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SegmentCRImage

Segments a directory of images with a method tuned for HE images.

Method described in "Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling" by Y. Yuan, H. Failmezger, O. M. Rueda, H. R. Ali, S. Graf, S.-F. Chin, R. F. Schwarz, C. Curtis, Mark J. Dunning, Helen Bardwell, Nicola Johnson, Sarah Doyle, Gulisa Turashvili, Elena Provenzano, Sam Aparicio, Carlos Caldas and Florian Markowetz - November 21, 2012

Version 1.0
Bundle anima
Categories
Authors Ville Rantanen (ville.rantanen@helsinki.fi)
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Requires R ; libtiff5-dev (DEB) ; libfftw3-dev (DEB) ; EBImage (R-package) ; CRImage (R-package)
Source files component.xml segment.crimage.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in ImageList Mandatory A directory with image files.

Outputs

Name Type Description
mask ImageList BW PNG images.
perimeter ImageList BW PNG images of the perimeter of the mask.
features CSV Featured measured from images.

Parameters

Name Type Default Description
failureRegion float 2000 Dark regions which exceed this value will be deleted
maxArea float 800 Maximum accepted pixel area in all methods.
method string "Otsu" Method for image segmentation. Choose from 'Otsu', 'Phansalkar'.
minArea float 1 Minimum accepted pixel area in all methods.
numWindows int 5 Number of separate thresholdings

Test cases

Test case Parameters IN
in
OUT
mask
OUT
perimeter
OUT
features
test1_basic (missing) in mask perimeter features

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