CellProfiler Pipeline: http://www.cellprofiler.org
Version:4
DateRevision:318
GitHash:
ModuleCount:10
HasImagePlaneDetails:False

Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    :\xff\xfe
    Filter images?:\xff\xfeI\x00m\x00a\x00g\x00e\x00s\x00 \x00o\x00n\x00l\x00y\x00
    Select the rule criteria:\xff\xfea\x00n\x00d\x00 \x00(\x00e\x00x\x00t\x00e\x00n\x00s\x00i\x00o\x00n\x00 \x00d\x00o\x00e\x00s\x00 \x00i\x00s\x00i\x00m\x00a\x00g\x00e\x00)\x00 \x00(\x00d\x00i\x00r\x00e\x00c\x00t\x00o\x00r\x00y\x00 \x00d\x00o\x00e\x00s\x00n\x00o\x00t\x00 \x00c\x00o\x00n\x00t\x00a\x00i\x00n\x00r\x00e\x00g\x00e\x00x\x00p\x00 \x00"\x00\x5B\x00\\\x00\\\x00\\\x00\\\x00/\x00\x5D\x00\\\x00\\\x00.\x00"\x00)\x00

Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Extract metadata?:\xff\xfeY\x00e\x00s\x00
    Metadata data type:\xff\xfeT\x00e\x00x\x00t\x00
    Metadata types:\xff\xfe{\x00}\x00
    Extraction method count:\xff\xfe1\x00
    Metadata extraction method:\xff\xfeE\x00x\x00t\x00r\x00a\x00c\x00t\x00 \x00f\x00r\x00o\x00m\x00 \x00f\x00i\x00l\x00e\x00/\x00f\x00o\x00l\x00d\x00e\x00r\x00 \x00n\x00a\x00m\x00e\x00s\x00
    Metadata source:\xff\xfeF\x00i\x00l\x00e\x00 \x00n\x00a\x00m\x00e\x00
    Regular expression to extract from file name:\xff\xfe^\x00(\x00?\x00P\x00<\x00P\x00l\x00a\x00t\x00e\x00>\x00.\x00*\x00)\x00_\x00(\x00?\x00P\x00<\x00W\x00e\x00l\x00l\x00>\x00\x5B\x00A\x00-\x00P\x00\x5D\x00\x5B\x000\x00-\x009\x00\x5D\x00{\x002\x00}\x00)\x00_\x00s\x00(\x00?\x00P\x00<\x00S\x00i\x00t\x00e\x00>\x00\x5B\x000\x00-\x009\x00\x5D\x00)\x00_\x00w\x00(\x00?\x00P\x00<\x00C\x00h\x00a\x00n\x00n\x00e\x00l\x00N\x00u\x00m\x00b\x00e\x00r\x00>\x00\x5B\x000\x00-\x009\x00\x5D\x00)\x00
    Regular expression to extract from folder name:\xff\xfe(\x00?\x00P\x00<\x00D\x00a\x00t\x00e\x00>\x00\x5B\x000\x00-\x009\x00\x5D\x00{\x004\x00}\x00_\x00\x5B\x000\x00-\x009\x00\x5D\x00{\x002\x00}\x00_\x00\x5B\x000\x00-\x009\x00\x5D\x00{\x002\x00}\x00)\x00$\x00
    Extract metadata from:\xff\xfeA\x00l\x00l\x00 \x00i\x00m\x00a\x00g\x00e\x00s\x00
    Select the filtering criteria:\xff\xfea\x00n\x00d\x00 \x00(\x00f\x00i\x00l\x00e\x00 \x00d\x00o\x00e\x00s\x00 \x00c\x00o\x00n\x00t\x00a\x00i\x00n\x00 \x00"\x00"\x00)\x00
    Metadata file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00
    Match file and image metadata:\xff\xfe\x5B\x00\x5D\x00
    Use case insensitive matching?:\xff\xfeN\x00o\x00
    Metadata file name:\xff\xfe

NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Assign a name to:\xff\xfeI\x00m\x00a\x00g\x00e\x00s\x00 \x00m\x00a\x00t\x00c\x00h\x00i\x00n\x00g\x00 \x00r\x00u\x00l\x00e\x00s\x00
    Select the image type:\xff\xfeG\x00r\x00a\x00y\x00s\x00c\x00a\x00l\x00e\x00 \x00i\x00m\x00a\x00g\x00e\x00
    Name to assign these images:\xff\xfeP\x00L\x00A\x00
    Match metadata:\xff\xfe\x5B\x00\x5D\x00
    Image set matching method:\xff\xfeO\x00r\x00d\x00e\x00r\x00
    Set intensity range from:\xff\xfeI\x00m\x00a\x00g\x00e\x00 \x00m\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00
    Assignments count:\xff\xfe2\x00
    Single images count:\xff\xfe0\x00
    Maximum intensity:\xff\xfe2\x005\x005\x00.\x000\x00
    Process as 3D?:\xff\xfeN\x00o\x00
    Relative pixel spacing in X:\xff\xfe1\x00.\x000\x00
    Relative pixel spacing in Y:\xff\xfe1\x00.\x000\x00
    Relative pixel spacing in Z:\xff\xfe1\x00.\x000\x00
    Select the rule criteria:\xff\xfea\x00n\x00d\x00 \x00(\x00f\x00i\x00l\x00e\x00 \x00d\x00o\x00e\x00s\x00 \x00c\x00o\x00n\x00t\x00a\x00i\x00n\x00 \x00"\x00c\x004\x00.\x00"\x00)\x00
    Name to assign these images:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00
    Name to assign these objects:\xff\xfeC\x00e\x00l\x00l\x00
    Select the image type:\xff\xfeG\x00r\x00a\x00y\x00s\x00c\x00a\x00l\x00e\x00 \x00i\x00m\x00a\x00g\x00e\x00
    Set intensity range from:\xff\xfeI\x00m\x00a\x00g\x00e\x00 \x00m\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00
    Maximum intensity:\xff\xfe2\x005\x005\x00.\x000\x00
    Select the rule criteria:\xff\xfea\x00n\x00d\x00 \x00(\x00f\x00i\x00l\x00e\x00 \x00d\x00o\x00e\x00s\x00 \x00c\x00o\x00n\x00t\x00a\x00i\x00n\x00 \x00"\x00c\x003\x00.\x00"\x00)\x00
    Name to assign these images:\xff\xfeO\x00r\x00i\x00g\x00G\x00r\x00e\x00e\x00n\x00
    Name to assign these objects:\xff\xfeN\x00u\x00c\x00l\x00e\x00u\x00s\x00
    Select the image type:\xff\xfeG\x00r\x00a\x00y\x00s\x00c\x00a\x00l\x00e\x00 \x00i\x00m\x00a\x00g\x00e\x00
    Set intensity range from:\xff\xfeI\x00m\x00a\x00g\x00e\x00 \x00m\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00
    Maximum intensity:\xff\xfe2\x005\x005\x00.\x000\x00

Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Do you want to group your images?:\xff\xfeY\x00e\x00s\x00
    grouping metadata count:\xff\xfe1\x00
    Metadata category:\xff\xfeF\x00i\x00l\x00e\x00L\x00o\x00c\x00a\x00t\x00i\x00o\x00n\x00

IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\'Identify the nuclei from the nuclear stain image. \'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:\xff\xfeO\x00r\x00i\x00g\x00B\x00l\x00u\x00e\x00
    Name the primary objects to be identified:\xff\xfeN\x00u\x00c\x00l\x00e\x00i\x00
    Typical diameter of objects, in pixel units (Min,Max):\xff\xfe1\x002\x000\x00,\x003\x000\x000\x00
    Discard objects outside the diameter range?:\xff\xfeY\x00e\x00s\x00
    Discard objects touching the border of the image?:\xff\xfeY\x00e\x00s\x00
    Method to distinguish clumped objects:\xff\xfeS\x00h\x00a\x00p\x00e\x00
    Method to draw dividing lines between clumped objects:\xff\xfeS\x00h\x00a\x00p\x00e\x00
    Size of smoothing filter:\xff\xfe1\x000\x00
    Suppress local maxima that are closer than this minimum allowed distance:\xff\xfe7\x00.\x000\x00
    Speed up by using lower-resolution image to find local maxima?:\xff\xfeY\x00e\x00s\x00
    Fill holes in identified objects?:\xff\xfeA\x00f\x00t\x00e\x00r\x00 \x00b\x00o\x00t\x00h\x00 \x00t\x00h\x00r\x00e\x00s\x00h\x00o\x00l\x00d\x00i\x00n\x00g\x00 \x00a\x00n\x00d\x00 \x00d\x00e\x00c\x00l\x00u\x00m\x00p\x00i\x00n\x00g\x00
    Automatically calculate size of smoothing filter for declumping?:\xff\xfeY\x00e\x00s\x00
    Automatically calculate minimum allowed distance between local maxima?:\xff\xfeY\x00e\x00s\x00
    Handling of objects if excessive number of objects identified:\xff\xfeC\x00o\x00n\x00t\x00i\x00n\x00u\x00e\x00
    Maximum number of objects:\xff\xfe5\x000\x000\x00
    Use advanced settings?:\xff\xfeY\x00e\x00s\x00
    Threshold setting version:\xff\xfe1\x000\x00
    Threshold strategy:\xff\xfeG\x00l\x00o\x00b\x00a\x00l\x00
    Thresholding method:\xff\xfeO\x00t\x00s\x00u\x00
    Threshold smoothing scale:\xff\xfe1\x00.\x003\x004\x008\x008\x00
    Threshold correction factor:\xff\xfe1\x00.\x000\x00
    Lower and upper bounds on threshold:\xff\xfe0\x00.\x000\x00,\x001\x00.\x000\x00
    Manual threshold:\xff\xfe0\x00.\x000\x00
    Select the measurement to threshold with:\xff\xfeN\x00o\x00n\x00e\x00
    Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00
    Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00
    Size of adaptive window:\xff\xfe5\x000\x00
    Lower outlier fraction:\xff\xfe0\x00.\x000\x005\x00
    Upper outlier fraction:\xff\xfe0\x00.\x000\x005\x00
    Averaging method:\xff\xfeM\x00e\x00a\x00n\x00
    Variance method:\xff\xfeS\x00t\x00a\x00n\x00d\x00a\x00r\x00d\x00 \x00d\x00e\x00v\x00i\x00a\x00t\x00i\x00o\x00n\x00
    # of deviations:\xff\xfe2\x00.\x000\x00
    Thresholding method:\xff\xfeO\x00t\x00s\x00u\x00

EnhanceOrSuppressFeatures:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Use filtering to enhance the foci speckles in the image. The feature size setting should be specified to be at least as large as the largest feature to be enhanced.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:\xff\xfeO\x00r\x00i\x00g\x00G\x00r\x00e\x00e\x00n\x00
    Name the output image:\xff\xfeE\x00n\x00h\x00a\x00n\x00c\x00e\x00d\x00G\x00r\x00e\x00e\x00n\x00
    Select the operation:\xff\xfeE\x00n\x00h\x00a\x00n\x00c\x00e\x00
    Feature size:\xff\xfe1\x000\x00
    Feature type:\xff\xfeS\x00p\x00e\x00c\x00k\x00l\x00e\x00s\x00
    Range of hole sizes:\xff\xfe1\x00,\x001\x000\x00
    Smoothing scale:\xff\xfe2\x00.\x000\x00
    Shear angle:\xff\xfe0\x00.\x000\x00
    Decay:\xff\xfe0\x00.\x009\x005\x00
    Enhancement method:\xff\xfeT\x00u\x00b\x00e\x00n\x00e\x00s\x00s\x00
    Speed and accuracy:\xff\xfeF\x00a\x00s\x00t\x00

MaskImage:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Mask the foci image using the nuclei objects.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:\xff\xfeE\x00n\x00h\x00a\x00n\x00c\x00e\x00d\x00G\x00r\x00e\x00e\x00n\x00
    Name the output image:\xff\xfeM\x00a\x00s\x00k\x00e\x00d\x00G\x00r\x00e\x00e\x00n\x00
    Use objects or an image as a mask?:\xff\xfeO\x00b\x00j\x00e\x00c\x00t\x00s\x00
    Select object for mask:\xff\xfeN\x00u\x00c\x00l\x00e\x00i\x00
    Select image for mask:\xff\xfeN\x00o\x00n\x00e\x00
    Invert the mask?:\xff\xfeN\x00o\x00

IdentifyPrimaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\'Identify the foci using per-object thresholding to compute a threshold for each individual nuclei object. Some manual adjustment of the smoothing filter size and maxima supression distance is required to optimize segmentation.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:\xff\xfeM\x00a\x00s\x00k\x00e\x00d\x00G\x00r\x00e\x00e\x00n\x00
    Name the primary objects to be identified:\xff\xfeh\x002\x00a\x00x\x00
    Typical diameter of objects, in pixel units (Min,Max):\xff\xfe4\x00,\x002\x000\x00
    Discard objects outside the diameter range?:\xff\xfeY\x00e\x00s\x00
    Discard objects touching the border of the image?:\xff\xfeY\x00e\x00s\x00
    Method to distinguish clumped objects:\xff\xfeI\x00n\x00t\x00e\x00n\x00s\x00i\x00t\x00y\x00
    Method to draw dividing lines between clumped objects:\xff\xfeI\x00n\x00t\x00e\x00n\x00s\x00i\x00t\x00y\x00
    Size of smoothing filter:\xff\xfe4\x00
    Suppress local maxima that are closer than this minimum allowed distance:\xff\xfe4\x00
    Speed up by using lower-resolution image to find local maxima?:\xff\xfeY\x00e\x00s\x00
    Fill holes in identified objects?:\xff\xfeA\x00f\x00t\x00e\x00r\x00 \x00b\x00o\x00t\x00h\x00 \x00t\x00h\x00r\x00e\x00s\x00h\x00o\x00l\x00d\x00i\x00n\x00g\x00 \x00a\x00n\x00d\x00 \x00d\x00e\x00c\x00l\x00u\x00m\x00p\x00i\x00n\x00g\x00
    Automatically calculate size of smoothing filter for declumping?:\xff\xfeN\x00o\x00
    Automatically calculate minimum allowed distance between local maxima?:\xff\xfeN\x00o\x00
    Handling of objects if excessive number of objects identified:\xff\xfeC\x00o\x00n\x00t\x00i\x00n\x00u\x00e\x00
    Maximum number of objects:\xff\xfe5\x000\x000\x00
    Use advanced settings?:\xff\xfeY\x00e\x00s\x00
    Threshold setting version:\xff\xfe1\x000\x00
    Threshold strategy:\xff\xfeG\x00l\x00o\x00b\x00a\x00l\x00
    Thresholding method:\xff\xfeR\x00o\x00b\x00u\x00s\x00t\x00B\x00a\x00c\x00k\x00g\x00r\x00o\x00u\x00n\x00d\x00
    Threshold smoothing scale:\xff\xfe1\x00.\x003\x004\x008\x008\x00
    Threshold correction factor:\xff\xfe1\x00.\x000\x00
    Lower and upper bounds on threshold:\xff\xfe0\x00.\x000\x00,\x001\x00.\x000\x00
    Manual threshold:\xff\xfe0\x00.\x000\x00
    Select the measurement to threshold with:\xff\xfeN\x00o\x00n\x00e\x00
    Two-class or three-class thresholding?:\xff\xfeT\x00w\x00o\x00 \x00c\x00l\x00a\x00s\x00s\x00e\x00s\x00
    Assign pixels in the middle intensity class to the foreground or the background?:\xff\xfeF\x00o\x00r\x00e\x00g\x00r\x00o\x00u\x00n\x00d\x00
    Size of adaptive window:\xff\xfe5\x000\x00
    Lower outlier fraction:\xff\xfe0\x00.\x000\x005\x00
    Upper outlier fraction:\xff\xfe0\x00.\x000\x005\x00
    Averaging method:\xff\xfeM\x00e\x00a\x00n\x00
    Variance method:\xff\xfeS\x00t\x00a\x00n\x00d\x00a\x00r\x00d\x00 \x00d\x00e\x00v\x00i\x00a\x00t\x00i\x00o\x00n\x00
    # of deviations:\xff\xfe2\x00.\x000\x00
    Thresholding method:\xff\xfeO\x00t\x00s\x00u\x00

RelateObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'Establish a parent-child between the foci (\\xe2\\x80\\x9cchildren\\xe2\\x80\\x9d) and the nuclei (\\xe2\\x80\\x9cparents\\xe2\\x80\\x9d) in order to determine which foci belong to which nuclei. Then, calculate mean foci measurements for each nucleus.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Parent objects:\xff\xfeN\x00u\x00c\x00l\x00e\x00i\x00
    Child objects:\xff\xfeh\x002\x00a\x00x\x00
    Name the output object:\xff\xfeR\x00e\x00l\x00a\x00t\x00e\x00O\x00b\x00j\x00e\x00c\x00t\x00s\x00
    Calculate child-parent distances?:\xff\xfeC\x00e\x00n\x00t\x00r\x00o\x00i\x00d\x00
    Calculate per-parent means for all child measurements?:\xff\xfeY\x00e\x00s\x00
    Calculate distances to other parents?:\xff\xfeN\x00o\x00
    Parent name:\xff\xfeN\x00o\x00n\x00e\x00
    Parent name:\xff\xfeN\x00o\x00n\x00e\x00

ExportToSpreadsheet:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\'Export any measurements to a comma-delimited file (.csv). The measurements made for the nuclei and foci objects will be saved to separate .csv files, in addition to the per-image .csv.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the column delimiter:\xff\xfeC\x00o\x00m\x00m\x00a\x00 \x00(\x00"\x00,\x00"\x00)\x00
    Add image metadata columns to your object data file?:\xff\xfeN\x00o\x00
    Select the measurements to export:\xff\xfeY\x00e\x00s\x00
    Calculate the per-image mean values for object measurements?:\xff\xfeY\x00e\x00s\x00
    Calculate the per-image median values for object measurements?:\xff\xfeY\x00e\x00s\x00
    Calculate the per-image standard deviation values for object measurements?:\xff\xfeY\x00e\x00s\x00
    Output file location:\xff\xfeE\x00l\x00s\x00e\x00w\x00h\x00e\x00r\x00e\x00.\x00.\x00.\x00\x7C\x00T\x00\x3A\x00\\\x00\\\x00L\x00M\x00G\x00\\\x00\\\x00L\x00M\x00G\x00S\x00e\x00c\x00t\x00i\x00o\x00n\x00s\x00\\\x00\\\x00G\x00e\x00n\x00e\x00_\x00T\x00a\x00r\x00g\x00e\x00t\x00i\x00n\x00g\x00\\\x00\\\x000\x000\x00_\x00L\x00A\x00B\x00\\\x00\\\x001\x004\x00_\x00c\x00e\x00l\x00l\x00p\x00r\x00o\x00f\x00i\x00l\x00e\x00r\x00\\\x00\\\x00P\x00i\x00p\x00e\x00l\x00i\x00n\x00e\x00s\x00
    Create a GenePattern GCT file?:\xff\xfeN\x00o\x00
    Select source of sample row name:\xff\xfeM\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00
    Select the image to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00
    Select the metadata to use as the identifier:\xff\xfeN\x00o\x00n\x00e\x00
    Export all measurement types?:\xff\xfeN\x00o\x00
    Press button to select measurements:\xff\xfeN\x00u\x00c\x00l\x00e\x00i\x00\x7C\x00C\x00h\x00i\x00l\x00d\x00r\x00e\x00n\x00_\x00h\x002\x00a\x00x\x00_\x00C\x00o\x00u\x00n\x00t\x00
    Representation of Nan/Inf:\xff\xfeN\x00a\x00N\x00
    Add a prefix to file names?:\xff\xfeY\x00e\x00s\x00
    Filename prefix:\xff\xfeb\x00i\x00n\x00_\x00t\x00e\x00s\x00t\x00
    Overwrite existing files without warning?:\xff\xfeY\x00e\x00s\x00
    Data to export:\xff\xfeN\x00u\x00c\x00l\x00e\x00i\x00
    Combine these object measurements with those of the previous object?:\xff\xfeN\x00o\x00
    File name:\xff\xfeD\x00A\x00T\x00A\x00.\x00c\x00s\x00v\x00
    Use the object name for the file name?:\xff\xfeY\x00e\x00s\x00