3DNucleiPipelineComputeConsumingFinal.cppipe

CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:421
GitHash:
ModuleCount:17
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:Nuclei
    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?:Yes
    Relative pixel spacing in X:0.129
    Relative pixel spacing in Y:0.129
    Relative pixel spacing in Z:0.2
    Select the rule criteria:and (file does contain "c00")
    Name to assign these images:c00
    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:FileLocation

GaussianFilter:[module_num:5|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Nuclei
    Name the output image:GaussianFilter
    Sigma:1

ReduceNoise:[module_num:6|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:GaussianFilter
    Name the output image:ReduceNoise
    Size:5
    Distance:2
    Cut-off distance:0.2

Threshold:[module_num:7|svn_version:'Unknown'|variable_revision_number:12|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:ReduceNoise
    Name the output image:Threshold
    Threshold strategy:Global
    Thresholding method:Otsu
    Threshold smoothing scale:1.5
    Threshold correction factor:1
    Lower and upper bounds on threshold:0,1.0
    Manual threshold:0.0
    Select the measurement to threshold with:None
    Two-class or three-class thresholding?:Three classes
    Log transform before thresholding?:No
    Assign pixels in the middle intensity class to the foreground or the background?:Background
    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:Otsu

Watershed:[module_num:8|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Threshold
    Name the output object:Watershed
    Use advanced settings?:No
    Generate from:Distance
    Markers:None
    Mask:Leave blank
    Connectivity:1
    Compactness:0.0
    Footprint:10
    Downsample:3
    Separate watershed labels:No
    Declump method:Intensity
    Reference Image:GaussianFilter
    Segmentation distance transform smoothing factor:0
    Minimum distance between seeds:1
    Minimum absolute internal distance:0.0
    Pixels from border to exclude:0
    Maximum number of seeds:-1
    Structuring element for seed dilation:ball,3

DilateObjects:[module_num:9|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input object:Watershed
    Name the output object:RealsizeNuclei
    Structuring element:octahedron,1

MeasureObjectIntensity:[module_num:10|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:Nuclei
    Select objects to measure:RealsizeNuclei

MeasureObjectSizeShape:[module_num:11|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:RealsizeNuclei
    Calculate the Zernike features?:No
    Calculate the advanced features?:No

RescaleIntensity:[module_num:12|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input image:Nuclei
    Name the output image:RescaleIntensityNuclei
    Rescaling method:Stretch each image to use the full intensity range
    Method to calculate the minimum intensity:Custom
    Method to calculate the maximum intensity:Custom
    Lower intensity limit for the input image:0.0
    Upper intensity limit for the input image:1.0
    Intensity range for the input image:0.0,1.0
    Intensity range for the output image:0.0,1.0
    Select image to match in maximum intensity:None
    Divisor value:1.0
    Divisor measurement:None

OverlayObjects:[module_num:13|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Input:RescaleIntensityNuclei
    Name the output image:OverlayObjects
    Objects:RealsizeNuclei
    Opacity:0.3

SaveImages:[module_num:14|svn_version:'Unknown'|variable_revision_number:16|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:True]
    Select the type of image to save:Image
    Select the image to save:OverlayObjects
    Select method for constructing file names:From image filename
    Select image name for file prefix:Nuclei
    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:Overlay
    Saved file format:tiff
    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

ConvertObjectsToImage:[module_num:15|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the input objects:RealsizeNuclei
    Name the output image:NucleiObjects3D
    Select the color format:Grayscale
    Select the colormap:Default

SaveImages:[module_num:16|svn_version:'Unknown'|variable_revision_number:16|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:NucleiObjects3D
    Select method for constructing file names:From image filename
    Select image name for file prefix:Nuclei
    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:3D
    Saved file format:tiff
    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:17|svn_version:'Unknown'|variable_revision_number:13|show_window:True|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:Yes
    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:RealsizeNuclei|AreaShape_Center_Y,RealsizeNuclei|AreaShape_Center_Z,RealsizeNuclei|AreaShape_Center_X,RealsizeNuclei|AreaShape_Volume,RealsizeNuclei|Intensity_IntegratedIntensity_Nuclei
    Representation of Nan/Inf:NaN
    Add a prefix to file names?:Yes
    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