analysis.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20160418141927
GitHash:9969f42
ModuleCount:23
HasImagePlaneDetails:False

LoadData:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Input data file location:Default Input Folder\x7C
    Name of the file:load_data_with_illum.csv
    Load images based on this data?:Yes
    Base image location:Default Input Folder\x7C
    Process just a range of rows?:No
    Rows to process:1,100000
    Group images by metadata?:Yes
    Select metadata tags for grouping:Plate,Well,Site
    Rescale intensities?:Yes

CorrectIlluminationApply:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:OrigDNA
    Name the output image:DNA
    Select the illumination function:IllumDNA
    Select how the illumination function is applied:Divide
    Select the input image:OrigER_RNA
    Name the output image:ER_RNA
    Select the illumination function:IllumER_RNA
    Select how the illumination function is applied:Divide
    Select the input image:OrigAGP
    Name the output image:AGP
    Select the illumination function:IllumAGP
    Select how the illumination function is applied:Divide
    Select the input image:OrigMito
    Name the output image:Mito
    Select the illumination function:IllumMito
    Select how the illumination function is applied:Divide

MeasureImageQuality:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Calculate metrics for which images?:All loaded images
    Image count:1
    Scale count:4
    Threshold count:1
    Select the images to measure:
    Include the image rescaling value?:Yes
    Calculate blur metrics?:Yes
    Spatial scale for blur measurements:5
    Spatial scale for blur measurements:10
    Spatial scale for blur measurements:20
    Spatial scale for blur measurements:50
    Calculate saturation metrics?:Yes
    Calculate intensity metrics?:Yes
    Calculate thresholds?:No
    Use all thresholding methods?:No
    Select a thresholding method:Otsu
    Typical fraction of the image covered by objects:0.1
    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

MeasureImageQuality:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Calculate metrics for which images?:Select...
    Image count:2
    Scale count:1
    Threshold count:1
    Scale count:1
    Threshold count:1
    Select the images to measure:OrigDNA
    Include the image rescaling value?:Yes
    Calculate blur metrics?:No
    Spatial scale for blur measurements:20
    Calculate saturation metrics?:No
    Calculate intensity metrics?:No
    Calculate thresholds?:Yes
    Use all thresholding methods?:No
    Select a thresholding method:Otsu
    Typical fraction of the image covered by objects:0.1
    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
    Select the images to measure:OrigAGP
    Include the image rescaling value?:Yes
    Calculate blur metrics?:No
    Spatial scale for blur measurements:20
    Calculate saturation metrics?:No
    Calculate intensity metrics?:No
    Calculate thresholds?:Yes
    Use all thresholding methods?:No
    Select a thresholding method:Otsu
    Typical fraction of the image covered by objects:0.1
    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

FlagImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:False|wants_pause:False]
    Hidden:2
    Hidden:1
    Name the flag\'s category:Metadata
    Name the flag:QCFlag_isEmpty
    How should measurements be linked?:Flag if any fail
    Skip image set if flagged?:Yes
    Flag is based on:Rules
    Select the object to be used for flagging:None
    Which measurement?:None
    Flag images based on low values?:Yes
    Minimum value:0.0
    Flag images based on high values?:Yes
    Maximum value:1.0
    Rules file location:Default Input Folder\x7CDesktop/SQLITE
    Rules file name:rules.txt
    Class number:1
    Hidden:1
    Name the flag\'s category:Metadata
    Name the flag:QCFlag_isBlurry
    How should measurements be linked?:Flag if any fail
    Skip image set if flagged?:No
    Flag is based on:Rules
    Select the object to be used for flagging:None
    Which measurement?:None
    Flag images based on low values?:Yes
    Minimum value:0.0
    Flag images based on high values?:Yes
    Maximum value:1.0
    Rules file location:Default Input Folder\x7CDesktop
    Rules file name:rules.txt
    Class number:2

IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:10|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:DNA
    Name the primary objects to be identified:Nuclei
    Typical diameter of objects, in pixel units (Min,Max):40,200
    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?:Yes
    Method to distinguish clumped objects:Shape
    Method to draw dividing lines between clumped objects:Shape
    Size of smoothing filter:12
    Suppress local maxima that are closer than this minimum allowed distance:30
    Speed up by using lower-resolution image to find local maxima?:Yes
    Name the outline image:PrimaryOutlines
    Fill holes in identified objects?:After both thresholding and declumping
    Automatically calculate size of smoothing filter for declumping?:No
    Automatically calculate minimum allowed distance between local maxima?:No
    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:2
    Threshold strategy:Adaptive
    Thresholding method:Otsu
    Select the smoothing method for thresholding:Automatic
    Threshold smoothing scale:10.0
    Threshold correction factor:1.0
    Lower and upper bounds on threshold:0.0,1.0
    Approximate fraction of image covered by objects?:0.9
    Manual threshold:0.0
    Select the measurement to threshold with:None
    Select binary image:None
    Masking objects:None
    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:Custom
    Size of adaptive window:40
    Use default parameters?:Custom
    Lower outlier fraction:0.05
    Upper outlier fraction:0.05
    Averaging method:Mean
    Variance method:Median absolute deviation
    # of deviations:0.5

Smooth:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:AGP
    Name the output image:smooth_AGP
    Select smoothing method:Median Filter
    Calculate artifact diameter automatically?:No
    Typical artifact diameter:5.0
    Edge intensity difference:0.1
    Clip intensities to 0 and 1?:Yes

IdentifySecondaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:9|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the input objects:Nuclei
    Name the objects to be identified:Cells
    Select the method to identify the secondary objects:Propagation
    Select the input image:smooth_AGP
    Number of pixels by which to expand the primary objects:28
    Regularization factor:0.001
    Name the outline image:SecondaryOutlines
    Retain outlines of the identified secondary objects?:No
    Discard secondary objects touching the border of the image?:No
    Discard the associated primary objects?:No
    Name the new primary objects:FilteredNuclei
    Retain outlines of the new primary objects?:No
    Name the new primary object outlines:FilteredNucleiOutlines
    Fill holes in identified objects?:Yes
    Threshold setting version:2
    Threshold strategy:Global
    Thresholding method:Otsu
    Select the smoothing method for thresholding:No smoothing
    Threshold smoothing scale:1.0
    Threshold correction factor:1.0
    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:Custom
    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

IdentifyTertiaryObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the larger identified objects:Cells
    Select the smaller identified objects:Nuclei
    Name the tertiary objects to be identified:Cytoplasm
    Name the outline image:CytoplasmOutlines
    Retain outlines of the tertiary objects?:No
    Shrink smaller object prior to subtraction?:Yes

MeasureCorrelation:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Hidden:4
    Hidden:3
    Select an image to measure:DNA
    Select an image to measure:ER_RNA
    Select an image to measure:AGP
    Select an image to measure:Mito
    Set threshold as percentage of maximum intensity for the images:15.0
    Select where to measure correlation:Within objects
    Select an object to measure:Nuclei
    Select an object to measure:Cytoplasm
    Select an object to measure:Cells

MeasureGranularity:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Image count:4
    Object count:1
    Select an image to measure:DNA
    Subsampling factor for granularity measurements:0.25
    Subsampling factor for background reduction:0.25
    Radius of structuring element:10
    Range of the granular spectrum:16
    Select objects to measure:Nuclei
    Object count:2
    Select an image to measure:ER_RNA
    Subsampling factor for granularity measurements:0.25
    Subsampling factor for background reduction:0.25
    Radius of structuring element:10
    Range of the granular spectrum:16
    Select objects to measure:Nuclei
    Select objects to measure:Cytoplasm
    Object count:2
    Select an image to measure:AGP
    Subsampling factor for granularity measurements:0.25
    Subsampling factor for background reduction:0.25
    Radius of structuring element:10
    Range of the granular spectrum:16
    Select objects to measure:Nuclei
    Select objects to measure:Cytoplasm
    Object count:2
    Select an image to measure:Mito
    Subsampling factor for granularity measurements:0.25
    Subsampling factor for background reduction:0.25
    Radius of structuring element:10
    Range of the granular spectrum:16
    Select objects to measure:Nuclei
    Select objects to measure:Cytoplasm

MeasureObjectIntensity:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Hidden:4
    Select an image to measure:DNA
    Select an image to measure:ER_RNA
    Select an image to measure:AGP
    Select an image to measure:Mito
    Select objects to measure:Nuclei
    Select objects to measure:Cytoplasm
    Select objects to measure:Cells

MeasureObjectNeighbors:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select objects to measure:Cells
    Select neighboring objects to measure:Cells
    Method to determine neighbors:Within a specified distance
    Neighbor distance:5
    Retain the image of objects colored by numbers of neighbors?:No
    Name the output image:ObjectNeighborCount
    Select colormap:Default
    Retain the image of objects colored by percent of touching pixels?:No
    Name the output image:PercentTouching
    Select a colormap:Default

MeasureObjectNeighbors:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select objects to measure:Nuclei
    Select neighboring objects to measure:Nuclei
    Method to determine neighbors:Within a specified distance
    Neighbor distance:2
    Retain the image of objects colored by numbers of neighbors?:No
    Name the output image:ObjectNeighborCount
    Select colormap:Default
    Retain the image of objects colored by percent of touching pixels?:No
    Name the output image:PercentTouching
    Select a colormap:Default

MeasureObjectNeighbors:[module_num:15|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select objects to measure:Cells
    Select neighboring objects to measure:Cells
    Method to determine neighbors:Adjacent
    Neighbor distance:2
    Retain the image of objects colored by numbers of neighbors?:No
    Name the output image:ObjectNeighborCount
    Select colormap:Default
    Retain the image of objects colored by percent of touching pixels?:No
    Name the output image:PercentTouching
    Select a colormap:Default

MeasureObjectIntensityDistribution:[module_num:16|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Hidden:4
    Hidden:3
    Hidden:1
    Hidden:0
    Calculate intensity Zernikes?:None
    Maximum zernike moment:9
    Select an image to measure:DNA
    Select an image to measure:ER_RNA
    Select an image to measure:AGP
    Select an image to measure:Mito
    Select objects to measure:Nuclei
    Object to use as center?:These objects
    Select objects to use as centers:None
    Select objects to measure:Cytoplasm
    Object to use as center?:These objects
    Select objects to use as centers:None
    Select objects to measure:Cells
    Object to use as center?:These objects
    Select objects to use as centers:None
    Scale the bins?:Yes
    Number of bins:4
    Maximum radius:100

MeasureObjectSizeShape:[module_num:17|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select objects to measure:Cells
    Select objects to measure:Nuclei
    Select objects to measure:Cytoplasm
    Calculate the Zernike features?:No

MeasureTexture:[module_num:18|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Hidden:4
    Hidden:3
    Hidden:1
    Select an image to measure:DNA
    Select an image to measure:ER_RNA
    Select an image to measure:AGP
    Select an image to measure:Mito
    Select objects to measure:Nuclei
    Select objects to measure:Cytoplasm
    Select objects to measure:Cells
    Texture scale to measure:3
    Angles to measure:Horizontal,Vertical,Diagonal
    Measure Gabor features?:No
    Number of angles to compute for Gabor:4
    Measure images or objects?:Both

OverlayOutlines:[module_num:19|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|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:OrigDNA
    Name the output image:NucleiOutlines
    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

OverlayOutlines:[module_num:20|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|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:OrigAGP
    Name the output image:CellOutlines
    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:#24EF2F
    Load outlines from an image or objects?:Objects
    Select objects to display:Cells

SaveImages:[module_num:21|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<Well>_f\\\\g<Site>_nuclei_outlines
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:png
    Output file location:Default Output Folder sub-folder\x7CNuclei_Outlines
    Image bit depth:16-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

SaveImages:[module_num:22|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:CellOutlines
    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<Well>_f\\\\g<Site>_cell_outlines
    Number of digits:4
    Append a suffix to the image file name?:No
    Text to append to the image name:
    Saved file format:png
    Output file location:Default Output Folder sub-folder\x7CCell_outlines
    Image bit depth:16-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

ExportToSpreadsheet:[module_num:23|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 column delimiter:Comma (",")
    Add image metadata columns to your object data file?:No
    Limit output to a size that is allowed in Excel?:No
    Select the 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\x7C
    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 measurement types?:Yes
    :
    Representation of Nan/Inf:NaN
    Add a prefix to file names?:No
    Filename prefix:MyExpt_
    Overwrite existing files without warning?:No
    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
    
CreateBatchFiles:[module_num:24|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:/Users/habbasi/Documents/CellProfiler 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:/Users/habbasi
    Hidden\x3A revision number:0
    Hidden\x3A from old matlab:No
    Launch BatchProfiler:No