Index

_

__getnewargs__() (LabelRecord method) __getstate__() (LabelRecord method)

__repr__() (LabelRecord method)

A

acronym (LabelRecord attribute) acronym() (LabelInfo method) acronyms (LabelInfo attribute)

alignData() (in module ClearMap.Alignment.Elastix) AlignmentParameter (in module ClearMap.Parameter)

C

calculateChunkSize() (in module ClearMap.ImageProcessing.StackProcessing) calculateStatistics() (in module ClearMap.ImageProcessing.ImageStatistics) calculateStatisticsOnStack() (in module ClearMap.ImageProcessing.ImageStatistics) calculateSubStacks() (in module ClearMap.ImageProcessing.StackProcessing) checkElastixInitialized() (in module ClearMap.Alignment.Elastix) checkInitialized() (in module ClearMap.ImageProcessing.IlastikClassification) classifyCells() (in module ClearMap.ImageProcessing.IlastikClassification) classifyPixel() (in module ClearMap.ImageProcessing.IlastikClassification) ClearMap (module) ClearMap.Alignment (module) ClearMap.Alignment.Elastix (module) ClearMap.Alignment.Resampling (module) ClearMap.Analysis (module) ClearMap.Analysis.Label (module) ClearMap.Analysis.Statistics (module) ClearMap.Analysis.Tools (module) ClearMap.Analysis.Tools.Extrapolate (module) ClearMap.Analysis.Tools.MultipleComparisonCorrection (module) ClearMap.Analysis.Tools.StatisticalTests (module) ClearMap.Analysis.Voxelization (module) ClearMap.ImageProcessing (module) ClearMap.ImageProcessing.BackgroundRemoval (module) ClearMap.ImageProcessing.CellDetection (module) ClearMap.ImageProcessing.CellSizeDetection (module) ClearMap.ImageProcessing.Filter (module) ClearMap.ImageProcessing.Filter.Convolution (module) ClearMap.ImageProcessing.Filter.DoGFilter (module) ClearMap.ImageProcessing.Filter.FilterKernel (module) ClearMap.ImageProcessing.Filter.LinearFilter (module) ClearMap.ImageProcessing.Filter.StructureElement (module) ClearMap.ImageProcessing.GreyReconstruction (module) ClearMap.ImageProcessing.IlastikClassification (module) ClearMap.ImageProcessing.IlluminationCorrection (module) ClearMap.ImageProcessing.ImageStatistics (module) ClearMap.ImageProcessing.MaximaDetection (module) ClearMap.ImageProcessing.SpotDetection (module) ClearMap.ImageProcessing.StackProcessing (module)

ClearMap.IO (module) ClearMap.IO.CSV (module) ClearMap.IO.FileList (module) ClearMap.IO.Imaris (module) ClearMap.IO.IO (module) ClearMap.IO.NPY (module) ClearMap.IO.NRRD (module) ClearMap.IO.RAW (module) ClearMap.IO.TIF (module) ClearMap.IO.VTK (module) ClearMap.Parameter (module) ClearMap.Settings (module) ClearMap.Utils (module) ClearMap.Utils.ParameterTools (module) ClearMap.Utils.ProcessWriter (module) ClearMap.Utils.Timer (module) ClearMap.Visualization (module) ClearMap.Visualization.Plot (module) ClearMapPath (in module ClearMap.Settings) clearMapPath() (in module ClearMap.Settings) closeFile() (in module ClearMap.IO.Imaris) collapse (LabelInfo attribute) (LabelRecord attribute) collapseMap (LabelInfo attribute) color (LabelRecord attribute) color() (LabelInfo method) colorPValues() (in module ClearMap.Analysis.Statistics) colors (LabelInfo attribute) convertData() (in module ClearMap.IO.IO) convolve() (in module ClearMap.ImageProcessing.Filter.Convolution) copyData() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.RAW) (in module ClearMap.IO.TIF) copyFile() (in module ClearMap.IO.IO) correctIllumination() (in module ClearMap.ImageProcessing.IlluminationCorrection) correctPValues() (in module ClearMap.Analysis.Tools.MultipleComparisonCorrection) countPointsGroupInRegions() (in module ClearMap.Analysis.Statistics) countPointsInRegions() (in module ClearMap.Analysis.Label) createDirectory() (in module ClearMap.IO.IO) cutoffPValues() (in module ClearMap.Analysis.Statistics)

D

dataFileExtensions (in module ClearMap.IO.IO) dataFileExtensionToType (in module ClearMap.IO.IO) dataFileNameToModule() (in module ClearMap.IO.IO) dataFileNameToType() (in module ClearMap.IO.IO) dataFileTypes (in module ClearMap.IO.IO) dataSize() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.RAW) (in module ClearMap.IO.TIF) dataSizeFromDataRange() (in module ClearMap.IO.IO) dataToRange() (in module ClearMap.IO.IO) dataZSize() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.RAW) (in module ClearMap.IO.TIF)

DefaultAnnotationFile (in module ClearMap.Analysis.Label) DefaultFlatFieldLineFile (in module ClearMap.ImageProcessing.IlluminationCorrection) DefaultLabeledImageFile (in module ClearMap.Analysis.Label) deformationDistance() (in module ClearMap.Alignment.Elastix) deformationField() (in module ClearMap.Alignment.Elastix) detectCellParameter (in module ClearMap.Parameter) detectCells() (in module ClearMap.ImageProcessing.CellDetection) detectCellShape() (in module ClearMap.ImageProcessing.CellSizeDetection) detectSpots() (in module ClearMap.ImageProcessing.SpotDetection)

E

elapsedTime() (Timer method) ElastixBinary (in module ClearMap.Alignment.Elastix) ElastixLib (in module ClearMap.Alignment.Elastix) ElastixPath (in module ClearMap.Settings)

estimateQValues() (in module ClearMap.Analysis.Tools.MultipleComparisonCorrection) extendedMax() (in module ClearMap.ImageProcessing.MaximaDetection) extrap1d() (in module ClearMap.Analysis.Tools.Extrapolate) extrap1dFromInterp1d() (in module ClearMap.Analysis.Tools.Extrapolate)

F

fileExpressionToFileName() (in module ClearMap.IO.FileList) fileExtension() (in module ClearMap.IO.IO) filterDoG() (in module ClearMap.ImageProcessing.Filter.DoGFilter) filterKernel() (in module ClearMap.ImageProcessing.Filter.FilterKernel) filterKernel2D() (in module ClearMap.ImageProcessing.Filter.FilterKernel) filterKernel3D() (in module ClearMap.ImageProcessing.Filter.FilterKernel) filterLinear() (in module ClearMap.ImageProcessing.Filter.LinearFilter) findCellIntensity() (in module ClearMap.ImageProcessing.CellSizeDetection) findCellSize() (in module ClearMap.ImageProcessing.CellSizeDetection)

findCenterOfMaxima() (in module ClearMap.ImageProcessing.MaximaDetection) findExtendedMaxima() (in module ClearMap.ImageProcessing.MaximaDetection) findIntensity() (in module ClearMap.ImageProcessing.MaximaDetection) findPixelCoordinates() (in module ClearMap.ImageProcessing.MaximaDetection) fixInterpolation() (in module ClearMap.Alignment.Resampling) fixOrientation() (in module ClearMap.Alignment.Resampling) flatfieldFromLine() (in module ClearMap.ImageProcessing.IlluminationCorrection) flatfieldLineFromRegression() (in module ClearMap.ImageProcessing.IlluminationCorrection) formatElapsedTime() (Timer method)

G

getDataExtent() (in module ClearMap.IO.Imaris) getDataSize() (in module ClearMap.IO.Imaris) getParameter() (in module ClearMap.Utils.ParameterTools) getResultDataFile() (in module ClearMap.Alignment.Elastix)

getScaleAndOffset() (in module ClearMap.IO.Imaris) getTransformFileSizeAndSpacing() (in module ClearMap.Alignment.Elastix) getTransformParameterFile() (in module ClearMap.Alignment.Elastix) greyReconstruction() (in module ClearMap.ImageProcessing.GreyReconstruction)

H

hMaxTransform() (in module ClearMap.ImageProcessing.MaximaDetection)

I

id (LabelRecord attribute) ids (LabelInfo attribute) IlastikParameter (in module ClearMap.Parameter) IlastikPath (in module ClearMap.Settings) initialize() (in module ClearMap.Analysis.Label) (LabelInfo method) Initialized (in module ClearMap.Alignment.Elastix) initializeElastix() (in module ClearMap.Alignment.Elastix)

inverseOrientation() (in module ClearMap.Alignment.Resampling) isDataFile() (in module ClearMap.IO.IO) isFile() (in module ClearMap.IO.IO) isFileExpression() (in module ClearMap.IO.IO) isInitialized() (in module ClearMap.ImageProcessing.IlastikClassification) isPointFile() (in module ClearMap.IO.IO)

J

joinParameter() (in module ClearMap.Utils.ParameterTools) joinPoints() (in module ClearMap.ImageProcessing.StackProcessing)

joinStatistics() (in module ClearMap.ImageProcessing.ImageStatistics)

L

Label (in module ClearMap.Analysis.Label) labelAtCollapse() (in module ClearMap.Analysis.Label) labelAtLevel() (in module ClearMap.Analysis.Label) LabelInfo (class in ClearMap.Analysis.Label) labelPoints() (in module ClearMap.Analysis.Label) LabelRecord (class in ClearMap.Analysis.Label)

labelToAcronym() (in module ClearMap.Analysis.Label) labelToColor() (in module ClearMap.Analysis.Label) labelToName() (in module ClearMap.Analysis.Label) level() (LabelInfo method) levels (LabelInfo attribute) localMax() (in module ClearMap.ImageProcessing.MaximaDetection)

M

makeColorAnnotations() (in module ClearMap.Analysis.Label) makeColorPalette() (in module ClearMap.Analysis.Label)

mean() (in module ClearMap.Analysis.Statistics)

N

name (LabelRecord attribute) name() (LabelInfo method) names (LabelInfo attribute)

noProcessing() (in module ClearMap.ImageProcessing.StackProcessing) NrrdError

O

openFile() (in module ClearMap.IO.Imaris) orientationToPermuation() (in module ClearMap.Alignment.Resampling) orientDataSize() (in module ClearMap.Alignment.Resampling) orientDataSizeInverse() (in module ClearMap.Alignment.Resampling)

orientResolution() (in module ClearMap.Alignment.Resampling) orientResolutionInverse() (in module ClearMap.Alignment.Resampling) overlayLabel() (in module ClearMap.Visualization.Plot) overlayPoints() (in module ClearMap.Visualization.Plot)

P

parallelProcessStack() (in module ClearMap.ImageProcessing.StackProcessing) parent (LabelRecord attribute) parent() (LabelInfo method) parents (LabelInfo attribute) parse_nrrdvector() (in module ClearMap.IO.NRRD) parse_optional_nrrdvector() (in module ClearMap.IO.NRRD) parseElastixOutputPoints() (in module ClearMap.Alignment.Elastix) plotOverlayLabel() (in module ClearMap.Visualization.Plot) plotOverlayPoints() (in module ClearMap.Visualization.Plot) plotTiling() (in module ClearMap.Visualization.Plot) pointFileExtensions (in module ClearMap.IO.IO) pointFileExtensionToType (in module ClearMap.IO.IO) pointFileNameToModule() (in module ClearMap.IO.IO) pointFileNameToType() (in module ClearMap.IO.IO)

pointFileTypes (in module ClearMap.IO.IO) pointShiftFromRange() (in module ClearMap.IO.IO) pointsToCoordinates() (in module ClearMap.IO.IO) pointsToCoordinatesAndProperties() (in module ClearMap.IO.IO) pointsToCoordinatesAndPropertiesFileNames() (in module ClearMap.IO.IO) pointsToProperties() (in module ClearMap.IO.IO) pointsToRange() (in module ClearMap.IO.IO) printElapsedTime() (Timer method) printSettings() (in module ClearMap.Alignment.Elastix) printSubStackInfo() (in module ClearMap.ImageProcessing.StackProcessing) process (ProcessWriter attribute) processStackParameter (in module ClearMap.Parameter) ProcessWriter (class in ClearMap.Utils.ProcessWriter)

R

readData() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.RAW) (in module ClearMap.IO.TIF) readDataFiles() (in module ClearMap.IO.FileList) readDataGroup() (in module ClearMap.Analysis.Statistics) readDataSet() (in module ClearMap.IO.Imaris) readFileList() (in module ClearMap.IO.FileList) readHeader() (in module ClearMap.IO.NRRD) readPoints() (in module ClearMap.IO.CSV) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NPY) (in module ClearMap.IO.VTK) readPointsGroup() (in module ClearMap.Analysis.Statistics) reconstruct() (in module ClearMap.ImageProcessing.GreyReconstruction) removeBackground() (in module ClearMap.ImageProcessing.BackgroundRemoval)

resampleData() (in module ClearMap.Alignment.Resampling) resampleDataInverse() (in module ClearMap.Alignment.Resampling) resampleDataSize() (in module ClearMap.Alignment.Resampling) resamplePoints() (in module ClearMap.Alignment.Resampling) resamplePointsInverse() (in module ClearMap.Alignment.Resampling) resampleXY() (in module ClearMap.Alignment.Resampling) ResamplingParameter (in module ClearMap.Parameter) rescaleSizeAndSpacing() (in module ClearMap.Alignment.Elastix) reset() (Timer method)

S

sagittalToCoronalData() (in module ClearMap.Alignment.Resampling) sequentiallyProcessStack() (in module ClearMap.ImageProcessing.StackProcessing) setElastixLibraryPath() (in module ClearMap.Alignment.Elastix) setPathTransformParameterFiles() (in module ClearMap.Alignment.Elastix) setTransformFileSizeAndSpacing() (in module ClearMap.Alignment.Elastix) setup() (in module ClearMap.Settings) splitFileExpression() (in module ClearMap.IO.FileList)

start() (Timer method) std() (in module ClearMap.Analysis.Statistics) structureElement() (in module ClearMap.ImageProcessing.Filter.StructureElement) structureElement2D() (in module ClearMap.ImageProcessing.Filter.StructureElement) structureElement3D() (in module ClearMap.ImageProcessing.Filter.StructureElement) structureElementOffsets() (in module ClearMap.ImageProcessing.Filter.StructureElement)

T

test() (in module ClearMap.Alignment.Elastix) (in module ClearMap.Analysis.Label) (in module ClearMap.Analysis.Statistics) (in module ClearMap.Analysis.Voxelization) (in module ClearMap.IO.CSV) (in module ClearMap.IO.FileList) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NPY) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.RAW) (in module ClearMap.IO.TIF) (in module ClearMap.ImageProcessing.Filter.FilterKernel) (in module ClearMap.ImageProcessing.SpotDetection) (in module ClearMap.Visualization.Plot) testCompletedCumulatives() (in module ClearMap.Analysis.Statistics) testCompletedCumulativesInSpheres() (in module ClearMap.Analysis.Statistics) testCompletedInvertedCumulatives() (in module ClearMap.Analysis.Statistics) testCramerVonMises2Sample() (in module ClearMap.Analysis.Tools.StatisticalTests) thresholdPoints() (in module ClearMap.Analysis.Statistics) time (Timer attribute) Timer (class in ClearMap.Utils.Timer) toDataRange() (in module ClearMap.IO.IO) toDataSize() (in module ClearMap.IO.IO)

toLabelAtCollapse() (LabelInfo method) toLabelAtCollapseMap() (LabelInfo method) toLabelAtLevel() (LabelInfo method) toMultiChannelData() (in module ClearMap.IO.IO) transformData() (in module ClearMap.Alignment.Elastix) TransformixBinary (in module ClearMap.Alignment.Elastix) transformPoints() (in module ClearMap.Alignment.Elastix) transformPointsToImaris() (in module ClearMap.IO.Imaris) tTestPointsInRegions() (in module ClearMap.Analysis.Statistics) tTestVoxelization() (in module ClearMap.Analysis.Statistics)

V

var() (in module ClearMap.Analysis.Statistics) VoxelizationParameter (in module ClearMap.Parameter)

voxelize() (in module ClearMap.Analysis.Voxelization) voxelizePixel() (in module ClearMap.Analysis.Voxelization)

W

weightsFromPrecentiles() (in module ClearMap.Analysis.Statistics) write() (ProcessWriter method) writeData() (in module ClearMap.IO.FileList) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NRRD) (in module ClearMap.IO.RAW) (in module ClearMap.IO.TIF) writeHeader() (in module ClearMap.IO.RAW) writeLUT() (in module ClearMap.Analysis.Label) writePAL() (in module ClearMap.Analysis.Label)

writeParameter() (in module ClearMap.Utils.ParameterTools) writePoints() (in module ClearMap.Alignment.Elastix) (in module ClearMap.IO.CSV) (in module ClearMap.IO.IO) (in module ClearMap.IO.Imaris) (in module ClearMap.IO.NPY) (in module ClearMap.IO.VTK) writeRawData() (in module ClearMap.IO.RAW) writeString() (ProcessWriter method) writeSubStack() (in module ClearMap.ImageProcessing.StackProcessing) writeTable() (in module ClearMap.IO.IO)