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

LoadImages:[module_num:1|svn_version:\'10951\'|variable_revision_number:11|show_window:True|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?:None
    Input image file location:Default Input Folder\x7C.
    Check image sets for missing or duplicate files?:
    Group images by metadata?:No
    Exclude certain files?:No
    Specify metadata fields to group by:
    Select subfolders to analyze:
    Image count:2
    Text that these images have in common (case-sensitive):d0.TIF
    Position of this image in each group:d0.TIF
    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:Ch0
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:NucleiOutlines
    Channel number:1
    Rescale intensities?:Yes
    Text that these images have in common (case-sensitive):d2.TIF
    Position of this image in each group:d2.TIF
    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:Ch2
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:NucleiOutlines
    Channel number:1
    Rescale intensities?:Yes

CorrectIlluminationCalculate:[module_num:2|svn_version:\'10458\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the input image:Ch0
    Name the output image:IllumCh0
    Select how the illumination function is calculated:Regular
    Dilate objects in the final averaged image?:No
    Dilation radius:0
    Block size:60
    Rescale the illumination function?:Yes
    Calculate function for each image individually, or based on all images?:All\x3A First cycle
    Smoothing method:Gaussian Filter
    Method to calculate smoothing filter size:Object size
    Approximate object size:150
    Smoothing filter size:10
    Retain the averaged image for use later in the pipeline (for example, in SaveImages)?:Yes
    Name the averaged image:Do not save
    Retain the dilated image for use later in the pipeline (for example, in SaveImages)?:Yes
    Name the dilated image:Do not save
    Automatically calculate spline parameters?:Yes
    Background mode:auto
    Number of spline points:5
    Background threshold:2
    Image resampling factor:2
    Maximum number of iterations:40
    Residual value for convergence:0.001

SaveImages:[module_num:3|svn_version:\'10822\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D]
    Select the type of image to save:Image
    Select the image to save:IllumCh0
    Select the objects to save:None
    Select the module display window to save:IllumCh0
    Select method for constructing file names:Single name
    Select image name for file prefix:Other..
    Enter single file name:ILLUM_Ch0
    Do you want to add a suffix to the image file name?:Yes
    Text to append to the image name:_2008_04_22_Gaussian150
    Select file format to use:mat
    Output file location:Default Output Folder\x7CNone
    Image bit depth:8
    Overwrite existing files without warning?:No
    Select how often to save:Last cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Store file and path information to the saved image?:No
    Create subfolders in the output folder?:n/a

CorrectIlluminationCalculate:[module_num:4|svn_version:\'10458\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Select the input image:Ch2
    Name the output image:IllumCh2
    Select how the illumination function is calculated:Regular
    Dilate objects in the final averaged image?:No
    Dilation radius:0
    Block size:60
    Rescale the illumination function?:Yes
    Calculate function for each image individually, or based on all images?:All\x3A First cycle
    Smoothing method:Gaussian Filter
    Method to calculate smoothing filter size:Object size
    Approximate object size:150
    Smoothing filter size:10
    Retain the averaged image for use later in the pipeline (for example, in SaveImages)?:Yes
    Name the averaged image:Do not save
    Retain the dilated image for use later in the pipeline (for example, in SaveImages)?:Yes
    Name the dilated image:Do not save
    Automatically calculate spline parameters?:Yes
    Background mode:auto
    Number of spline points:5
    Background threshold:2
    Image resampling factor:2
    Maximum number of iterations:40
    Residual value for convergence:0.001

SaveImages:[module_num:5|svn_version:\'10822\'|variable_revision_number:7|show_window:True|notes:\x5B\x5D]
    Select the type of image to save:Image
    Select the image to save:IllumCh2
    Select the objects to save:None
    Select the module display window to save:IllumCh2
    Select method for constructing file names:Single name
    Select image name for file prefix:ILLUM_Ch2
    Enter single file name:ILLUM_Ch2
    Do you want to add a suffix to the image file name?:Yes
    Text to append to the image name:_2008_04_22_Gaussian150
    Select file format to use:mat
    Output file location:Default Output Folder\x7CNone
    Image bit depth:8
    Overwrite existing files without warning?:No
    Select how often to save:Last cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Store file and path information to the saved image?:No
    Create subfolders in the output folder?:n/a
