CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:10997

LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D]
    Input data file location:Default Input Folder\x7C/imaging/analysis/2006_09_29_ScreeningPaper/Roche/platemap
    Name of the file:Metadata_with_GRK_as_PosCtrl.csv
    Load images based on this data?:Yes
    Base image location:Default Input Folder\x7C.
    Process just a range of rows?:No
    Rows to process:1,100000
    Group images by metadata?:No
    Select metadata fields for grouping:
    Rescale intensities?:Yes

LoadSingleImage:[module_num:2|svn_version:\'10884\'|variable_revision_number:5|show_window:True|notes:\x5B\x5D]
    Input image file location:Default Input Folder\x7C/imaging/analysis/2006_09_29_ScreeningPaper/Roche/images/../CP2_output/IllumCorr
    Filename of the image to load (Include the extension, e.g., .tif):ILLUM_Ch0.mat
    Load as images or objects?:Images
    Name the image that will be loaded:IllumDNA
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outlines:NucleiOutlines
    Rescale intensities?:Yes
    Filename of the image to load (Include the extension, e.g., .tif):ILLUM_Ch2.mat
    Load as images or objects?:Images
    Name the image that will be loaded:IllumGFP
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outlines:NucleiOutlines
    Rescale intensities?:Yes

CorrectIlluminationApply:[module_num:3|svn_version:\'10300\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D]
    Select the input image:OrigDNA
    Name the output image:CorrDNA
    Select the illumination function:IllumDNA
    Select how the illumination function is applied:Divide
    Select the input image:OrigGFP
    Name the output image:CorrGFP
    Select the illumination function:IllumGFP
    Select how the illumination function is applied:Divide

IdentifyPrimaryObjects:[module_num:4|svn_version:\'10826\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D]
    Select the input image:CorrDNA
    Name the primary objects to be identified:Nuclei
    Typical diameter of objects, in pixel units (Min,Max):20,80
    Discard objects outside the diameter range?:Yes
    Try to merge too small objects with nearby larger objects?:No
    Discard objects touching the border of the image?:Yes
    Select the thresholding method:Otsu Global
    Threshold correction factor:1.0
    Lower and upper bounds on threshold:0,1
    Approximate fraction of image covered by objects?:0.1
    Method to distinguish clumped objects:Shape
    Method to draw dividing lines between clumped objects:Shape
    Size of smoothing filter:10
    Suppress local maxima that are closer than this minimum allowed distance:5
    Speed up by using lower-resolution image to find local maxima?:Yes
    Name the outline image:Do not save
    Fill holes in identified objects?:Yes
    Automatically calculate size of smoothing filter?:Yes
    Automatically calculate minimum allowed distance between local maxima?:Yes
    Manual threshold:0.0
    Select binary image:Otsu Global
    Retain outlines of the identified objects?:Yes
    Automatically calculate the threshold using the Otsu method?:Yes
    Enter Laplacian of Gaussian threshold:.5
    Two-class or three-class thresholding?:Two classes
    Minimize the weighted variance or the entropy?:Weighted variance
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes
    Enter LoG filter diameter:5
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Select the measurement to threshold with:None

IdentifySecondaryObjects:[module_num:5|svn_version:\'10826\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D]
    Select the input objects:Nuclei
    Name the objects to be identified:Cells
    Select the method to identify the secondary objects:Distance - N
    Select the input image:CorrGFP
    Select the thresholding method:Otsu Global
    Threshold correction factor:1
    Lower and upper bounds on threshold:0,1
    Approximate fraction of image covered by objects?:10%
    Number of pixels by which to expand the primary objects:30
    Regularization factor:0.05
    Name the outline image:Do not save
    Manual threshold:0
    Select binary image:Do not use
    Retain outlines of the identified secondary objects?:Yes
    Two-class or three-class thresholding?:Two classes
    Minimize the weighted variance or the entropy?:Weighted variance
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Discard secondary objects that touch the edge of the image?:No
    Discard the associated primary objects?:No
    Name the new primary objects:FilteredNuclei
    Retain outlines of the new primary objects?:No
    Name the new primary object outlines:FilteredNucleiOutlines
    Select the measurement to threshold with:None
    Fill holes in identified objects?:No

EnhanceOrSuppressFeatures:[module_num:6|svn_version:\'10591\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the input image:CorrGFP
    Name the output image:SpecklesGFP
    Select the operation:Enhance
    Feature size:7
    Feature type:Speckles
    Range of hole sizes:1,10

IdentifyPrimaryObjects:[module_num:7|svn_version:\'10826\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D]
    Select the input image:SpecklesGFP
    Name the primary objects to be identified:Speckles
    Typical diameter of objects, in pixel units (Min,Max):3,7
    Discard objects outside the diameter range?:No
    Try to merge too small objects with nearby larger objects?:No
    Discard objects touching the border of the image?:No
    Select the thresholding method:Otsu Global
    Threshold correction factor:6.0
    Lower and upper bounds on threshold:0.000000,1.000000
    Approximate fraction of image covered by objects?:0.01
    Method to distinguish clumped objects:Shape
    Method to draw dividing lines between clumped objects:Shape
    Size of smoothing filter:4
    Suppress local maxima that are closer than this minimum allowed distance:7
    Speed up by using lower-resolution image to find local maxima?:Yes
    Name the outline image:PrimaryOutlines
    Fill holes in identified objects?:Yes
    Automatically calculate size of smoothing filter?:No
    Automatically calculate minimum allowed distance between local maxima?:Yes
    Manual threshold:0.0
    Select binary image:None
    Retain outlines of the identified objects?:No
    Automatically calculate the threshold using the Otsu method?:Yes
    Enter Laplacian of Gaussian threshold:0.5
    Two-class or three-class thresholding?:Two classes
    Minimize the weighted variance or the entropy?:Weighted variance
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes
    Enter LoG filter diameter:5
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Select the measurement to threshold with:None

Crop:[module_num:8|svn_version:\'10804\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the input image:CorrGFP
    Name the output image:CropGFP
    Select the cropping shape:Objects
    Select the cropping method:Coordinates
    Apply which cycle\'s cropping pattern?:Every
    Left and right rectangle positions:0,end
    Top and bottom rectangle positions:0,end
    Coordinates of ellipse center:500,500
    Ellipse radius, X direction:400
    Ellipse radius, Y direction:200
    Use Plate Fix?:No
    Remove empty rows and columns?:No
    Select the masking image:None
    Select the image with a cropping mask:None
    Select the objects:Cells

IdentifyPrimaryObjects:[module_num:9|svn_version:\'10826\'|variable_revision_number:8|show_window:True|notes:\x5B\x5D]
    Select the input image:CropGFP
    Name the primary objects to be identified:SpklPerObj
    Typical diameter of objects, in pixel units (Min,Max):3,7
    Discard objects outside the diameter range?:No
    Try to merge too small objects with nearby larger objects?:No
    Discard objects touching the border of the image?:No
    Select the thresholding method:Otsu PerObject
    Threshold correction factor:1.4
    Lower and upper bounds on threshold:0.000000,1.000000
    Approximate fraction of image covered by objects?:0.01
    Method to distinguish clumped objects:Shape
    Method to draw dividing lines between clumped objects:Shape
    Size of smoothing filter:4
    Suppress local maxima that are closer than this minimum allowed distance:7
    Speed up by using lower-resolution image to find local maxima?:Yes
    Name the outline image:PrimaryOutlines
    Fill holes in identified objects?:Yes
    Automatically calculate size of smoothing filter?:No
    Automatically calculate minimum allowed distance between local maxima?:Yes
    Manual threshold:0.0
    Select binary image:None
    Retain outlines of the identified objects?:No
    Automatically calculate the threshold using the Otsu method?:Yes
    Enter Laplacian of Gaussian threshold:0.5
    Two-class or three-class thresholding?:Two classes
    Minimize the weighted variance or the entropy?:Weighted variance
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes
    Enter LoG filter diameter:5
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Select the measurement to threshold with:None

MeasureObjectSizeShape:[module_num:10|svn_version:\'1\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
    Select objects to measure:Nuclei
    Select objects to measure:Cells
    Select objects to measure:Speckles
    Select objects to measure:SpklPerObj
    Calculate the Zernike features?:Yes

MeasureObjectIntensity:[module_num:11|svn_version:\'10816\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D]
    Hidden:2
    Select an image to measure:CorrDNA
    Select an image to measure:CorrGFP
    Select objects to measure:Nuclei
    Select objects to measure:Cells
    Select objects to measure:Speckles
    Select objects to measure:SpklPerObj

MeasureTexture:[module_num:12|svn_version:\'1\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Hidden:1
    Hidden:2
    Hidden:2
    Select an image to measure:CorrGFP
    Select objects to measure:Cells
    Select objects to measure:Nuclei
    Texture scale to measure:3
    Texture scale to measure:1
    Measure Gabor features?:Yes
    Number of angles to compute for Gabor:4

MeasureImageIntensity:[module_num:13|svn_version:\'10816\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the image to measure:CorrDNA
    Measure the intensity only from areas enclosed by objects?:No
    Select the input objects:None
    Select the image to measure:CorrGFP
    Measure the intensity only from areas enclosed by objects?:No
    Select the input objects:None

MeasureCorrelation:[module_num:14|svn_version:\'10300\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Hidden:2
    Hidden:4
    Select an image to measure:CorrDNA
    Select an image to measure:CorrGFP
    Select where to measure correlation:Both
    Select an object to measure:Nuclei
    Select an object to measure:Cells
    Select an object to measure:Speckles
    Select an object to measure:SpklPerObj

MeasureObjectRadialDistribution:[module_num:15|svn_version:\'10798\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
    Hidden:1
    Hidden:1
    Hidden:1
    Select an image to measure:CorrGFP
    Select objects to measure:Cells
    Object to use as center?:Other objects
    Select objects to use as centers:Nuclei
    Number of bins:4

MeasureGranularity:[module_num:16|svn_version:\'10300\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D]
    Image count:1
    Object count:0
    Select an image to measure:CorrGFP
    Subsampling factor for granularity measurements:0.25
    Subsampling factor for background reduction:0.25
    Radius of structuring element:2
    Range of the granular spectrum:12

RelateObjects:[module_num:17|svn_version:\'10300\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the input child objects:Speckles
    Select the input parent objects:Cells
    Calculate distances?:None
    Calculate per-parent means for all child measurements?:Yes
    Calculate distances to other parents?:No
    Parent name:Do not use

RelateObjects:[module_num:18|svn_version:\'10300\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the input child objects:SpklPerObj
    Select the input parent objects:Cells
    Calculate distances?:Centroid
    Calculate per-parent means for all child measurements?:Yes
    Calculate distances to other parents?:No
    Parent name:None

CalculateStatistics:[module_num:19|svn_version:\'10599\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Where is information about the positive and negative control status of each image?:Metadata_PosNegCtrls
    Where is information about the treatment dose for each image?:Metadata_Dose
    Log-transform dose values?:No
    Create dose/response plots?:No
    Figure prefix:
    Output file location:Default Output Folder\x7C.

ExportToSpreadsheet:[module_num:20|svn_version:\'10880\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D]
    Select or enter the column delimiter:Comma (",")
    Prepend the output file name to the data file names?:Yes
    Add image metadata columns to your object data file?:No
    Limit output to a size that is allowed in Excel?:No
    Select the columns of measurements to export?:No
    Calculate the per-image mean values for object measurements?:No
    Calculate the per-image median values for object measurements?:No
    Calculate the per-image standard deviation values for object measurements?:No
    Output file location:Elsewhere...\x7C/imaging/analysis/2006_09_29_ScreeningPaper/Roche/CP2_output/2010_01_22_output_adding_CalcStats_module/.
    Create a GenePattern GCT file?:No
    Select source of sample row name:Metadata
    Select the image to use as the identifier:None
    Select the metadata to use as the identifier:None
    Export all measurements, using default file names?:No
    Press button to select measurements to export:None\x7CNone
    Data to export:Image
    Combine these object measurements with those of the previous object?:No
    File name:Image.csv
    Use the object name for the file name?:No
    Data to export:Experiment
    Combine these object measurements with those of the previous object?:No
    File name:Experiment.csv
    Use the object name for the file name?:No
    Data to export:Cells
    Combine these object measurements with those of the previous object?:No
    File name:Cells.csv
    Use the object name for the file name?:No
    Data to export:Nuclei
    Combine these object measurements with those of the previous object?:No
    File name:Nuclei.csv
    Use the object name for the file name?:No
    Data to export:Speckles
    Combine these object measurements with those of the previous object?:No
    File name:Speckles.csv
    Use the object name for the file name?:No
    Data to export:SpklPerObj
    Combine these object measurements with those of the previous object?:No
    File name:SpklPerObj.csv
    Use the object name for the file name?:No
