\indexentry{test() (in module ClearMap.ImageProcessing.Filter.FilterKernel)|hyperpage}{73}
\indexentry{ClearMap.ImageProcessing.Filter.StructureElement (module)|hyperpage}{73}
\indexentry{structureElement() (in module ClearMap.ImageProcessing.Filter.StructureElement)|hyperpage}{73}
\indexentry{structureElementOffsets() (in module ClearMap.ImageProcessing.Filter.StructureElement)|hyperpage}{74}
\indexentry{structureElement2D() (in module ClearMap.ImageProcessing.Filter.StructureElement)|hyperpage}{74}
\indexentry{structureElement3D() (in module ClearMap.ImageProcessing.Filter.StructureElement)|hyperpage}{74}
\indexentry{ClearMap.ImageProcessing.IlluminationCorrection (module)|hyperpage}{74}
\indexentry{DefaultFlatFieldLineFile (in module ClearMap.ImageProcessing.IlluminationCorrection)|hyperpage}{74}
\indexentry{correctIllumination() (in module ClearMap.ImageProcessing.IlluminationCorrection)|hyperpage}{74}
\indexentry{flatfieldFromLine() (in module ClearMap.ImageProcessing.IlluminationCorrection)|hyperpage}{75}
\indexentry{flatfieldLineFromRegression() (in module ClearMap.ImageProcessing.IlluminationCorrection)|hyperpage}{75}
\indexentry{ClearMap.ImageProcessing.BackgroundRemoval (module)|hyperpage}{76}
\indexentry{removeBackground() (in module ClearMap.ImageProcessing.BackgroundRemoval)|hyperpage}{76}
\indexentry{ClearMap.ImageProcessing.GreyReconstruction (module)|hyperpage}{76}
\indexentry{reconstruct() (in module ClearMap.ImageProcessing.GreyReconstruction)|hyperpage}{76}
\indexentry{greyReconstruction() (in module ClearMap.ImageProcessing.GreyReconstruction)|hyperpage}{77}
\indexentry{ClearMap.ImageProcessing.SpotDetection (module)|hyperpage}{77}
\indexentry{detectSpots() (in module ClearMap.ImageProcessing.SpotDetection)|hyperpage}{78}
\indexentry{test() (in module ClearMap.ImageProcessing.SpotDetection)|hyperpage}{79}
\indexentry{ClearMap.ImageProcessing.MaximaDetection (module)|hyperpage}{79}
\indexentry{hMaxTransform() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{79}
\indexentry{localMax() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{79}
\indexentry{extendedMax() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{79}
\indexentry{findExtendedMaxima() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{79}
\indexentry{findCenterOfMaxima() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{80}
\indexentry{findPixelCoordinates() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{80}
\indexentry{findIntensity() (in module ClearMap.ImageProcessing.MaximaDetection)|hyperpage}{80}
\indexentry{ClearMap.ImageProcessing.IlastikClassification (module)|hyperpage}{81}
\indexentry{isInitialized() (in module ClearMap.ImageProcessing.IlastikClassification)|hyperpage}{81}
\indexentry{checkInitialized() (in module ClearMap.ImageProcessing.IlastikClassification)|hyperpage}{81}
\indexentry{classifyPixel() (in module ClearMap.ImageProcessing.IlastikClassification)|hyperpage}{81}
\indexentry{classifyCells() (in module ClearMap.ImageProcessing.IlastikClassification)|hyperpage}{82}
\indexentry{ClearMap.ImageProcessing.ImageStatistics (module)|hyperpage}{82}
\indexentry{calculateStatistics() (in module ClearMap.ImageProcessing.ImageStatistics)|hyperpage}{82}
\indexentry{calculateStatisticsOnStack() (in module ClearMap.ImageProcessing.ImageStatistics)|hyperpage}{83}
\indexentry{joinStatistics() (in module ClearMap.ImageProcessing.ImageStatistics)|hyperpage}{83}
\indexentry{ClearMap.Analysis (module)|hyperpage}{84}
\indexentry{ClearMap.Analysis.Tools (module)|hyperpage}{84}
\indexentry{ClearMap.Analysis.Tools.Extrapolate (module)|hyperpage}{84}
\indexentry{extrap1d() (in module ClearMap.Analysis.Tools.Extrapolate)|hyperpage}{84}
\indexentry{extrap1dFromInterp1d() (in module ClearMap.Analysis.Tools.Extrapolate)|hyperpage}{84}
\indexentry{ClearMap.Analysis.Tools.MultipleComparisonCorrection (module)|hyperpage}{85}
\indexentry{correctPValues() (in module ClearMap.Analysis.Tools.MultipleComparisonCorrection)|hyperpage}{85}
\indexentry{estimateQValues() (in module ClearMap.Analysis.Tools.MultipleComparisonCorrection)|hyperpage}{85}
\indexentry{ClearMap.Analysis.Tools.StatisticalTests (module)|hyperpage}{86}
\indexentry{testCramerVonMises2Sample() (in module ClearMap.Analysis.Tools.StatisticalTests)|hyperpage}{86}
\indexentry{ClearMap.Analysis.Label (module)|hyperpage}{86}
\indexentry{DefaultLabeledImageFile (in module ClearMap.Analysis.Label)|hyperpage}{86}
\indexentry{DefaultAnnotationFile (in module ClearMap.Analysis.Label)|hyperpage}{86}
\indexentry{LabelRecord (class in ClearMap.Analysis.Label)|hyperpage}{86}
\indexentry{\_\_getnewargs\_\_() (LabelRecord method)|hyperpage}{87}
\indexentry{\_\_getstate\_\_() (LabelRecord method)|hyperpage}{87}
\indexentry{\_\_repr\_\_() (LabelRecord method)|hyperpage}{87}
\indexentry{acronym (LabelRecord attribute)|hyperpage}{87}
\indexentry{collapse (LabelRecord attribute)|hyperpage}{87}
\indexentry{color (LabelRecord attribute)|hyperpage}{87}
\indexentry{id (LabelRecord attribute)|hyperpage}{87}
\indexentry{name (LabelRecord attribute)|hyperpage}{87}
\indexentry{parent (LabelRecord attribute)|hyperpage}{87}
\indexentry{LabelInfo (class in ClearMap.Analysis.Label)|hyperpage}{87}
\indexentry{ids (LabelInfo attribute)|hyperpage}{87}
\indexentry{names (LabelInfo attribute)|hyperpage}{87}
\indexentry{acronyms (LabelInfo attribute)|hyperpage}{87}
\indexentry{colors (LabelInfo attribute)|hyperpage}{87}
\indexentry{parents (LabelInfo attribute)|hyperpage}{87}
\indexentry{levels (LabelInfo attribute)|hyperpage}{87}
\indexentry{collapse (LabelInfo attribute)|hyperpage}{87}
\indexentry{collapseMap (LabelInfo attribute)|hyperpage}{87}
\indexentry{initialize() (LabelInfo method)|hyperpage}{87}
\indexentry{name() (LabelInfo method)|hyperpage}{87}
\indexentry{acronym() (LabelInfo method)|hyperpage}{87}
\indexentry{color() (LabelInfo method)|hyperpage}{87}
\indexentry{parent() (LabelInfo method)|hyperpage}{87}
\indexentry{level() (LabelInfo method)|hyperpage}{87}
\indexentry{toLabelAtLevel() (LabelInfo method)|hyperpage}{87}
\indexentry{toLabelAtCollapseMap() (LabelInfo method)|hyperpage}{87}
\indexentry{toLabelAtCollapse() (LabelInfo method)|hyperpage}{87}
\indexentry{Label (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{initialize() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{labelAtLevel() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{labelAtCollapse() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{labelPoints() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{countPointsInRegions() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{labelToName() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{labelToAcronym() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{labelToColor() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{writePAL() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{writeLUT() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{makeColorPalette() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{makeColorAnnotations() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{test() (in module ClearMap.Analysis.Label)|hyperpage}{88}
\indexentry{ClearMap.Analysis.Statistics (module)|hyperpage}{88}
\indexentry{readDataGroup() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{readPointsGroup() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{tTestVoxelization() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{cutoffPValues() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{colorPValues() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{mean() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{std() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{var() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{thresholdPoints() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{weightsFromPrecentiles() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{countPointsGroupInRegions() (in module ClearMap.Analysis.Statistics)|hyperpage}{88}
\indexentry{tTestPointsInRegions() (in module ClearMap.Analysis.Statistics)|hyperpage}{89}
\indexentry{testCompletedCumulatives() (in module ClearMap.Analysis.Statistics)|hyperpage}{89}
\indexentry{testCompletedInvertedCumulatives() (in module ClearMap.Analysis.Statistics)|hyperpage}{89}
\indexentry{testCompletedCumulativesInSpheres() (in module ClearMap.Analysis.Statistics)|hyperpage}{89}
\indexentry{test() (in module ClearMap.Analysis.Statistics)|hyperpage}{89}
\indexentry{ClearMap.Analysis.Voxelization (module)|hyperpage}{89}
\indexentry{voxelize() (in module ClearMap.Analysis.Voxelization)|hyperpage}{89}
\indexentry{voxelizePixel() (in module ClearMap.Analysis.Voxelization)|hyperpage}{89}
\indexentry{test() (in module ClearMap.Analysis.Voxelization)|hyperpage}{90}
\indexentry{ClearMap.Visualization (module)|hyperpage}{90}
\indexentry{ClearMap.Visualization.Plot (module)|hyperpage}{90}
\indexentry{plotTiling() (in module ClearMap.Visualization.Plot)|hyperpage}{90}
\indexentry{overlayLabel() (in module ClearMap.Visualization.Plot)|hyperpage}{90}
\indexentry{plotOverlayLabel() (in module ClearMap.Visualization.Plot)|hyperpage}{91}
\indexentry{overlayPoints() (in module ClearMap.Visualization.Plot)|hyperpage}{91}
\indexentry{plotOverlayPoints() (in module ClearMap.Visualization.Plot)|hyperpage}{91}
\indexentry{test() (in module ClearMap.Visualization.Plot)|hyperpage}{91}
\indexentry{ClearMap.Parameter (module)|hyperpage}{92}
\indexentry{detectCellParameter (in module ClearMap.Parameter)|hyperpage}{92}
\indexentry{IlastikParameter (in module ClearMap.Parameter)|hyperpage}{92}
\indexentry{processStackParameter (in module ClearMap.Parameter)|hyperpage}{92}
\indexentry{AlignmentParameter (in module ClearMap.Parameter)|hyperpage}{92}
\indexentry{ResamplingParameter (in module ClearMap.Parameter)|hyperpage}{93}
\indexentry{VoxelizationParameter (in module ClearMap.Parameter)|hyperpage}{93}
\indexentry{ClearMap.Settings (module)|hyperpage}{93}
\indexentry{IlastikPath (in module ClearMap.Settings)|hyperpage}{93}
\indexentry{ElastixPath (in module ClearMap.Settings)|hyperpage}{93}
\indexentry{setup() (in module ClearMap.Settings)|hyperpage}{94}
\indexentry{clearMapPath() (in module ClearMap.Settings)|hyperpage}{94}
\indexentry{ClearMapPath (in module ClearMap.Settings)|hyperpage}{94}
\indexentry{ClearMap.Utils (module)|hyperpage}{94}
\indexentry{ClearMap.Utils.ParameterTools (module)|hyperpage}{94}
\indexentry{getParameter() (in module ClearMap.Utils.ParameterTools)|hyperpage}{94}
\indexentry{writeParameter() (in module ClearMap.Utils.ParameterTools)|hyperpage}{94}
\indexentry{joinParameter() (in module ClearMap.Utils.ParameterTools)|hyperpage}{94}
\indexentry{ClearMap.Utils.ProcessWriter (module)|hyperpage}{95}
\indexentry{ProcessWriter (class in ClearMap.Utils.ProcessWriter)|hyperpage}{95}
\indexentry{process (ProcessWriter attribute)|hyperpage}{95}
\indexentry{writeString() (ProcessWriter method)|hyperpage}{95}
\indexentry{write() (ProcessWriter method)|hyperpage}{95}
\indexentry{ClearMap.Utils.Timer (module)|hyperpage}{95}
\indexentry{Timer (class in ClearMap.Utils.Timer)|hyperpage}{95}
\indexentry{time (Timer attribute)|hyperpage}{95}
\indexentry{start() (Timer method)|hyperpage}{95}
\indexentry{reset() (Timer method)|hyperpage}{95}
\indexentry{elapsedTime() (Timer method)|hyperpage}{95}
\indexentry{printElapsedTime() (Timer method)|hyperpage}{96}
\indexentry{formatElapsedTime() (Timer method)|hyperpage}{96}