ClearMap.Parameter module

ClearMap default parameter module.

This module defines default parameter used by various sub-packages.

See also

Settings

detectCellParameter = {'findExtendedMaximaParameter': {'threshold': 0, 'save': None, 'verbose': False, 'hMax': 20, 'size': 5}, 'correctIlluminationParameter': {'scaling': 'Mean', 'flatfield': True, 'save': None, 'verbose': False, 'background': None}, 'removeBackgroundParameter': {'save': None, 'verbose': False, 'size': (15, 15)}, 'filterDoGParameter': {'save': None, 'sigma2': None, 'sigma': None, 'verbose': False, 'size': (7, 7, 11)}, 'detectCellShapeParameter': {'threshold': 700, 'save': None, 'verbose': False}, 'findIntensityParameter': {'method': 'Max', 'size': (3, 3, 3)}}

dict: Paramters for cell detection using the spot detection algorithm

See also

IlastikParameter, StackProcessingParameter

IlastikParameter = {'rescale': None, 'backgroundSize': (15, 15), 'classifier': '/Test/Ilastik/classifier.h5'}

dict: Paramters for cell detection using Ilastik classification

  • “classifier”: ilastic classifier to use
  • “rescale”: rescale images before classification
  • “backgroundSize”: Background correctoin: None or (y,x) which is size of disk for gray scale opening

See also

SpotDetectionParameter, StackProcessingParameter

processStackParameter = {'chunkOptimizationSize': <built-in function all>, 'processes': 2, 'chunkSizeMin': 30, 'chunkOptimization': True, 'cChunkOverlap': 15, 'chunkSizeMax': 100}
dict: Parameter for processing an image stack in parallel
  • “processes”: max number of parallel processes
  • “chunkSizeMax” : maximal chunk size in z
  • “chunkSizeMin” : minimal chunk size in z,
  • “chunkOverlap” : overlap between two chunks,
  • “chunkOptimization”: optimize chunk size and number to number of processes
  • “chunkOptimizationSize”: increase chunk size for optimizaition (True, False or all = automatic)

See also

SpotDetectionParameter, IlastikParameter

AlignmentParameter = {'fixedImageMask': None, 'alignmentDirectory': None, 'movingImage': '/Test/Data/Elastix/150524_0_8X-s3-20HFautofluor_18-51-1-warpable.tif', 'affineParameterFile': '/Test/Elastix/ElastixParameterAffine.txt', 'bSplineParameterFile': '/Test/Elastix/ElastixParameterBSpline.txt', 'fixedImage': '/Test/Data/Elastix/OstenRefARA_v2_lowerHalf.tif'}

dict: Parameter for Elastix alignment

  • “alignmentDirectory” : directory to save the alignment result
  • “movingImage”: image to be aligned
  • “fixedImage”: reference image
  • “affineParameterFile”: elastix parameter files for affine alignment
  • “bSplineParameterFile” : elastix parameter files for non-linear alignment

See also

Elastix

ResamplingParameter = {'orientation': None, 'source': None, 'resolutionSink': (25, 25, 25), 'sink': None, 'resolutionSource': (4.0625, 4.0625, 3)}

dict: Parameter for resampling data

  • “source” : data source file
  • “sink” : data output file

“resolutionSource”: resolution of the raw data (in um / pixel) as (x,y,z)

“resolutionSink” : resolution of the reference / atlas image (in um/ pixel) as (x,y,z)

“orientation” : Orientation of the data set wrt reference as (x=1,y=2,z=3)
(-axis will invert the orientation, for other hemisphere use (-1, 2, 3), to exchnge x,y use (2,1,3) etc)

See also

Resampling

VoxelizationParameter = {'method': 'Spherical', 'voxelizationSize': (1, 1, 1)}

dict: Parameter to calculate density voxelization

  • “method”: Method to voxelize: ‘Spherical’,’Rectangular, ‘Gaussian’
  • “voxelizationSize”: max size of the volume to be voxelized

See also

voxelization