CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20160418141927
GitHash:9969f42
ModuleCount:13
HasImagePlaneDetails:False

Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|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.\', \'\\xe2\\x80\\x94\', \'Settings converted from legacy pipeline.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    :
    Filter images?:No filtering
    Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.")

Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|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.\', \'\\xe2\\x80\\x94\', \'Settings converted from legacy pipeline.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Extract metadata?:No
    Metadata data type:Text
    Metadata types:{}
    Extraction method count:1
    Metadata extraction method:Extract from file/folder names
    Metadata source:File name
    Regular expression:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)
    Regular expression:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$
    Extract metadata from:All images
    Select the filtering criteria:and (file does contain "")
    Metadata file location:
    Match file and image metadata:\x5B\x5D
    Use case insensitive matching?:No

NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\', \'\\xe2\\x80\\x94\', \'Settings converted from legacy pipeline.\', \'Please change any color images from \\xe2\\x80\\x9cLoad as Grayscale image\\xe2\\x80\\x9d to \\xe2\\x80\\x9cLoad as Color image\\xe2\\x80\\x9d\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Assign a name to:Images matching rules
    Select the image type:Grayscale image
    Name to assign these images:DNA
    Match metadata:\x5B\x5D
    Image set matching method:Order
    Set intensity range from:Image metadata
    Assignments count:2
    Single images count:0
    Maximum intensity:255.0
    Select the rule criteria:and (file does contain "C2-")
    Name to assign these images:H2B
    Name to assign these objects:Cell
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Retain outlines of loaded objects?:No
    Name the outline image:LoadedOutlines
    Maximum intensity:255.0
    Select the rule criteria:and (file does contain "C1-")
    Name to assign these images:ERKKTR
    Name to assign these objects:Nucleus
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Retain outlines of loaded objects?:No
    Name the outline image:LoadedOutlines
    Maximum intensity:255.0

Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|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.\', \'\\xe2\\x80\\x94\', \'Settings converted from legacy pipeline.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Do you want to group your images?:No
    grouping metadata count:1
    Metadata category:None

IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:H2B
    Name the primary objects to be identified:PreNuclei
    Typical diameter of objects, in pixel units (Min,Max):20,100
    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?:No
    Method to distinguish clumped objects:Intensity
    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:7.0
    Speed up by using lower-resolution image to find local maxima?:No
    Name the outline image:PrimaryOutlines
    Fill holes in identified objects?:After both thresholding and declumping
    Automatically calculate size of smoothing filter for declumping?:Yes
    Automatically calculate minimum allowed distance between local maxima?:Yes
    Retain outlines of the identified objects?:No
    Automatically calculate the threshold using the Otsu method?:Yes
    Enter Laplacian of Gaussian threshold:0.5
    Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes
    Enter LoG filter diameter:5.0
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Threshold setting version:1
    Threshold strategy:Automatic
    Thresholding method:RobustBackground
    Select the smoothing method for thresholding:Automatic
    Threshold smoothing scale:1.0
    Threshold correction factor:1
    Lower and upper bounds on threshold:0.0,1.0
    Approximate fraction of image covered by objects?:0.01
    Manual threshold:0.0
    Select the measurement to threshold with:None
    Select binary image:None
    Masking objects:None
    Two-class or three-class thresholding?:Three classes
    Minimize the weighted variance or the entropy?:Weighted variance
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Method to calculate adaptive window size:Image size
    Size of adaptive window:10
    Use default parameters?:Default
    Lower outlier fraction:0.05
    Upper outlier fraction:0.05
    Averaging method:Mean
    Variance method:Standard deviation
    # of deviations:2.0

ExpandOrShrinkObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:True]
    Select the input objects:PreNuclei
    Name the output objects:nuclei
    Select the operation:Shrink objects by a specified number of pixels
    Number of pixels by which to expand or shrink:1
    Fill holes in objects so that all objects shrink to a single point?:No
    Retain the outlines of the identified objects?:No
    Name the outline image:ShrunkenNucleiOutlines

SaveImages:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:11|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Objects
    Select the image to save:None
    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:H2B
    Enter single file name:OrigBlue
    Number of digits:4
    Append a suffix to the image file name?:Yes
    Text to append to the image name:_nuclei
    Saved file format:jpg
    Output file location:Default Output Folder\x7C
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:Yes
    When to save:Every cycle
    Rescale the images? :No
    Save as grayscale or color image?:Color
    Select colormap:gist_rainbow
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C
    Saved movie format:avi

OverlayOutlines:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Display outlines on a blank image?:No
    Select image on which to display outlines:ERKKTR
    Name the output image:OrigOverlay
    Outline display mode:Color
    Select method to determine brightness of outlines:Max of image
    Width of outlines:1
    Select outlines to display:None
    Select outline color:Red
    Load outlines from an image or objects?:Objects
    Select objects to display:nuclei

DisplayDataOnImage:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:6|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Display object or image measurements?:Object
    Select the input objects:nuclei
    Measurement to display:Number_Object_Number
    Select the image on which to display the measurements:OrigOverlay
    Text color:red
    Name the output image that has the measurements displayed:Numbered_nuclei
    Font size (points):12
    Number of decimals:0
    Image elements to save:Image
    Annotation offset (in pixels):5
    Display mode:Text
    Color map:Default
    Display background image?:Yes
    Color map scale:Use this image\'s measurement range
    Color map range:0.0,1.0

SaveImages:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:Numbered_nuclei
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:From image filename
    Select image name for file prefix:ERKKTR
    Enter single file name:OrigBlue
    Number of digits:4
    Append a suffix to the image file name?:Yes
    Text to append to the image name:numbered
    Saved file format:tif
    Output file location:Default Output Folder\x7C
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:No
    When to save:Every cycle
    Rescale the images? :No
    Save as grayscale or color image?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...\x7C
    Saved movie format:avi

MeasureObjectIntensity:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Hidden:2
    Select an image to measure:H2B
    Select an image to measure:ERKKTR
    Select objects to measure:nuclei