Nuclear_Localisation.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:426
GitHash:
ModuleCount:15
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?:Custom
    Select the rule criteria:and (extension does istif) (file doesnot contain "OTF")

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?:Yes
    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<Well>[A-P][0-9]{2})_.*F(?P<Field>[0-9]{3}).*A(?P<ChannelNumber>[0-9]{2}).*.tif
    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?:Yes

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:Images matching rules
    Select the image type:Grayscale image
    Name to assign these images:DNA
    Match metadata:[]
    Image set matching method:Order
    Set intensity range from:Image metadata
    Assignments count:4
    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 (metadata does ChannelNumber "01")
    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
    Select the rule criteria:and (metadata does ChannelNumber "02")
    Name to assign these images:Fascin
    Name to assign these objects:Nucleus
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0
    Select the rule criteria:and (metadata does ChannelNumber "03")
    Name to assign these images:Actin
    Name to assign these objects:Cytoplasm
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Maximum intensity:255.0
    Select the rule criteria:and (metadata does ChannelNumber "04")
    Name to assign these images:NuclearActin
    Name to assign these objects:Speckle
    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:Well

Smooth:[module_num:5|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:DNA
    Name the output image:SmoothedDNA
    Select smoothing method:Gaussian Filter
    Calculate artifact diameter automatically?:No
    Typical artifact diameter:2
    Edge intensity difference:0.1
    Clip intensities to 0 and 1?:Yes

Smooth:[module_num:6|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Actin
    Name the output image:SmoothedActin
    Select smoothing method:Gaussian Filter
    Calculate artifact diameter automatically?:No
    Typical artifact diameter:2
    Edge intensity difference:0.1
    Clip intensities to 0 and 1?:Yes

IdentifyPrimaryObjects:[module_num:7|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:SmoothedDNA
    Name the primary objects to be identified:Nuclei
    Typical diameter of objects, in pixel units (Min,Max):15,50
    Discard objects outside the diameter range?:Yes
    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: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?:Yes
    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

IdentifySecondaryObjects:[module_num:8|svn_version:'Unknown'|variable_revision_number:10|show_window:False|notes:[]|batch_state:array([], 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:SmoothedActin
    Number of pixels by which to expand the primary objects:10
    Regularization factor:0.05
    Discard secondary objects touching the border of the image?:No
    Discard the associated primary objects?:No
    Name the new primary objects:FilteredNuclei
    Fill holes in identified objects?:Yes
    Threshold setting version:12
    Threshold strategy:Global
    Thresholding method:Minimum Cross-Entropy
    Threshold smoothing scale:0.0
    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

IdentifyTertiaryObjects:[module_num:9|svn_version:'Unknown'|variable_revision_number:3|show_window:False|notes:[]|batch_state:array([], 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
    Shrink smaller object prior to subtraction?:Yes

MeasureObjectIntensity:[module_num:10|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select images to measure:Fascin, NuclearActin
    Select objects to measure:Cells, Cytoplasm, Nuclei

OverlayOutlines:[module_num:11|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Display outlines on a blank image?:No
    Select image on which to display outlines:DNA
    Name the output image:NucleiOverlay
    Outline display mode:Grayscale
    Select method to determine brightness of outlines:Max of image
    How to outline:Inner
    Select outline color:Red
    Select objects to display:Nuclei

OverlayOutlines:[module_num:12|svn_version:'Unknown'|variable_revision_number:4|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Display outlines on a blank image?:No
    Select image on which to display outlines:Actin
    Name the output image:CellOverlay
    Outline display mode:Grayscale
    Select method to determine brightness of outlines:Max of image
    How to outline:Inner
    Select outline color:Red
    Select objects to display:Cells

SaveImages:[module_num:13|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:True]
    Select the type of image to save:Image
    Select the image to save:NucleiOverlay
    Select method for constructing file names:Sequential numbers
    Select image name for file prefix:DNA
    Enter file prefix: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|
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:No
    When to save:Every cycle
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...|
    How to save the series:T (Time)
    Save with lossless compression?:Yes

SaveImages:[module_num:14|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:CellOverlay
    Select method for constructing file names:Sequential numbers
    Select image name for file prefix:None
    Enter file prefix: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|
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:No
    When to save:Every cycle
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...|
    How to save the series:T (Time)
    Save with lossless compression?:Yes

ExportToSpreadsheet:[module_num:15|svn_version:'Unknown'|variable_revision_number:13|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the column delimiter:Comma (",")
    Add image metadata columns to your object data file?:No
    Add image file and folder names to your object data file?: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|
    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
    Press button to select measurements:
    Representation of Nan/Inf:NaN
    Add a prefix to file names?:No
    Filename prefix:MyExpt_
    Overwrite existing files without warning?:Yes
    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