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

LoadImages:[module_num:1|svn_version:\'10951\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D]
    File type to be loaded:individual images
    File selection method:Text-Exact match
    Number of images in each group?:3
    Type the text that the excluded images have in common:Do not use
    Analyze all subfolders within the selected folder?:All
    Input image file location:Default Input Folder\x7C.
    Check image sets for missing or duplicate files?:No
    Group images by metadata?:No
    Exclude certain files?:No
    Specify metadata fields to group by:
    Select subfolders to analyze:
    Image count:1
    Text that these images have in common (case-sensitive):_origihc.jpg
    Position of this image in each group:blue
    Extract metadata from where?:None
    Regular expression that finds metadata in the file name:None
    Type the regular expression that finds metadata in the subfolder path:None
    Channel count:1
    Group the movie frames?:No
    Grouping method:Interleaved
    Number of channels per group:2
    Load the input as images or objects?:Images
    Name this loaded image:OrigIHC
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:NucleiOutlines
    Channel number:1
    Rescale intensities?:Yes

ColorToGray:[module_num:2|svn_version:\'10318\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D]
    Select the input image:OrigIHC
    Conversion method:Combine
    Image type\x3A:RGB
    Name the output image:OrigGray
    Relative weight of the red channel:1
    Relative weight of the green channel:1
    Relative weight of the blue channel:1
    Convert red to gray?:Yes
    Name the output image:OrigRed
    Convert green to gray?:Yes
    Name the output image:OrigGreen
    Convert blue to gray?:Yes
    Name the output image:OrigBlue
    Channel count:1
    Channel number\x3A:Red\x3A 1
    Relative weight of the channel:1
    Image name\x3A:Channel1

UnmixColors:[module_num:3|svn_version:\'10829\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D]
    Stain count:2
    Color image:OrigIHC
    Image name:dabIM
    Stain:DAB
    Red absorbance:0.2139392
    Green absorbance:0.8511267
    Blue absorbance:0.47794023
    Image name:hemIM
    Stain:Hematoxylin
    Red absorbance:0.7489029
    Green absorbance:0.6062416
    Blue absorbance:0.26731083

Resize:[module_num:4|svn_version:\'10627\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D]
    Select the input image:hemIM
    Name the output image:ResizedH
    Select resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:0.50
    Width of the final image, in pixels:100
    Height of the final image, in pixels:100
    Interpolation method:Nearest Neighbor
    How do you want to specify the dimensions?:Manual
    Select the image with the desired dimensions:None
    Additional image count:2
    Select the additional image?:dabIM
    Name the output image:DAB_resize
    Select the additional image?:OrigGray
    Name the output image:Gray_resize

ApplyThreshold:[module_num:5|svn_version:\'6746\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D]
    Select the input image:DAB_resize
    Name the output image:ThreshDAB
    Select the output image type:Binary (black and white)
    Set pixels below or above the threshold to zero?:Below threshold
    Subtract the threshold value from the remaining pixel intensities?:No
    Number of pixels by which to expand the thresholding around those excluded bright pixels:0.0
    Select the thresholding method:Manual
    Manual threshold:0.6
    Lower and upper bounds on threshold:0.000000,1.000000
    Threshold correction factor:1
    Approximate fraction of image covered by objects?:0.01
    Select the input objects:None
    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
    Select the measurement to threshold with:None

ApplyThreshold:[module_num:6|svn_version:\'6746\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D]
    Select the input image:Gray_resize
    Name the output image:ThreshTissue
    Select the output image type:Binary (black and white)
    Set pixels below or above the threshold to zero?:Below threshold
    Subtract the threshold value from the remaining pixel intensities?:No
    Number of pixels by which to expand the thresholding around those excluded bright pixels:0.0
    Select the thresholding method:Manual
    Manual threshold:0.9
    Lower and upper bounds on threshold:0.000000,1.000000
    Threshold correction factor:1
    Approximate fraction of image covered by objects?:0.01
    Select the input objects:None
    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
    Select the measurement to threshold with:None

Morph:[module_num:7|svn_version:\'10300\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D]
    Select the input image:ThreshDAB
    Name the output image:MorphBlue
    Select the operation to perform:fill
    Number of times to repeat operation:Custom
    Repetition number:2
    Scale:5
    Select the operation to perform:fill
    Number of times to repeat operation:Custom
    Repetition number:3
    Scale:3
    Select the operation to perform:close
    Number of times to repeat operation:Custom
    Repetition number:4
    Scale:5
    Select the operation to perform:fill
    Number of times to repeat operation:Custom
    Repetition number:3
    Scale:3

Morph:[module_num:8|svn_version:\'10300\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D]
    Select the input image:ThreshTissue
    Name the output image:MorphBlueTissue
    Select the operation to perform:invert
    Number of times to repeat operation:Once
    Repetition number:2
    Scale:5
    Select the operation to perform:fill small holes
    Number of times to repeat operation:Once
    Maximum hole area:9
    Scale:3
    Select the operation to perform:erode
    Number of times to repeat operation:Once
    Repetition number:2
    Scale:3
    Select the operation to perform:dilate
    Number of times to repeat operation:Once
    Repetition number:2
    Scale:3

MaskImage:[module_num:9|svn_version:\'10428\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D]
    Select the input image:MorphBlueTissue
    Name the output image:MaskNegTissueBin
    Use objects or an image as a mask?:Image
    Select object for mask:None
    Select image for mask:MorphBlue
    Invert the mask?:Yes

Resize:[module_num:10|svn_version:\'10627\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D]
    Select the input image:MorphBlue
    Name the output image:ResizedDABbin
    Select resizing method:Resize by a fraction or multiple of the original size
    Resizing factor:2
    Width of the final image, in pixels:100
    Height of the final image, in pixels:100
    Interpolation method:Nearest Neighbor
    How do you want to specify the dimensions?:Manual
    Select the image with the desired dimensions:None
    Additional image count:1
    Select the additional image?:MaskNegTissueBin
    Name the output image:ResizedHEMBin

SaveImages:[module_num:11|svn_version:\'10822\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D]
    Select the type of image to save:Image
    Select the image to save:ResizedDABbin
    Select the objects to save:Nuclei
    Select the module display window to save:None
    Select method for constructing file names:From image filename
    Select image name for file prefix:OrigIHC
    Enter single file name:OrigBlue
    Do you want to add a suffix to the image file name?:Yes
    Text to append to the image name:_DAB
    Select file format to use:jpg
    Output file location:Default Output Folder\x7CNone
    Image bit depth:8
    Overwrite existing files without warning?:Yes
    Select how often to save:Every cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:Greys
    Store file and path information to the saved image?:No
    Create subfolders in the output folder?:No

SaveImages:[module_num:12|svn_version:\'10822\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D]
    Select the type of image to save:Image
    Select the image to save:ResizedHEMBin
    Select the objects to save:Nuclei
    Select the module display window to save:None
    Select method for constructing file names:From image filename
    Select image name for file prefix:OrigIHC
    Enter single file name:OrigBlue
    Do you want to add a suffix to the image file name?:Yes
    Text to append to the image name:_HEM
    Select file format to use:jpg
    Output file location:Default Output Folder\x7CNone
    Image bit depth:8
    Overwrite existing files without warning?:Yes
    Select how often to save:Every cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:Greys
    Store file and path information to the saved image?:No
    Create subfolders in the output folder?:No