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

LoadImages:[module_num:1|svn_version:\'Unknown\'|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?:All
    Input image file location:Default Input Folder\x7CNone
    Check image sets for missing or duplicate files?:Yes
    Group images by metadata?:No
    Exclude certain files?:No
    Specify metadata fields to group by:
    Select subfolders to analyze:
    Image count:4
    Text that these images have in common (case-sensitive):DAPI
    Position of this image in each group:1
    Extract metadata from where?:None
    Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)
    Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
    Channel count:1
    Group the movie frames?:No
    Grouping method:Interleaved
    Number of channels per group:3
    Load the input as images or objects?:Images
    Name this loaded image:DNA
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:LoadedImageOutlines
    Channel number:1
    Rescale intensities?:Yes
    Text that these images have in common (case-sensitive):DsRed
    Position of this image in each group:2
    Extract metadata from where?:None
    Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)
    Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
    Channel count:1
    Group the movie frames?:No
    Grouping method:Interleaved
    Number of channels per group:3
    Load the input as images or objects?:Images
    Name this loaded image:Cd31
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:LoadedImageOutlines
    Channel number:1
    Rescale intensities?:Yes
    Text that these images have in common (case-sensitive):Cy5
    Position of this image in each group:3
    Extract metadata from where?:None
    Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)
    Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
    Channel count:1
    Group the movie frames?:No
    Grouping method:Interleaved
    Number of channels per group:3
    Load the input as images or objects?:Images
    Name this loaded image:PRG5
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:LoadedImageOutlines
    Channel number:1
    Rescale intensities?:Yes
    Text that these images have in common (case-sensitive):GFP
    Position of this image in each group:4
    Extract metadata from where?:None
    Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)
    Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
    Channel count:1
    Group the movie frames?:No
    Grouping method:Interleaved
    Number of channels per group:3
    Load the input as images or objects?:Images
    Name this loaded image:SMA
    Name this loaded object:Nuclei
    Retain outlines of loaded objects?:No
    Name the outline image:LoadedImageOutlines
    Channel number:1
    Rescale intensities?:Yes

MeasureCorrelation:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
    Hidden:2
    Hidden:1
    Select an image to measure:DNA
    Select an image to measure:Cd31
    Select where to measure correlation:Across entire image
    Select an object to measure:None

ExportToSpreadsheet:[module_num:3|svn_version:\'Unknown\'|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:Default Output Folder\x7CNone
    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?:Yes
    Press button to select measurements to export:
    Data to export:Do not use
    Combine these object measurements with those of the previous object?:No
    File name:DATA.csv
    Use the object name for the file name?:Yes