CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20160418141927
GitHash:9969f42
ModuleCount:8
HasImagePlaneDetails:False

LoadData:[module_num:1|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]
    Input data file location:Elsewhere...\x7C/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Images
    Name of the file:Filelist_local.csv
    Load images based on this data?:Yes
    Base image location:Elsewhere...\x7C/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Images
    Process just a range of rows?:Yes
    Rows to process:12289,13056
    Group images by metadata?:No
    Select metadata tags for grouping:
    Rescale intensities?:Yes

IdentifyPrimaryObjects:[module_num:2|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:OrigDAPI
    Name the primary objects to be identified:Nuclei
    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:Intensity
    Size of smoothing filter:10
    Suppress local maxima that are closer than this minimum allowed distance:7
    Speed up by using lower-resolution image to find local maxima?:Yes
    Name the outline image:NucleiOutlines
    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?:Yes
    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
    Handling of objects if excessive number of objects identified:Continue
    Maximum number of objects:500
    Threshold setting version:1
    Threshold strategy:Global
    Thresholding method:Otsu
    Select the smoothing method for thresholding:Automatic
    Threshold smoothing scale:1
    Threshold correction factor:1
    Lower and upper bounds on threshold:0.000000,1.000000
    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:From image
    Two-class or three-class thresholding?:Two 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

ConvertObjectsToImage:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input objects:Nuclei
    Name the output image:Nuclei
    Select the color format:Grayscale
    Select the colormap:Default

MaskImage:[module_num:4|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]
    Select the input image:Nuclei
    Name the output image:LabelOutlines
    Use objects or an image as a mask?:Image
    Select object for mask:None
    Select image for mask:NucleiOutlines
    Invert the mask?:No

SaveImages:[module_num:5|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:Nuclei
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<Plate>_\\\\g<Well>_s\\\\g<Site>
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:Do not use
    Saved file format:png
    Output file location:Elsewhere...\x7C/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Output/Segmentation/Labels/z_\\\\g<ZStep>
    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?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Default Input Folder
    Saved movie format:avi

SaveImages:[module_num:6|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:NucleiOutlines
    Select the objects to save:None
    Select the module display window to save:None
    Select method for constructing file names:Single name
    Select image name for file prefix:None
    Enter single file name:\\\\g<Plate>_\\\\g<Well>_s\\\\g<Site>
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:Do not use
    Saved file format:png
    Output file location:Elsewhere...\x7C/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Output/Segmentation/Outlines/z_\\\\g<ZStep>
    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?:Grayscale
    Select colormap:gray
    Record the file and path information to the saved image?:Yes
    Create subfolders in the output folder?:No
    Base image folder:Default Input Folder
    Saved movie format:avi

ExportToDatabase:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:27|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Database type:MySQL
    Database name:2008_11_05_QualityControlForScreens
    Add a prefix to table names?:Yes
    Table prefix:U2OS_Segmetation_2011_03_22_
    SQL file prefix:SQL_
    Output file location:Elsewhere...\x7C/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Output
    Create a CellProfiler Analyst properties file?:Yes
    Database host:
    Username:
    Password:
    Name the SQLite database file:DefaultDB.db
    Calculate the per-image mean values of object measurements?:No
    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?:None
    Select the objects:Cells,Nuclei
    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:http\x3A//imageweb/images/CPALinks
    Write image thumbnails directly to the database?:Yes
    Select the images for which you want to save thumbnails:OrigDAPI,OrigPhalloidin
    Auto-scale thumbnail pixel intensities?:Yes
    Select the plate type:384
    Select the plate metadata:ZStep
    Select the well metadata:Well
    Include information for all images, using default values?:No
    Properties image group count:2
    Properties group field count:1
    Properties filter field count:0
    Workspace measurement count:1
    Experiment name:Experiment_U2OS
    Which objects should be used for locations?:None
    Enter a phenotype class table name if using the classifier tool:
    Export object relationships?:No
    Overwrite without warning?:Data only
    Access CPA images via URL?:Yes
    Select the classification type:Object
    Select an image to include:OrigDAPI
    Use the image name for the display?:No
    Image name:DAPI
    Channel color:red
    Select an image to include:NucleiOutlines
    Use the image name for the display?:No
    Image name:Nuclei
    Channel color:none
    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?:Yes
    Automatically create a filter for each plate?:Yes
    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:Image
    Select the X-axis measurement:
    Select the X-axis index:ImageNumber
    Type of measurement to plot on the Y-axis:Image
    Enter the object name:Image
    Select the Y-axis measurement:
    Select the Y-axis index:ImageNumber

CreateBatchFiles:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Store batch files in default output folder?:Yes
    Output folder path:/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Output
    Are the cluster computers running Windows?:No
    Hidden\x3A in batch mode:No
    Hidden\x3A in distributed mode:No
    Hidden\x3A default input folder at time of save:/imaging/analysis/2008_11_05_QualityControlForScreens_ImagingPlatform/2011_03_22_DemoPlate_ImagingPlatform/Images
    Hidden\x3A revision number:11502
    Hidden\x3A from old matlab:No
    Launch BatchProfiler:No
    Local root path:\\\\\\\\iodine\\\\imaging_analysis
    Cluster root path:/imaging/analysis
    Local root path:\\\\\\\\sunexa06\\\\cbimage2\\\\hcs
    Cluster root path:/cbnt/cbimage2/hcs