CW_Pipeline_Extracted.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:425
GitHash:
ModuleCount:8
HasImagePlaneDetails:False

Images:[module_num:1|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['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.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    :
    Filter images?:Images only
    Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "[\\\\/]\\.")

Metadata:[module_num:2|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:['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.']|batch_state:array([], 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 to extract from file name:^(?P<Plate>.*)_(?P<Well>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])
    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
    Extract metadata from:All images
    Select the filtering criteria:and (file does contain "")
    Metadata file location:Elsewhere...|
    Match file and image metadata:[]
    Use case insensitive matching?:No
    Metadata file name:None
    Does cached metadata exist?:No

NamesAndTypes:[module_num:3|svn_version:'Unknown'|variable_revision_number:8|show_window:False|notes:['The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Assign a name to:All images
    Select the image type:Grayscale image
    Name to assign these images:Fig1
    Match metadata:[]
    Image set matching method:Order
    Set intensity range from:Image metadata
    Assignments count:1
    Single images count:0
    Maximum intensity:255.0
    Process as 3D?:No
    Relative pixel spacing in X:1.0
    Relative pixel spacing in Y:1.0
    Relative pixel spacing in Z:1.0
    Select the rule criteria:and (file does contain "")
    Name to assign these images:DNA
    Name to assign these objects:Cell
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0

Groups:[module_num:4|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['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.']|batch_state:array([], 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:15|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Fig1
    Name the primary objects to be identified:IdentifyPrimaryObjects
    Typical diameter of objects, in pixel units (Min,Max):30,100
    Discard objects outside the diameter range?:Yes
    Discard objects touching the border of the image?:Yes
    Method to distinguish clumped objects:Intensity
    Method to draw dividing lines between clumped objects:Intensity
    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?:Yes
    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
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Use advanced settings?:No
    Threshold setting version:12
    Threshold strategy:Global
    Thresholding method:Minimum Cross-Entropy
    Threshold smoothing scale:1.3488
    Threshold correction factor:1.0
    Lower and upper bounds on threshold:0.0,1.0
    Manual threshold:0.0
    Select the measurement to threshold with:None
    Two-class or three-class thresholding?:Two classes
    Log transform before thresholding?:No
    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
    Size of adaptive window:50
    Lower outlier fraction:0.05
    Upper outlier fraction:0.05
    Averaging method:Mean
    Variance method:Standard deviation
    # of deviations:2.0
    Thresholding method:Minimum Cross-Entropy

MeasureObjectIntensity:[module_num:6|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select images to measure:Fig1
    Select objects to measure:IdentifyPrimaryObjects

MeasureObjectSizeShape:[module_num:7|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select object sets to measure:IdentifyPrimaryObjects
    Calculate the Zernike features?:Yes
    Calculate the advanced features?:No

ExportToDatabase:[module_num:8|svn_version:'Unknown'|variable_revision_number:28|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Database type:SQLite
    Database name:DefaultDB
    Add a prefix to table names?:Yes
    Table prefix:MyExpt_
    Output file location:Default Output Folder|
    Create a CellProfiler Analyst properties file?:No
    Database host:
    Username:
    Password:
    Name the SQLite database file:DefaultDB.db
    Calculate the per-image mean values of object measurements?:Yes
    Calculate the per-image median values of object measurements?:No
    Calculate the per-image standard deviation values of object measurements?:No
    Calculate the per-well mean values of object measurements?:No
    Calculate the per-well median values of object measurements?:No
    Calculate the per-well standard deviation values of object measurements?:No
    Export measurements for all objects to the database?:All
    Select the objects:
    Maximum # of characters in a column name:64
    Create one table per object, a single object table or a single object view?:Single object table
    Enter an image url prepend if you plan to access your files via http:
    Write image thumbnails directly to the database?:No
    Select the images for which you want to save thumbnails:
    Auto-scale thumbnail pixel intensities?:Yes
    Select the plate type:None
    Select the plate metadata:None
    Select the well metadata:None
    Include information for all images, using default values?:Yes
    Properties image group count:1
    Properties group field count:1
    Properties filter field count:0
    Workspace measurement count:1
    Experiment name:MyExpt
    Which objects should be used for locations?:None
    Enter a phenotype class table name if using the Classifier tool in CellProfiler Analyst:
    Export object relationships?:Yes
    Overwrite without warning?:Never
    Access CellProfiler Analyst images via URL?:No
    Select the classification type:Object
    Select an image to include:None
    Use the image name for the display?:Yes
    Image name:Channel1
    Channel color:red
    Do you want to add group fields?:No
    Enter the name of the group:
    Enter the per-image columns which define the group, separated by commas:ImageNumber, Image_Metadata_Plate, Image_Metadata_Well
    Do you want to add filter fields?:No
    Automatically create a filter for each plate?:No
    Create a CellProfiler Analyst workspace file?:No
    Select the measurement display tool:ScatterPlot
    Type of measurement to plot on the X-axis:Image
    Enter the object name:None
    Select the X-axis measurement:None
    Select the X-axis index:ImageNumber
    Type of measurement to plot on the Y-axis:Image
    Enter the object name:None
    Select the Y-axis measurement:None
    Select the Y-axis index:ImageNumber